Characterisation of host growth after infection with a broad-range freshwater cyanopodophage

Freshwater cyanophages are poorly characterised in comparison to their marine counterparts, however, the level of genetic diversity that exists in freshwater cyanophage communities is likely to exceed that found in marine environments, due to the habitat heterogeneity within freshwater systems. Many cyanophages are specialists, infecting a single host species or strain; however, some are less fastidious and infect a number of different host genotypes within the same species or even hosts from different genera. Few instances of host growth characterisation after infection by broad host-range phages have been described. Here we provide an initial characterisation of interactions between a cyanophage isolated from a freshwater fishing lake in the south of England and its hosts. Designated ΦMHI42, the phage is able to infect isolates from two genera of freshwater cyanobacteria, Planktothrix and Microcystis. Transmission Electron Microscopy and Atomic Force Microscopy indicate that ΦMHI42 is a member of the Podoviridae, albeit with a larger than expected capsid. The kinetics of host growth after infection with ΦMHI42 differed across host genera, species and strains in a way that was not related to the growth rate of the uninfected host. To our knowledge, this is the first characterisation of the growth of cyanobacteria in the presence of a broad host-range freshwater cyanophage

Physico-chemical and microbial factors affecting the operation of a package wastewater treatment plant

The Biologically Engineered Single Sludge Treatment (BESST) system is a small package wastewater treatment plant, which is designed to reduce influent concentrations of ammoniacal nitrogen, biochemical oxygen demand and total suspended solids, to a standard fit for discharge into controlled waterways. This thesis examines the treatment performance of the BESST, while operating under steady state and disruptive conditions, and assesses the contribution of physicochemical and microbiological factors to treatment efficacy. The design of the BESST was based on principles of activated sludge processes, and comprised of an anoxic area, an aerobic area, and an upflow clarifier. In each area of the system, physico-chemical and microbiological profiles were distinct from the other areas. The influent delivered to the system was municipal sewage, delivered from the start of the wastewater treatment works within which the prototype BESST was located. The influent was generally high in concentrations of biochemical oxygen demand, and was highly variable in nature. At times, this was reflected in effluent quality, particularly when disruptive events were occurring, such as mechanical failure. However, good levels of reduction in concentrations of ammoniacal nitrogen, biochemical oxygen demand and total suspended solids were observed throughout the treatment period, and the system demonstrated a good level of robustness with regard to mechanical failure and experimental changes to sewage control parameters. Transformations of nitrogen and phosphorus were performed by bacteria in the biomass of the system, and were analysed throughout the sampling period by qualitative, culture based and molecular microbiological methods. Culture based techniques were shown to be a valuable monitoring tool, but were not representative of the actual community in the BESST. Molecular methods provided a higher resolution of microbial populations present during treatment, but it was not possible to correlate data obtained from culture based methodology with that obtained using molecular techniques. Enhanced phosphorus removal trials were performed during the study period, in order to facilitate the production of an effluent very low in concentrations of total phosphorus. The trial suggested that enhanced removal of phosphorus was possible in the BESST, and found the most dominant morphotype accumulating polyphosphate, to be that of filamentous bacteria. The study produced a large and complex dataset, which presented difficulties in the analysis of interactions between variables. Suggestions are presented to overcome such difficulties. The BESST is presented in this study as a package wastewater system which is able to successfully perform biological nutrient removal in a robust manner, the interrogation of which has led to a greater contribution to knowledge of small wastewater treatment systems and the reactive nature of the chemical and biological processes occurring within them.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

PhagePhisher: a Pipeline for the Discovery of Covert Viral Sequences in Complex Genomic Datasets

Obtaining meaningful viral information from large sequencing datasets presents unique challenges distinct from prokaryotic and eukaryotic sequencing efforts. The difficulties surrounding this issue can be ascribed in part to the genomic plasticity of viruses themselves as well as the scarcity of existing information in genomic databases. The open-source software PhagePhisher (http://www.putonti-lab.com/phagephisher) has been designed as a simple pipeline to extract relevant information from complex and mixed datasets, and will improve the examination of bacteriophages, viruses, and virally related sequences, in a range of environments. Key aspects of the software include speed and ease of use; PhagePhisher can be used with limited operator knowledge of bioinformatics on a standard workstation. As a proof-of-concept, PhagePhisher was successfully implemented with bacteria–virus mixed samples of varying complexity. Furthermore, viral signals within microbial metagenomic datasets were easily and quickly identified by PhagePhisher, including those from prophages as well as lysogenic phages, an important and often neglected aspect of examining phage populations in the environment. PhagePhisher resolves viral-related sequences which may be obscured by or imbedded in bacterial genomes

Seven Bacteriophages Isolated from the Female Urinary Microbiota

Recent research has debunked the myth that urine is sterile, having uncovered bacteria within the bladders of healthy individuals. However, the identity, diversity, and putative roles of bacteriophages in the bladder are unknown. We report the draft genome sequences of seven bacteriophages isolated from microbial communities from adult female bladders

Bacteriophages isolated from Lake Michigan demonstrate broad host-range across several bacterial phyla

BACKGROUND: The study of bacteriophages continues to generate key information about microbial interactions in the environment. Many phenotypic characteristics of bacteriophages cannot be examined by sequencing alone, further highlighting the necessity for isolation and examination of phages from environmental samples. While much of our current knowledge base has been generated by the study of marine phages, freshwater viruses are understudied in comparison. Our group has previously conducted metagenomics-based studies samples collected from Lake Michigan - the data presented in this study relate to four phages that were extracted from the same samples. FINDINGS: Four phages were extracted from Lake Michigan on the same bacterial host, exhibiting similar morphological characteristics as shown under transmission electron microscopy. Growth characteristics of the phages were unique to each isolate. Each phage demonstrated a host-range spanning several phyla of bacteria - to date, such a broad host-range is yet to be reported. Genomic data reveals genomes of a similar size, and close similarities between the Lake Michigan phages and the Pseudomonas phage PB1, however, the majority of annotated genes present were ORFans and little insight was offered into mechanisms for host-range. CONCLUSIONS: The phages isolated from Lake Michigan are capable of infecting several bacterial phyla, and demonstrate varied phenotypic characteristics despite similarities in host preference, and at the genomic level. We propose that such a broad host-range is likely related to the oligotrophic nature of Lake Michigan, and the competitive benefit that this characteristic may lend to phages in nature

Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges

Advances in bioinformatics and sequencing technologies have allowed for the analysis of complex microbial communities at an unprecedented rate. While much focus is often placed on the cellular members of these communities, viruses play a pivotal role, particularly bacteria-infecting viruses (bacteriophages); phages mediate global biogeochemical processes and drive microbial evolution through bacterial grazing and horizontal gene transfer. Despite their importance and ubiquity in nature, very little is known about the diversity and structure of viral communities. Though the need for culture-based methods for viral identification has been somewhat circumvented through metagenomic techniques, the analysis of metaviromic data is marred with many unique issues. In this review, we examine the current bioinformatic approaches for metavirome analyses and the inherent challenges facing the field as illustrated by the ongoing efforts in the exploration of freshwater phage populations

Assessment of a Metaviromic Dataset Generated from Nearshore Lake Michigan

Bacteriophages are powerful ecosystem engineers. They drive bacterial mortality rates and genetic diversity, and affect microbially mediated biogeochemical processes on a global scale. This has been demonstrated in marine environments; however, phage communities have been less studied in freshwaters, despite representing a potentially more diverse environment. Lake Michigan is one of the largest bodies of freshwater on the planet, yet to date the diversity of its phages has yet to be examined. Here, we present a composite survey of viral ecology in the nearshore waters of Lake Michigan. Sequence analysis was performed using a web server previously used to analyse similar data. Our results revealed a diverse community of DNA phages, largely comprising the order Caudovirales. Within the scope of the current study, the Lake Michigan virome demonstrates a distinct community. Although several phages appeared to hold dominance, further examination highlighted the importance of interrogating metagenomic data at the genome level. We present our study as baseline information for further examination of the ecology of the lake. In the current study we discuss our results and highlight issues of data analysis which may be important for freshwater studies particularly, in light of the complexities associated with examining phage ecology generall

A UK survey of COVID‐19 related social support closures and their effects on older people, people with dementia, and carers

Abstract Objectives The aim of this national survey was to explore the impact of COVID‐19 public health measures on access to social support services and the effects of closures of services on the mental well‐being of older people and those affected by dementia. Methods A UK‐wide online and telephone survey was conducted with older adults, people with dementia, and carers between April and May 2020.The survey captured demographic and postcode data, social support service usage before and after COVID‐19 public health measures, current quality of life, depression, and anxiety. Multiple linear regression analysis was used to explore the relationship between social support service variations and anxiety and well‐being. Results 569 participants completed the survey (61 people with dementia, 285 unpaid carers, and 223 older adults). Paired samples t‐tests and X2‐tests showed that the mean hour of weekly social support service usage and the number of people having accessed various services was significantly reduced post COVID‐19. Multiple regression analyses showed that higher variations in social support service hours significantly predicted increased levels of anxiety in people with dementia and older adults, and lower levels of mental well‐being in unpaid carers and older adults. Conclusions Being unable to access social support services due to COVID contributed to worse quality of life and anxiety in those affected by dementia and older adults across the UK. Social support services need to be enabled to continue providing support in adapted formats, especially in light of continued public health restrictions for the foreseeable future. This article is protected by copyright. All rights reserved

UK consensus guidelines for the delivery of unexpected news in obstetric ultrasound: The ASCKS framework

Background: Studies indicate there is a need to improve the delivery of unexpected news via obstetric ultrasound, but there have been few advances in this area. One factor preventing improvement has been a lack of consensus regarding the appropriate phrases and behaviours which sonographers and ultrasound practitioners should use in these situations. Aims: To develop consensus guidelines for unexpected news delivery in Early Pregnancy Unit and Fetal Anomaly Screening Programme NHS settings. Methods: A workshop was conducted to identify priorities and reach consensus on areas of contention. Contributors included interdisciplinary healthcare professionals, policy experts, representatives from third-sector organisations, lay experts and academic researchers (n = 28). Written and verbal feedback was used to draft initial guidance which was then circulated amongst the wider writing group (n = 39). Revisions were undertaken until consensus was reached. Results: Consensus guidelines were developed outlining the behaviours and phrases which should be used during scans where unexpected findings are identified. Specific recommendations included that: honest and clear communication should be prioritised, even with uncertain findings; technical terms should be used, but these should be written down together with their lay interpretations; unless expectant parents use other terminology (e.g. ‘foetus’), the term ‘baby’ should be used as a default, even in early pregnancy; at the initial news disclosure, communication should focus on information provision. Expectant parents should not be asked to make decisions during the scan. Conclusions: These recommendations can be used to develop and improve news delivery interventions in obstetric ultrasound settings. The full guidelines can be accessed online as supplemental material and at https://doi.org/10.5518/100/24

Spontaneous DNA damage to the nuclear genome promotes senescence, T redox imbalance and aging

Accumulation of senescent cells over time contributes to aging and age-related diseases. However, what drives senescence in vivo is not clear. Here we used a genetic approach to determine if spontaneous nuclear DNA damage is sufficient to initiate senescence in mammals. Ercc1-/Δ mice with reduced expression of ERCC1-XPF endonuclease have impaired capacity to repair the nuclear genome. Ercc1-/Δ mice accumulated spontaneous, oxidative DNA damage more rapidly than wild-type (WT) mice. As a consequence, senescent cells accumulated more rapidly in Ercc1-/Δ mice compared to repair-competent animals. However, the levels of DNA damage and senescent cells in Ercc1-/Δ mice never exceeded that observed in old WT mice. Surprisingly, levels of reactive oxygen species (ROS) were increased in tissues of Ercc1-/Δ mice to an extent identical to naturally-aged WT mice. Increased enzymatic production of ROS and decreased antioxidants contributed to the elevation in oxidative stress in both Ercc1-/Δ and aged WT mice. Chronic treatment of Ercc1-/Δ mice with the mitochondrial-targeted radical scavenger XJB-5–131 attenuated oxidative DNA damage, senescence and age-related pathology. Our findings indicate that nuclear genotoxic stress arises, at least in part, due to mitochondrial-derived ROS, and this spontaneous DNA damage is sufficient to drive increased levels of ROS, cellular senescence, and the consequent age-related physiological decline