Investigating the DNA methylation landscape of Staphylococcus aureus

Staphylococcus aureus is a leading causative agent of healthcare-associated infections. One aspect of the organism that remains unknown is the methylome, specifically that of the whole genome. In prokaryotes, methylation is facilitated by methyltransferases, usually part of the organism’s Restriction Modification system (RM). It is well established that RM are involved in cellular defense but have also been attributed to have secondary regulatory functions in host physiology and virulence by modulating gene expression through DNA methylation in numerous bacterial species. In S. aureus the main RM present are Type I RM Sau1, which potential epigenetic role has not yet been studied. Using PacBio SMRT sequencing this study investigates the variability and distribution of sau1 DNA binding specificity unit (hsdS) alleles and explores the frequency of whole genome 6mA methylation within the species using a historically and phylogenetically variable collection of S. aureus isolates part of the NCTC3000 project. The results revealed lineage specific methylation patterns randomly distributed throughout the chromosome, but preferential methylation of the coding sequence and the core genome. Between the 24 represented STs, the detailed protein structure of 40 different HsdS homologs were characterised and matched to corresponding 6mA target recognition sequences, greatly augmenting the current knowledge of Sau1 methylation signatures. Differential methylation was also investigated in novel ST622 hybrid strains as a natural experiment (variable methylation signatures across an identical sequence region between chimeric and closely related ST45 and ST22 donor strains) effectively looking at the effect of large-scale recombination on whole genome methylation using RNA-Sequencing. Mutagenesis of hsdS and further transcriptomic studies revealed that deletion of 6mA methylation by Sau1 in a set of isogenic mutants in multiple sequence backgrounds causes a pleotropic shift in expression of metabolic genes. This is not likely due to an epigenetic regulatory mechanism, but rather and induced global stress response.""I would first like to acknowledge that this work was funded by the Wellcome ISSF Fund of the University of St Andrews (School of Medicine)."--Acknowledgement

CRISPR antiphage defence mediated by the cyclic nucleotide-binding membrane protein Csx23

Funding: Biotechnology and Biological Sciences Research Council [BB/T004789/1 to M.F.W., T.M.G.]; European Research Council Advanced Grant [101018608 to M.F.W.]; Engineering and Physical Sciences Research Council [EP/X016455/1 to K.A., B.E.B., M.F.W.]; BBSRC equipment grants [BB/R013780/1, BB/T017740/1 to B.E.B.]. Funding for open access charge: University of St Andrews block grant.CRISPR-Cas provides adaptive immunity in prokaryotes. Type III CRISPR systems detect invading RNA and activate the catalytic Cas10 subunit, which generates a range of nucleotide second messengers to signal infection. These molecules bind and activate a diverse range of effector proteins that provide immunity by degrading viral components and/or by disturbing key aspects of cellular metabolism to slow down viral replication. Here, we focus on the uncharacterised effector Csx23, which is widespread in Vibrio cholerae. Csx23 provides immunity against plasmids and phage when expressed in Escherichia coli along with its cognate type III CRISPR system. The Csx23 protein localises in the membrane using an N-terminal transmembrane α-helical domain and has a cytoplasmic C-terminal domain that binds cyclic tetra-adenylate (cA4), activating its defence function. Structural studies reveal a tetrameric structure with a novel fold that binds cA4 specifically. Using pulse EPR, we demonstrate that cA4 binding to the cytoplasmic domain of Csx23 results in a major perturbation of the transmembrane domain, consistent with the opening of a pore and/or disruption of membrane integrity. This work reveals a new class of cyclic nucleotide binding protein and provides key mechanistic detail on a membrane-associated CRISPR effector.Peer reviewe

Tailoring electrocatalytic activity of titanate perovskite oxides for enhancing oxygen and hydrogen evolution reactions

This thesis focuses on the preparation, characterization, and optimization of Ti-based perovskites for water splitting, particularly for OER. These materials are synthesized primarily via a modified sol-gel method. The development and implementation of a double E strategy resulted in a significant enhancement of the catalytic activity of Ti-based perovskites for water splitting. A series of La₀.₂₊₂ₓCa₀.₇₋₂ₓTi₁₋ₓCoₓO₃ (LCTCoₓ) perovskites with different Co doping levels are synthesized. Reduced LCTCo₀.₁₁ (R-LCTCo₀.₁₁) is identified as a superior OER catalyst by controlling reduction time and temperature. It exhibits excellent mass activity (based on Co), achieving approximately 1700 mA mg⁻¹ at an overpotential of 450 mV, surpassing the benchmark catalyst RuO₂. The process utilized to enhance the OER catalytic activity of Co-doped Ti-based perovskites is known as redox exsolution. Although the OER catalytic activity of La₀.₂₅Ca₀.₆₅Ti₀.₉₅Fe₀.₀₅O₃ (LCTFe) can be enhanced through redox exsolution, it is less effective than LCTCo. To further optimize the performance of LCTFe, a unique strategy, the double E strategy, is employed. This strategy combines redox exsolution and electrodeposition, resulting in R-LCTFe/Ni. This innovative approach, a novel contribution of this thesis, has proven effective. R-LCTFe/Ni demonstrates remarkable OER catalytic activity, achieving overpotentials of only 331 mV at a current density of 10 mA cm⁻². It also exhibits notable HER catalytic activity, making it a bifunctional catalyst for water splitting. Additionally, the successfully synthesized R-LCTFe/Co catalyst also shows exceptional water splitting catalytic activity, providing preliminary evidence of the transferability of the double E strategy. During the preparation of R-LCTNi/Co, the conditions for electrodeposition are carefully controlled and selected, leading to an optimization of the double E strategy. The resulting R-LCTNi/Co exhibits a low overpotential of 281 mV at a current density of 10 mA cm⁻², outperforming numerous state-of-the-art catalysts. This further substantiates the transferability of the double E strategy

Toward a Cenozoic history of atmospheric CO2

Funding: This work was supported by National Science Foundation grant OCE 16-36005 (B.H. and P.J.P.), Heising-Simons Foundation grant 2018-0996 (B.H. and V.F.), National Science Foundation grant EAR 21-21649 (B.H., V.F., J.J.M., and C.F.G.), National Science Foundation grant EAR 21-21170 (G.J.B.), National Science Foundation grant EAR 20-02370 (Y.C.), National Science Foundation grant 18-43285 (A.P.), Columbia University’s Center for Climate and Life (K.T.U.), the G. Unger Vetlesen Foundation (K.T.U.), National Science Foundation grant 21-00537 (A.P. and P.J.P.), National Science Foundation grant 21-00509 (P.J.P.), National Science Foundation grant EAR 21-21165 (A.R.), National Science Foundation grant EAR 18-06015 (Y.G.Z.), National Science Foundation grant DGE 16-44869 (S.R.P.), National Science Foundation grant 18-13703 (E.G.H.), National Science Foundation grant OCE 16-58023 (J.C.Z.), National Science Foundation grant 16-02905 (M.H.), Swedish Research Council grant NT7-2016 04905 (M.S.), European Research Council grant 101020824 (J.C.M.), SFI/RC/2092 (J.C.M.), UK Research and Innovation grant 101045371 (M.J.H.), Natural Environment Research Council grant NE/X000567/1 (M.P.S.B.), Royal Society grant DHF\R1\221014 (C.R.W.), Australian Research Council grant DP150104007 (P.J.F.), Deutsche Forschungsgemeinschaft grant RA 2068/4-1 (M.R.), European Research Council grant 805246 (J.W.B.R.), an ETH Fellowship (J.K.C.R.), National Science Foundation of China grant 42030503 (J.D.), the Sandal Society Museum (G.J.R.), a Royal Society Tata Fellowship (B.D.A.N.), and Natural Environment Research Council grant NE/P019048/1 (G.L.F.).INTRODUCTION Anthropogenic carbon dioxide (CO2) emissions have driven an increase in the global atmospheric CO2 concentration from 280 parts per million (ppm) before industrialization to an annual average of 419 ppm in 2022, corresponding to an increase in global mean surface temperature (GMST) of 1.1°C over the same period. If global CO2 emissions continue to rise, atmospheric CO2 could exceed 800 ppm by the year 2100. This begs the question of where our climate is headed. The geologic record is replete with both brief and extended intervals of CO2 concentration higher than today and thus provides opportunities to project the response of the future climate system to increasing CO2. For example, it has been estimated that global surface temperature 50 million years ago (Ma) was ~12°C higher than today, in tandem with atmospheric CO2 concentrations some 500 ppm higher (i.e., more than doubled) than present-day values. Consistent with these estimates, Antarctica and Greenland were free of ice at that time. However, reconstructing these values prior to direct instrumental measurements requires the use of paleoproxies—measurable properties of geological archives that are closely, but only indirectly, related to the parameter in question (e.g., temperature, CO2). To date, at least eight different proxies from both terrestrial and marine archives have been developed and applied to reconstruct paleo-CO2, but their underlying assumptions have been revised over time, and published reconstructions are not always consistent. This uncertainty complicates quantification of the climate responses to the ongoing rise of atmospheric CO2 concentrations. RATIONALE Although earlier studies have compiled published paleo-CO2 estimates, those studies typically applied only limited proxy vetting, included estimates that were made before the proxies were sufficiently validated, and/or focused on only a subset of available proxy data. The international consortium of the Cenozoic CO2 Proxy Integration Project (CenCO2PIP) has undertaken a 7-year effort to document, evaluate, and synthesize published paleo-CO2 records from all available archives, spanning the past 66 million years. The most reliable CO2 estimates were identified, some records were recalculated to conform with the latest proxy understanding, age models were updated where necessary and possible, and data were categorized according to the community’s level of confidence in each estimate. The highest-rated data were eventually combined into a reconstruction of the Cenozoic history of atmospheric CO2. RESULTS The resulting reconstruction illustrates a more quantitatively robust relationship between CO2 and global surface temperature, yielding greater clarity and confidence than previous syntheses. The new record suggests that early Cenozoic “hothouse” CO2 concentrations peaked around 1600 ppm at ~51 Ma. Near 33.9 Ma, the onset of continent-wide Antarctic glaciation coincided with an atmospheric CO2 concentration of 720 ppm. By ~32 Ma, atmospheric CO2 had dropped to 550 ppm, and this value coincided with the onset of radiation in plants with carbon-concentrating mechanisms that populate grasslands and deserts today. CO2 remained below this threshold for the remainder of the Cenozoic and continued its long-term decrease toward the present. Along this trajectory, the middle Miocene (~16 Ma) marks the last time that CO2 concentrations were consistently higher than at present; Greenland was not yet glaciated at that time, and independent estimates suggest that sea level was some 50 m higher than today. Values eventually dropped below 270 ppm at the Plio-Pleistocene boundary (2.6 Ma), when Earth approached our current “icehouse” state of bipolar glaciation. This and other climatic implications of the revised CO2 curve, including the evolution of the cryosphere, flora, and fauna, along with the cross-disciplinary data assessment process, are detailed in the full online article. CONCLUSION This community-vetted CO2 synthesis represents the most reliable data available to date and a means to improve our understanding of past changes in global climate and carbon cycling as well as organismal evolution. However, this effort is still incomplete. Data remain sparse during the earlier part of the record and in some instances are dominated by estimates from a single proxy system. Generating a paleo-CO2 record with even greater confidence will require further research using multiple proxies to fill in data gaps and increase overall data resolution, resolve discrepancies between estimates from contemporaneous proxy analyses, reduce uncertainty of established methods, and develop new proxies.Peer reviewe

Assessing the role of geographical access to health-care in colorectal cancer diagnosis and survival in Scotland

Geographical accessibility to healthcare services is important for the achievement of health equity. Lack of spatial access can result in delayed medical treatment and poor health outcomes. In this research, individual level data are used to assess how geographical accessibility to healthcare influences cancer diagnosis and survival in Scotland. Specifically, this thesis aims to address the following three research questions: • How does geographical accessibility to healthcare services vary according to area characteristics? • Is geographical accessibility to cancer treatment hospitals associated with rates of colorectal cancer survival? • Is geographical accessibility to General Practitioners (GPs) associated with the stage of diagnosis for colorectal cancer? To address the above research questions, this thesis develops a new Geographic Information System (GIS) measure of distance and time to health services at a fine-scale geography (i.e., postcode level) in Scotland. Three other major datasets are innovatively linked with the GIS- based accessibility measure to explore colorectal cancer diagnosis and survival in the Scottish context; these are the Scottish Longitudinal Study, NHS National Services Scotland, and Scottish Government data. This research found significant variation in travel time to GP and hospitals in Scotland at postcode level. After controlling for rurality, there is an area-level social gradient in distance to health services. Using survival analysis modelling and controlling for other social, demographic and economic correlates of diagnosis and survival for colorectal cancer, this thesis found that travel time to health services has no influence on colorectal cancer diagnosis or survival in Scotland. Unlike many previous studies, this study controlled for individual correlates of social circumstances. Early diagnosis, screening and having early treatment were found to be significant in determining cancer survival. The use of individual level data and the linkage of four major national datasets have opened new avenues for future health research to test hypotheses about geographical accessibility in other cancers."This PhD study is fully funded by the University of St Andrews, School of Geography and Sustainable Development (600th Anniversary Scholarship) to which we are deeply thankful."--Fundin

Fear of progression after cancer recurrence : a mixed methods study

Funding: This project was funded by the University of Stirling and an endowment (Cancer Care Research Legacy 98) as part of a PhD project.Background: The recurrence of cancer will significantly impact an individual’s quality of life (QoL) as they adjust to living with a condition that is often incurable. Patients remain at risk of further progression following recurrence, but fear of cancer progression (FOP) at this time is not commonly examined. Importantly, these fears are known to reach levels in which there are consequences for QoL. Methods: This study sought to explore levels of FOP, health-related QoL, anxiety, and depression in patients after a recurrence of their cancer in a longitudinal manner. With the study taking place throughout the COVID-19 pandemic, an assessment of fears related to cancer and the pandemic was included. A sequential mixed method approach was employed for complementarity and expansion purposes. A questionnaire was administered to 44 participants on three different occasions one month apart. A sub-sample of 10 participants then took part in semi-structured interviews. Findings: FOP was present at moderate levels in patients with a cancer recurrence, with over a third of the sample reaching levels considered dysfunctional. Levels of fear were stable over three months and were not predicted by select demographic or clinical factors. On average, depression was low, but anxiety reached mild levels. Challenges to health-related QoL were evident. Low levels of concern about COVID-19 in relation to cancer were reported. Integrated findings provided more nuanced answers to the research questions, including more specific worries about cancer progression. Implications: Findings support the development of psychosocial interventions to manage FOP, and future recommendations are provided. Identifying the presence of fears not commonly screened for after cancer recurrence adds to the existing knowledge in this area. Through acknowledging and attending to the psychosocial impact of FOP, healthcare professionals can provide tailored support to enhance the well-being of those with a recurrence of their cancer.Peer reviewe

Nocturnal avian migration drives high daily turnover but limited change in abundance on the ground

Funding: This research received support from the Swiss National Science Foundation (grant no. 191138 and 21787, to RN), through the GloBAM project as part of the 2017/2018 Belmont Forum and BiodivERsA joint call for research proposals (NSF no. 1927743 to AF and AMD), the Macrodemography project (NSF no. 2017817, to AMD) and the Lyda Hill Philanthropies (to AF).Every night during spring and autumn, the mass movement of migratory birds redistributes bird abundances found on the ground during the day. However, the connection between the magnitude of nocturnal migration and the resulting change in diurnal abundance remains poorly quantified. If departures and landings at the same location are balanced throughout the night, we expect high bird turnover but little change in diurnal abundance (stream-like migration). Alternatively, migrants may move simultaneously in spatial pulses, with well-separated areas of departure and landing that cause significant changes in the abundance of birds on the ground during the day (wave-like migration). Here, we apply a flow model to data from weather surveillance radars (WSR) to quantify the daily fluxes of nocturnally migrating birds landing and departing from the ground, characterizing the movement and stopover of birds in a comprehensive synoptic scale framework. We corroborate our results with independent observations of the diurnal abundances of birds on the ground from eBird. Furthermore, we estimate the abundance turnover, defined as the proportion of birds replaced overnight. We find that seasonal bird migration chiefly resembles a stream where bird populations on the ground are continuously replaced by new individuals. Large areas show similar magnitudes of take-off and landing, coupled with relatively small distances flown by birds each night, resulting in little change in bird densities on the ground. We further show that WSR-inferred landing and take-off fluxes predict changes in eBird-derived abundance turnover rate and turnover in species composition. We find that the daily turnover rate of birds is 13% on average but can reach up to 50% on peak migration nights. Our results highlight that WSR networks can provide real-time information on rapidly changing bird distributions on the ground. The flow model applied to WSR data can be a valuable tool for real-time conservation and public engagement focused on migratory birds' daytime stopovers.Peer reviewe

A women ambassador behind the scenesRosario Castellanos in Israel (1971-1974)

Peer reviewe

What does nihilism tell us about modal logic?

Brauer (Philos Stud 179:2751–2763, https://doi.org/10.1007/s11098-022-01793-7, 2022) has recently argued that if it is possible that there is nothing, then the correct modal logic for metaphysical modality cannot include D. Here, I argue that Brauer’s argument is unsuccessful; or at the very least significantly weaker than presented. First, I outline a simple argument for why it is not possible that there is nothing. I note that this argument has a well-known solution involving the distinction between truth in and truth at a possible world. However, I then argue that once the semantics presupposed by Brauer’s argument is reformulated in terms of truth at a world, we have good reasons to think that a crucial semantic premise in Brauer’s argument should be rejected in favour of an alternative. Brauer’s argument is, however, no longer valid with this alternative premise. Thus, plausibly Brauer’s argument against D is only valid, if it is not sound.Peer reviewe

Old ways, new names : identity, reciprocity and continuity in the northwestern Roman alae, 52 B.C.-A.D. 212

This thesis focuses on Rome’s desire to exploit the well-documented prowess of northwestern Iron Age groups in the area of cavalry, while also taking into consideration the dynamics of control and risk involved in such a process. How and why was the cavalry particularly important in the incorporation of northwestern tribal societies into the Roman system? What facilitated the transferal of martial culture to service under Roman authority? How did the mechanics of an existing reciprocal system enable the maintenance of loyalty and effectiveness? What made the peoples of northwestern Iron Age Europe the ideal cavalry recruit? How did provincial uprisings like the Batavian revolt in AD 69 impact imperial use of these populations? Could an auxiliary soldier ever truly ‘become Roman’? The author’s purpose is to investigate the origin, cultivation and maintenance of relations between Rome and specific areas which were important cavalry recruiting grounds, with a focus on the cultural import of equestrian status and the fluidity of martial values and loyalties. Aspects considered include the integration of ‘barbarian’ elites and their followers through Roman patronage and the careful construction of networks of reliance and friendship. The importance of existing societal circumstances in the process of merging different martial cultures into the Roman system is emphasized and extensively discussed. The Batvian revolt of AD 69 and its aftermath will be examined to determine how it affected the overall development of the Roman auxiliary system as manifested after the Flavian period and the impact on the identity of the auxiliary cavalryman. Archaeological evidence is used to investigate the early organization of the auxiliary and the lasting impact of various cultures in the development of Roman cavalry equipment, as well as the changes in frontier societal structure brought about by military installations. Where direct evidence is lacking, historical texts and comparative analysis can be used to infer what is not explicitly apparent in the sources and form a clearer picture of one branch of the complex responses to Roman influence. By employing a narrower approach to the subject, this thesis seeks to identify larger themes of incorporation and to further the understanding of interactions between certain non-Roman communities and the expanding influence of Rome. At the same time, this study will provide a more nuanced view of the experience of a particular group within the imperial system as well as a new way of dealing with the difficulty of interpreting ancient identity