Understanding community diversity on coastal defences : the role of key drivers and ecological enhancements

Coastal defences have become prevalent in the marine environment in response to rising sea levels and increasingly frequent coastal storms. However, due to insufficient habitat heterogeneity and physical complexity such structures support lower biodiversity than natural rocky shores. As a result, a range of ecological enhancements have been developed to address the diversity deficit. This thesis monitored colonization of an ecologically enhanced rock armour defence at Runswick Bay, North Yorkshire. Artificial rock pools and sandstone boulder habitats were incorporated into the defence design to increase habitat heterogeneity and groove microhabitats were engineered to increase small-scale complexity of granite boulders. Fourteen months after construction, diversity of sessile and mobile assemblages was significantly higher in artificial pool and sandstone boulder habitats than in unmodified granite boulder habitats. The community which developed on engineered grooves was not different to that of substrates without grooves. This thesis also examined whether fine-scale complexity (rugosity) and substrate orientation act as drivers of diversity on coastal defences. At both mid and upper shore height, the most rugose substrate had the highest diversity of sessile and mobile species. Over a regional scale, the age of defence was more important in determining community structure than rugosity. In addition, diversity and structure of communities differed significantly between North, North-east and East orientations at mid and upper shore height. This thesis demonstrates that increasing the habitat heterogeneity and incorporating natural substrata into rock armour defences can improve biodiversity. This thesis also demonstrates the importance of fine-scale complexity across tidal heights, and that environmental factors determined by orientation affect community structure. These results can be used to inform how ecological enhancements are applied in future developments

Characterisation of the terminal enzymes of haem biosynthesis from Staphylococcus aureus

Haem is an essential molecule that is required for a wide variety of functions in all forms of life. This molecule is required for oxygen transport in humans as a prosthetic group of haemoglobin and myoglobin and is also an integral component of various cytochromes as well as being a cofactor for peroxidases and catalases. Until very recently it was generally accepted that the haem biosynthetic pathway was a conserved process in most organisms that synthesise haem. This dogma has changed with the discovery of two new pathways by which haem can be synthesised. The most recently discovered of these pathways, known as the coproporphyrin-dependent pathway, is utilised by many actinobacteria and firmicutes (including Staphylococcus aureus) and is now thought to be an ancestral pathway to the now more widely distributed classical pathway. In light of this discovery, the current work seeks to examine the biochemical and kinetic properties of the enzymes involved in the terminal stages of haem synthesis in S. aureus (HemY, HemH and HemQ). HemY from S. aureus, which is classically known as a protoporphyrinogen IX oxidase, catalyses the antepenultimate step in a coproporphyrinogen-dependant pathway in vivo was shown for the first time to catalyse the oxidation of coproporphyrinogen III as well as protoporphyrinogen IX, demonstrating that this enzyme can catalyse steps in both classical and coproporphyrin-dependant haem biosynthesis in vitro. Kinetic analyses revealed that the previously-observed stimulation of HemY activity by the terminal pathway enzyme HemQ (a coprohaem decarboxylase) occurred via a peroxidase-mediated mechanism resulting in the generation of superoxide, although this stimulation was not observable when HemY is utilising the native coproporphyrinogen III substrate. This generation of toxic free radicals could explain why HemQ enzymes have not been identified in organisms that synthesise haem via the classical protoporphyrin IX pathway. The HemH enzyme, also known as ferrochelatase, has also been further characterised with its in vivo substrates (Fe2+ and coproporphyrin III), where activity was shown to be diminished by a regulatory metal binding site. The activity of this enzyme with a variety of alternative metal substrates was also assessed, with the enzyme being able to insert metals that are commonly inserted by other ferrochelatases. Kinetic constants for HemQ, a coprohaem decarboxylase, were determined for the first time and HemQ was further assessed for an ability to bind other tetrapyrroles: non-metallated porphyrins were found to bind much tighter than the metalloporphyrins that are the in vivo substrate and product for this enzyme. Together, these intriguing observations have implications for the divergent evolution of haem biosynthesis in ancestral microorganisms and provides new insights into the flux of intermediates through the terminal stages of haem biosynthesis in S. aureus

The coproporphyrin ferrochelatase of Staphylococcus aureus: mechanistic insights into a regulatory iron binding site

The majority of characterised ferrochelatase enzymes catalyse the final step of classical haem synthesis, inserting ferrous iron into protoporphyrin IX. However, for the recently-discovered coproporphyrin-dependent pathway, ferrochelatase catalyses the penultimate reaction where ferrous iron is inserted into coproporphyrin III. Ferrochelatase enzymes from the bacterial phyla Firmicutes and Actinobacteria have previously been shown to insert iron into coproporphyrin, and those from Bacillus subtilis and Staphylococcus aureus are known to be inhibited by elevated iron concentrations. The work herein reports a Km (coproporphyrin III) for S. aureus ferrochelatase of 1.5 µM and it is shown that elevating the iron concentration increases the Km for coproporphyrin III, providing a potential explanation for the observed iron-mediated substrate inhibition. Together, structural modelling, site-directed mutagenesis, and kinetic analyses confirm residue Glu271 as being essential for the binding of iron to the inhibitory regulatory site on S. aureus ferrochelatase, providing a molecular explanation for the observed substrate inhibition patterns. This work therefore has implications for how haem biosynthesis in S. aureus is regulated by iron availability

All-Sky Near Infrared Space Astrometry

Gaia is currently revolutionizing modern astronomy. However, much of the Galactic plane, center and the spiral arm regions are obscured by interstellar extinction, rendering them inaccessible because Gaia is an optical instrument. An all-sky near infrared (NIR) space observatory operating in the optical NIR, separated in time from the original Gaia would provide microarcsecond NIR astrometry and millimag photometry to penetrate obscured regions unraveling the internal dynamics of the Galaxy.Comment: 7 page

Depression and anxiety during the year before death from cancer.

OBJECTIVE: Previous studies of depression and anxiety during the year before death have reported different findings. We therefore aimed to study depression and anxiety in patients who had died from cancer and had previously attended cancer clinics. METHODS: We analysed routine data on 4869 deceased patients who had completed the Hospital Anxiety and Depression Scale (HADS) as part of their routine cancer care. The HADS data were linked with demographic, cancer and mortality data from national registries. We used data from all HADS completed in the last year of life to investigate the relationships between mean depression (HADS-D) and anxiety (HADS-A) scores and the percentages of high scores (≥11 on each subscale) and time to death (Analysis 1). This analysis used multivariable linear regression with cubic splines and robust standard errors to allow for multiple HADS from the same patients. We also investigated within-patient changes in scores (Analysis 2) in a subset of patients who had completed more than one HADS. RESULTS: In Analysis 1, modelled mean HADS-D scores increased by around 2.5 and the percentage of high HADS-D scores increased from 13% at six months before death to 30% at one month before death. Changes in HADS-A were smaller and occurred later. In Analysis 2, similar patterns were observed in individual patients' HADS scores. CONCLUSION: Depression should be looked for and treated in patients with cancer and a prognosis of six months or less, in order to maximise the quality of patients' remaining life

The HemQ coprohaem decarboxylase generates reactive oxygen species: implications for the evolution of classical haem biosynthesis

Bacteria require a haem biosynthetic pathway for the assembly of a variety of protein complexes including cytochromes, peroxidases, globins, and catalase. Haem is synthesised via a series of tetrapyrrole intermediates including non-metallated porphyrins such as protoporphyrin IX, which is well-known to generate reactive oxygen species (ROS) in the presence of light and oxygen. Staphylococcus aureus has an ancient haem biosynthetic pathway that proceeds via the formation of coproporphyrin III, a less reactive porphyrin. Herein, we demonstrate for the first time that HemY of S. aureus is able to generate both protoporphyrin IX and coproporphyrin III, and that the terminal enzyme of this pathway, HemQ, can stimulate the generation of protoporphyrin IX (but not coproporphyrin III). Assays with hydrogen peroxide, horseradish peroxidase, superoxide dismutase, and catalase confirm that this stimulatory effect is mediated by superoxide. Structural modelling reveals that HemQ enzymes do not possess the structural attributes that are common to peroxidases that form compound I [FeIV=O]+, which taken together with the superoxide data leaves Fenton chemistry as a likely route for the superoxide-mediated stimulation of protoporphyrinogen IX oxidase activity of HemY. This generation of toxic free radicals could explain why HemQ enzymes have not been identified in organisms that synthesise haem via the classical protoporphyrin IX pathway. This work has implications for the divergent evolution of haem biosynthesis in ancestral microorganisms and provides new structural and mechanistic insights into a recently discovered oxidative decarboxylase reaction

Deep Synoptic Array Science: Polarimetry of 25 New Fast Radio Bursts Provides Insights into their Origins

We report on a full-polarization analysis of the first 25 as yet non-repeating FRBs detected at 1.4 GHz by the 110-antenna Deep Synoptic Array (DSA-110) during commissioning observations. We present details of the data reduction, calibration, and analysis procedures developed for this novel instrument. The data have 32 $\mu$s time resolution and sensitivity to Faraday rotation measures (RMs) between $\pm10^{6}$rad m$^{-2}$. RMs are detected for 20 FRBs with magnitudes ranging from $4-4670$ rad m$^{-2}$. $9/25$ FRBs are found to have high ($\ge 70\%$) linear-polarization fractions. The remaining FRBs exhibit significant circular polarization ($3/25$), or are either partially depolarized ($8/25$) or unpolarized ($5/25$). We investigate the mechanism of depolarization, disfavoring stochastic RM variations within a scattering screen as a dominant cause. Polarization-state and possible RM variations are observed in the four FRBs with multiple sub-components, but only one other FRB shows a change in polarization state. We combine the DSA-110 sample with polarimetry of previously published FRBs, and compare the polarization properties of FRB sub-populations and FRBs with Galactic pulsars. Although FRBs are typically far more polarized than the average profiles of Galactic pulsars, and exhibit greater spread in polarization fractions than pulsar single pulses, we find a remarkable similarity between FRB polarization fractions and the youngest (characteristic ages $<10^{5}$ yr) pulsars. Our results support a scenario wherein FRB emission is intrinsically highly linearly polarized, and where propagation effects within progenitor magnetospheres can result in conversion to circular polarization and depolarization. Young pulsar emission and magnetospheric-propagation geometries may form a useful analogy for the origin of FRB polarization.Comment: 43 pages, 17 figure

Deep Synoptic Array Science: Implications of Faraday Rotation Measures of Localized Fast Radio Bursts

Faraday rotation measures (RMs) of fast radio bursts (FRBs) offer the prospect of directly measuring extragalactic magnetic fields. We present an analysis of the RMs of ten as yet non-repeating FRBs detected and localized to host galaxies by the 110-antenna Deep Synoptic Array (DSA-110). We combine this sample with published RMs of 15 localized FRBs, nine of which are repeating sources. For each FRB in the combined sample, we estimate the host-galaxy dispersion measure (DM) contributions and extragalactic RM. We find compelling evidence that the extragalactic components of FRB RMs are often dominated by contributions from the host-galaxy interstellar medium (ISM). Specifically, we find that both repeating and as yet non-repeating FRBs show a correlation between the host-DM and host-RM in the rest frame, and we find an anti-correlation between extragalactic RM (in the observer frame) and redshift for non-repeaters, as expected if the magnetized plasma is in the host galaxy. Important exceptions to the ISM origin include a dense, magnetized circum-burst medium in some repeating FRBs, and the intra-cluster medium (ICM) of host or intervening galaxy clusters. We find that the estimated ISM magnetic-field strengths, $B_{||}$, are characteristically larger than those inferred from Galactic radio pulsars. This suggests either increased ISM magnetization in FRB hosts in comparison with the Milky Way, or that FRBs preferentially reside in regions of increased magnetic-field strength within their hosts

Deep Synoptic Array science I: discovery of the host galaxy of FRB 20220912A

We report the detection and interferometric localization of the repeating fast radio burst (FRB) source FRB 20220912A during commissioning observations with the Deep Synoptic Array (DSA-110). Two bursts were detected from FRB 20220912A, one each on 2022 October 18 and 2022 October 25. The best-fit position is (R.A. J2000, decl. J2000) = (23:09:04.9, +48:42:25.4), with a 90% confidence error ellipse of $\pm2$ arcsec and $\pm1$ arcsec in right ascension and declination respectively. The two bursts have disparate polarization properties and temporal profiles. We find a Faraday rotation measure that is consistent with the low value of $+0.6$ rad m$^{-2}$ reported by CHIME/FRB. The DSA-110 localization overlaps with the galaxy PSO J347.2702+48.7066 at a redshift $z=0.0771$, which we identify as the likely host. PSO J347.2702$+$48.7066 has a stellar mass of approximately $10^{10}M_{\odot}$, modest internal dust extinction, and a star-formation rate likely in excess of $0.1\,M_{\odot}$ yr$^{-1}$. The host-galaxy contribution to the dispersion measure is likely $\lesssim50$ pc cm$^{-3}$. The FRB 20220912A source is therefore likely viewed along a tenuous plasma column through the host galaxy.Comment: 10 pages, 7 figures, 2 tables, submitted to AAS Journal