Singled Out: Genomic analysis of uncultured microbes in marine sediments

The vast majority of abundant taxa in marine sediment environments have not yielded to culture, leaving questions about their relationship to other taxa and their functional potential unanswered. However, in the absence of active cultures, careful application of various omics methods can be used to help us make useful inferences about their evolutionary history and how they have continued to survive in environments of extreme energy deprivation. For this dissertation, I have applied comparative genomics methods to members of two uncultured groups, the recently proposed Altiarchaeales order and a cosmopolitan taxon associated with the Actinobacteria phylum. Additionally, I combined transcript recruitment and metabolomic profiles to investigate metabolisms inferred from the single-cell amplified genomes extracted from members of a taxa that thrive in Baltic Sea sediment microbial communities. In Chapter II, I establish a phylogenetic relationship across distantly related members of the order Altiarchaeales and discuss environment-specific adaptations. In Chapter III, transcript recruitment and metabolite profiles support a community-wide focus on microbial persistence with active members of the uncultured Atribacteria phylum playing an important ecological role. In Chapter IV, my analysis leads to the proposal of the new class within the Actinobacteria. Osirisbacteria is a class of Actinobacteria that is specialized for life in anoxic environments. Overall, this work offers new insights into deeply-branching microbial taxa, improved understanding of recently considered branches of the evolutionary tree, and new perspective on metabolisms important for survival in low-energy marine sediment environments

Dispositions, rules, and finks

This paper discusses the prospects of a dispositional solution to the Kripke–Wittgenstein rule-following puzzle. Recent attempts to employ dispositional approaches to this puzzle have appealed to the ideas of finks and antidotes—interfering dispositions and conditions—to explain why the rule-following disposition is not always manifested. We argue that this approach fails: agents cannot be supposed to have straightforward dispositions to follow a rule which are in some fashion masked by other, contrary dispositions of the agent, because in all cases, at least some of the interfering dispositions are both relatively permanent and intrinsic to the agent. The presence of these intrinsic and relatively permanent states renders the ascription of a rule-following disposition to the agent fals

Effect of initiating drug treatment on the risk of drug-related poisoning death and acquisitive crime among offending heroin users.

BACKGROUND: A recent Cochrane review of randomised trials identified a lack of evidence for interventions provided to drug-using offenders. We use routine data to address whether contact with treatment services reduces heroin users' likelihood of a future acquisitive offence or drug-related poisoning (DRP) death. METHODS: Heroin-users were identified from probation assessments and linked to drug-treatment, mortality and offending records. The study cohort was selected to ensure that the subject was not: in prison, in treatment or had recently left treatment. Subjects were classed as initiators if they attended a triage appointment within two weeks of their assessment; non-initiators otherwise. Initiator and non-initiators were compared over a maximum of one year, with respect to their risk of recorded acquisitive offence or DRP-death. Balance was sought using propensity score matching and missing data were accounted for using multiple imputation. RESULTS: Nine percent of assessments identified for analysis were classed as initiators. Accounting for observed confounding and missing data, there was a reduction in DRPs associated with initiator assessments, however there was uncertainty around this estimate such that a null-effect could not be ruled out (HR: 0.42, 95% CI 0.17-1.04). There was no evidence of a decrease in the recidivism risk, in fact the analysis showed a small increase (HR: 1.10, 95% CI 1.02-1.18). CONCLUSION: For heroin-using offenders, initial contact with treatment services does not appear to reduce the likelihood of a future acquisitive offence

Formation of quasi-free-standing graphene on SiC(0001) through intercalation of erbium

Activation of the carbon buffer layer on 4H- and 6H-SiC substrates using elements with high magnetic moments may lead to novel graphene/SiC-based spintronic devices. In this work, we use a variety of surface analysis techniques to explore the intercalation of Er underneath the buffer layer showing evidence for the associated formation of quasi-free-standing graphene (QFSG). A combined analysis of low energy electron diffraction (LEED), atomic force microscopy (AFM), X-ray and ultraviolet photoemission spectroscopy (XPS and UPS), and metastable de-excitation spectroscopy (MDS) data reveals that annealing at temperatures up to 1073 K leads to deposited Er clustering at the surface. The data suggest that intercalation of Er occurs at 1273 K leading to the breaking of back-bonds between the carbon buffer layer and the underlying SiC substrate and the formation of QFSG. Further annealing at 1473 K does not lead to the desorption of Er atoms but does result in further graphitization of the surface

Enhancing the repeatability and sensitivity of low-cost PCB, pH-sensitive field-effect transistors

Discrete, extended gate pH-sensitive field-effect transistors (dEGFETs) fabricated on printed circuit boards (PCBs) are a low-cost, simple to manufacture analytical technology that can be applied to a wide range of applications. Electrodeposited iridium oxide (IrOx) films have emerged as promising pH-sensitive layers owing to their theoretically high pH sensitivity and facile deposition, but typically exhibit low pH sensitivity or lack repro- ducibility. Moreover, to date, a combined IrOx and dEGFET PCB system has not yet been realised. In this study, we demonstrate a dEGFET pH sensor based on an extended gate manufactured on PCB that is rendered pH sensitive through an electrodeposited IrOx film, which can reliably and repeatably display beyond-Nernstian pH response. Using a combination of complementary surface analysis techniques, we show that the high pH sensitivity and repeatability of the dEGFETs are dependent on both the chemical composition and critically the uniformity of the IrOx film. The IrOx film uniformity can be enhanced through electrochemical polishing of the extended gate electrode prior to electrodeposition, leading to dEGFETs that exhibit a median pH sensitivity of 70.7 ± 5 mV/pH (n = 56) compared to only 31.3 ± 14 mV/pH (n = 31) for IrOx electrodeposited on non- polished PCB electrodes. Finally, we demonstrate the applicability of these devices by demonstrating the detection and quantification of ampicillin due to β-Lactamase enzyme activity, thus laying the foundation for cheap and ubiquitous sensors which can be applied to a range of global challenges across healthcare and environmental monitoring

Retinitis Pigmentosa GTPase Regulator (RPGR) protein isoforms in mammalian retina:insights into X-linked Retinitis Pigmentosa and associated ciliopathies

AbstractMutations in the cilia-centrosomal protein Retinitis Pigmentosa GTPase Regulator (RPGR) are a frequent cause of retinal degeneration. The RPGR gene undergoes complex alternative splicing and encodes multiple protein isoforms. To elucidate the function of major RPGR isoforms (RPGR1–19 and RPGRORF15), we have generated isoform-specific antibodies and examined their expression and localization in the retina. Using sucrose-gradient centrifugation, immunofluorescence and co-immunoprecipitation methods, we show that RPGR isoforms localize to distinct sub-cellular compartments in mammalian photoreceptors and associate with a number of cilia-centrosomal proteins. The RCC1-like domain of RPGR, which is present in all major RPGR isoforms, is sufficient to target it to the cilia and centrosomes in cultured cells. Our findings indicate that multiple isotypes of RPGR may perform overlapping yet somewhat distinct transport-related functions in photoreceptors

Vega—A small, low cost, ground robot for nuclear decommissioning

From Wiley via Jisc Publications RouterHistory: received 2021-08-20, rev-recd 2021-11-03, accepted 2021-11-05, pub-electronic 2021-11-25Article version: VoRPublication status: PublishedFunder: Royal Academy of Engineering; Id: http://dx.doi.org/10.13039/501100000287Funder: Engineering and Physical Sciences Research Council; Id: http://dx.doi.org/10.13039/501100000266Abstract: This paper presents the Vega robot, which is a small, low cost, potentially disposable ground robot designed for nuclear decommissioning. Vega has been developed specifically to support characterization and inspection operations, such as 2D and 3D mapping, radiation scans and sample retrieval. The design and construction methodology that was followed to develop the robot is described and its capabilities detailed. Vega was designed to provide flexibility, both in software and hardware, is controlled via tele‐operation, although it can be extended to semi and full autonomy, and can be used in either tethered or untethered configurations. A version of the tethered robot was designed for extreme radiation tolerance, utilizing relay electronics and removing active electronic systems. Vega can be outfitted with a multitude of sensors and actuators, including gamma spectrometers, alpha/beta radiation sensors, LiDARs and robotic arms. To demonstrate its flexibility, a 5 degree‐of‐freedom manipulator has been successfully integrated onto Vega, facilitating deployments where handling is required. To assess the tolerance of Vega to the levels of ionizing radiation that may be found in decommissioning environments, its individual components were irradiated, allowing estimates to be made of the length of time Vega would be able to continue to operate in nuclear environments. Vega has been successfully deployed in an active environment at the Dounreay nuclear site in the UK, deployed in nonactive environments at the Atomic Weapons Establishment, and demonstrated to many other organizations in the UK nuclear industry including Sellafield Ltd, with the goal of moving to active deployments in the future

Functional Analysis of Retinitis Pigmentosa 2 (RP2) Protein Reveals Variable Pathogenic Potential of Disease-Associated Missense Variants

Genetic mutations are frequently associated with diverse phenotypic consequences, which limits the interpretation of the consequence of a variation in patients. Mutations in the retinitis pigmentosa 2 (RP2) gene are associated with X-linked RP, which is a phenotypically heterogenic form of retinal degeneration. The purpose of this study was to assess the functional consequence of disease-associated mutations in the RP2 gene using an in vivo assay. Morpholino-mediated depletion of rp2 in zebrafish resulted in perturbations in photoreceptor development and microphthalmia (small eye). Ultrastructural and immunofluorescence analyses revealed defective photoreceptor outer segment development and lack of expression of photoreceptor-specific proteins. The retinopathy phenotype could be rescued by expressing the wild-type human RP2 protein. Notably, the tested RP2 mutants exhibited variable degrees of rescue of rod versus cone photoreceptor development as well as microphthalmia. Our results suggest that RP2 plays a key role in photoreceptor development and maintenance in zebrafish and that the clinical heterogeneity associated with RP2 mutations may, in part, result from its potentially distinct functional relevance in rod versus cone photoreceptors

Defining Boundaries for Ecosystem-Based Management: A Multispecies Case Study of Marine Connectivity across the Hawaiian Archipelago

Determining the geographic scale at which to apply ecosystem-based management (EBM) has proven to be an obstacle for many marine conservation programs. Generalizations based on geographic proximity, taxonomy, or life history characteristics provide little predictive power in determining overall patterns of connectivity, and therefore offer little in terms of delineating boundaries for marine spatial management areas. Here, we provide a case study of 27 taxonomically and ecologically diverse species (including reef fishes, marine mammals, gastropods, echinoderms, cnidarians, crustaceans, and an elasmobranch) that reveal four concordant barriers to dispersal within the Hawaiian Archipelago which are not detected in single-species exemplar studies. We contend that this multispecies approach to determine concordant patterns of connectivity is an objective and logical way in which to define the minimum number of management units and that EBM in the Hawaiian Archipelago requires at least five spatially managed regions

Missense mutations in the copper transporter gene ATP7A cause X-Linked distal hereditary motor neuropathy

Distal hereditary motor neuropathies comprise a clinically and genetically heterogeneous group of disorders. We recently mapped an X-linked form of this condition to chromosome Xq13.1-q21 in two large unrelated families. The region of genetic linkage included ATP7A, which encodes a copper-transporting P-type ATPase mutated in patients with Menkes disease, a severe infantile-onset neurodegenerative condition. We identified two unique ATP7A missense mutations (p.P1386S and p.T994I) in males with distal motor neuropathy in two families. These molecular alterations impact highly conserved amino acids in the carboxyl half of ATP7A and do not directly involve the copper transporter's known critical functional domains. Studies of p.P1386S revealed normal ATP7A mRNA and protein levels, a defect in ATP7A trafficking, and partial rescue of a S. cerevisiae copper transport knockout. Although ATP7A mutations are typically associated with severe Menkes disease or its milder allelic variant, occipital horn syndrome, we demonstrate here that certain missense mutations at this locus can cause a syndrome restricted to progressive distal motor neuropathy without overt signs of systemic copper deficiency. This previously unrecognized genotype-phenotype correlation suggests an important role of the ATP7A copper transporter in motor-neuron maintenance and function