Current Performance of the SLD VXD3

During 1996, the SLD collaboration completed construction and began operation of a new charge-coupled device (CCD) vertex detector (VXD3). Since then, its performance has been studied in detail and a new topological vertexing technique has been developed. In this paper, we discuss the design of VXD3, procedures for aligning it, and the tracking and vertexing improvements that have led to its world-record performance.Comment: 17 pages latex including 10 figures, to appear in Proceedings Vertex99 Worksho

Aspects of southern ocean transport and mixing

Understanding and quantifying the circulation of the oceans and the driving mechanisms thereof is an important step in developing models which can accurately predict future climate change. In particular, model studies have shown that the spatial variability of diapycnal diffusivity, which represents the rate at which deep water returns to shallower depths by means of turbulent diapycnal mixing, is a critical factor controlling the strength and structure of the circulation. Efforts are therefore ongoing to measure diffusivity as extensively as possible, but temporal variability in diffusivity has not been widely addressed. Results from three Southern Ocean studies are presented in this thesis. Firstly, a high resolution hydrographic survey carried out on the northern flank of the Kerguelen Plateau identifies a complex meandering current system carrying a total eastward volume transport of 174 ± 22 Sv, mostly associated with the blended Subtropical Front/Subantarctic Front. Significant water mass transformation across isopycnals is not required to balance the budgets in this region. Secondly, results are presented which cast doubt on the advisability of using density profiles acquired using Conductivity-Temperature-Depth instruments to estimate diapycnal diffusivity (an attractive proposition due to low cost and widespread data availability) in areas of weak stratification such as the Southern Ocean, because the noise characteristics of the data result in inaccurate diffusivity estimates. Finally, a method is developed for estimating diffusivity from profiles of velocity shear acquired by moored acoustic Doppler current profilers. An 18-month time series of diffusivity estimates is derived with a median of 3.3 × 10−4 m2 s−1 and a range of 0.5 × 10−4 m2 s−1 to 57 × 10−4 m2 s−1. There is no significant signal at annual or semiannual periods, but there is evidence of signals at periods of approximately fourteen days (likely due to the spring-neaps tidal cycle), and at periods of 3.8 and 2.6 days most likely due to topographically-trapped waves propagating around the local seamount. More widespread application of this method would allow for an assessment of natural climate variability in diapycnal diffusivity

The vertical structure of upper ocean variability at the Porcupine Abyssal Plain during 2012-2013

This study presents the characterization of variability in temperature, salinity and oxygen concentration, including the vertical structure of the variability, in the upper 1000m of the ocean over a full year in the northeast Atlantic. Continuously profiling ocean gliders with vertical resolution between 0.5-1m provide more information on temporal variability throughout the water column than time series from moorings with sensors at a limited number of fixed depths. The heat, salt and dissolved oxygen content are quantified at each depth. While the near surface heat content is consistent with the net surface heat flux, heat content of the deeper layers is driven by gyre-scale water mass changes. Below ~150m, heat and salt content display intraseasonal variability which has not been resolved by previous studies. A mode-1 baroclinic internal tide is detected as a peak in the power spectra of water mass properties. The depth of minimum variability is at ~415m for both temperature and salinity, but this is a depth of high variability for oxygen concentration. The deep variability is dominated by the intermittent appearance of Mediterranean Water, which shows evidence of filamentation. Susceptibility to salt fingering occurs throughout much of the water column for much of the year. Between about 700-900m, the water column is susceptible to diffusive layering, particularly when Mediterranean Water is present. This unique ability to resolve both high vertical and temporal resolution highlights the importance of intraseasonal variability in upper ocean heat and salt content, variations that may be aliased by traditional observing techniques

The computational analysis of post-translational modifications

The post-translational modification (PTMs) of proteins presents a means to increase the proteome size and diversity of an organism through the inclusion of structural elements not encoded at the sequence-level alone. Their erroneous inclusion or exclusion has been linked to a variety of diseases and disorders thus their characterisation has the potential to present viable drug targets. The proliferation of newer high-throughput methods, such as mass spectrometry, to identify such modifications has led to a rapid increase in the number of databases and tools to display and analyse such vast amounts of data effectively. This study covers the development of one such tool; PTM Browser, and the construction of the underlying database that it is based upon. This new database was initially seeded with annotations from the Swiss-Prot and Phospho.ELM resources. The initial database of PTMs was then expanded to include a large repertoire of previously unannotated proteins for a selection of topical species (e.g. Danio rerio and Tetraodon nigroviridis). Orthologue assignments have also been added to the database – to allow for queries to be performed regarding the conservation of modifications between homologous proteins. The PTM Browser tool allows for a full exploration of this new database of PTMs – with a special focus on allowing users to identify modifications that are both shared between and are specific to particular species. This tool is freely available for non-commercial use at the following URL: http://www.ptmbrowser.org. An analysis is presented on the conservation of modifications between members of the tumour suppressor family, p53, using this new tool. This tool has also been used to analysis the conservation of modifications between super-kingdoms and Eukaryote species

Functional analysis of Rex, a sensor of the NADH/NAD+ redox poise in Streptomyces coelicolor

Maintenance of the intracellular NADH/NAD+ redox poise is vital for energy generation in cells. Gram-positive bacteria, including the antibiotic-producing organism, Streptomyces coelicolor, have evolved a regulatory protein Rex that both senses this ratio and mediates an adaptive response to changes in it. Rex is a dimeric redox-sensitive transcriptional repressor. It is capable of binding to both NAD+ and NADH, although only NADH is an effector, causing dissociation of the protein from operator (ROP) sites. As NADH levels rise during oxygen limitation Rex dissociates from its target genes allowing expression, which helps to restore the NADH/NAD+ ratio. Microarray-based expression studies had suggested that Rex regulated only a small number of genes. In this work, however, ChIP-on-chip analyses revealed 38 genes that are potential regulon members. Analysis of the Rex binding sites in S. coelicolor revealed new insights into the mode of binding and show that Rex can bind with low affinity to incomplete half sites. This work also focused on characterising two key Rex targets, ndh and nuoA-N, that encode non-proton-translocating and proton translocating NADH dehydrogenases, respectively. Whereas nuoAN is not essential and was not expressed in liquid media, ndh was essential for growth. Depletion of NDH from growing cells led to the induction of Rex target genes confirming that ndh and Rex play key roles in maintaining redox homeostasis. Structure-based dissection of Rex, via a close homologue in Thermus aquaticus, identified a key interaction between the NADH- and DNAbinding domains of Rex. An R29-D203’ salt-bridge, that traverses the NADH binding and DNA binding domains of Rex, appeared to stabilise the DNA-bound form of Rex, but is ‘broken’ in the presence of NADH. In the NADH-bound form of Rex, D203 alternatively interacts with Y111, which in turn interacts with the nicotinamide ring of NADH. In order to assess the importance of individual subunits in the dimeric Rex, a single-chain derivative was constructed and the NADH binding and DNA binding domains individually disrupted

CP asymmetries in scalar bottom quark decays

We propose CP asymmetries based on triple product correlations in the decays sbottom_m -> top chargino_j with subsequent decays of top and chargino_j. For the subsequent chargino_j decay into a leptonic final state l^- \nu neutralino_1 we consider the three possible decay chains chargino_j -> l^- sneutrino -> l^- \nu neutralino_1, chargino_j -> slepton_n \nu -> l^- \nu neutralino_1 and chargino_j -> W^- neutralino_1 -> l^- \nu neutralino_1. We consider two classes of CP asymmetries. In the first class it must be possible to distinguish between different leptonic chargino_j decay chains, whereas in the second class this is not necessary. We consider also the 2-body decay chargino_j -> W^- neutralino_1, and we assume that the momentum of the W boson can be measured. Our framework is the minimal supersymmetric standard model with complex parameters. The proposed CP asymmetries are non-vanishing due to non-zero phases for the parameters \mu and/or A_b. We present numerical results and estimate the observability of these CP asymmetries.Comment: 27 page

Bioeconomy and Circular Economy Approaches Need to Enhance the Focus on Biodiversity to Achieve Sustainability

Bioeconomy and circular economy approaches are being adopted by an increasing number of international organizations, governments and companies to enhance sustainability. Concerns have been raised about the implications for biodiversity. Here, we present a review of current research on the two approaches to determine their relationship to each other and to other economic models, their impact on sustainability and their relationship with biodiversity. Bioeconomy and circular economy are both poorly defined, inconsistently implemented and inadequately measured, and neither provides a clear pathway to sustainability. Many actors promote goals around economic growth above environmental issues. Biodiversity is often addressed indirectly or inadequately. Furthermore, many traditionally disadvantaged groups, including women and indigenous people, may be neglected and rarely engage or benefit. These challenges are compounded by capacity gaps and legal and governance complexities around implementation, influenced by traditional mindsets and approaches. Countries and companies need to plan their sustainability strategies more explicitly around the biodiversity they impact. Opportunities include the relevance and timeliness of sustainable economics for delivering Sustainable Development Goals in a post-COVID world, the existence of work to be built on, and the diversity of stakeholders already engaged. We propose five main steps to ensure the sustainability of economic approaches. Ultimately, we can ensure sustainability only by starting to shift mindsets and establishing a more focused agenda for bioeconomy and circular economy that puts species, ecosystems and the wellbeing of local people at the center

Estimating oceanic primary production using vertical irradiance and chlorophyll profiles from ocean gliders in the North Atlantic

An autonomous underwater vehicle (Seaglider) has been used to estimate marine primary production (PP) using a combination of irradiance and fluorescence vertical profiles. This method provides estimates for depth-resolved and temporally evolving PP on fine spatial scales in the absence of ship-based calibrations. We describe techniques to correct for known issues associated with long autonomous deployments such as sensor calibration drift and fluorescence quenching. Comparisons were made between the Seaglider, stable isotope (13C), and satellite estimates of PP. The Seaglider-based PP estimates were comparable to both satellite estimates and stable isotope measurements

Child-orientated environmental education influences adult knowledge and household behaviour

Environmental education is frequently undertaken as a conservation intervention designed to change the attitudes and behaviour of recipients. Much conservation education is aimed at children, with the rationale that children influence the attitudes of their parents, who will consequently change their behaviour. Empirical evidence to substantiate this suggestion is very limited, however. For the first time, we use a controlled trial to assess the influence of wetland-related environmental education on the knowledge of children and their parents and household behaviour. We demonstrate adults exhibiting greater knowledge of wetlands and improved reported household water management behaviour when their child has received wetland-based education at Seychelles wildlife clubs. We distinguish between 'folk' knowledge of wetland environments and knowledge obtained from formal education, with intergenerational transmission of each depending on different factors. Our study provides the first strong support for the suggestion that environmental education can be transferred between generations and indirectly induce targeted behavioural changes