Speciation and diversification of the beetle tribe Cratopini on the islands of the South West Indian Ocean area.

The aim of this thesis is to examine a spectacular radiation of phytophagous beetles (Curculionidae: Entiminae: Cratopini) that inhabit the islands of the South-Western Indian Ocean. As there are no previous molecular studies of these beetles, it was necessary to take a varied approach that employed both population genetic methods and phylogenetic methods to gain a broad understanding of the evolution of the group. Questions addressed range from aspects of the ecology of individual species to the relationships within islands amongst morphospecies and finally to the biogeography of the group as a whole. Throughout, where appropriate, reference is made to the current understanding of Indian Ocean geology and how this effects the interpretation of the patterns seen. The relationships amongst morphospecies are complex with many found to be paraphyletic within much larger monophyletic clades of multiple morphospecies. Coalescent model based species delimitation techniques are used to define the boundaries of putative species for future examination. The overall biogeography of the group is found to be highly complex with multiple colonisation events across islands and archipelagos. Flight is found to have been lost on multiple occasions and the taxonomy of the group is discussed. Finally many Cratopine lineages are found to display strong population structure despite being flighted, possible reasons for this are discussed

Merging DNA metabarcoding and ecological network analysis to understand and build resilient terrestrial ecosystems

Summary 1. Significant advances in both mathematical and molecular approaches in ecology offer unprecedented opportunities to describe and understand ecosystem functioning. Ecological networks describe interactions between species, the underlying structure of communities and the function and stability of ecosystems. They provide the ability to assess the robustness of complex ecological communities to species loss, as well as a novel way of guiding restoration. However, empirically quantifying the interactions between entire communities remains a significant challenge. 2. Concomitantly, advances in DNA sequencing technologies are resolving previously intractable questions in functional and taxonomic biodiversity and provide enormous potential to determine hitherto difficult to observe species interactions. Combining DNA metabarcoding approaches with ecological network analysis presents important new opportunities for understanding large-scale ecological and evolutionary processes, as well as providing powerful tools for building ecosystems that are resilient to environmental change. 3. We propose a novel ‘nested tagging’ metabarcoding approach for the rapid construction of large, phylogenetically structured species-interaction networks. Taking tree–insect–parasitoid ecological networks as an illustration, we show how measures of network robustness, constructed using DNA metabarcoding, can be used to determine the consequences of tree species loss within forests, and forest habitat loss within wider landscapes. By determining which species and habitats are important to network integrity, we propose new directions for forest management. 4. Merging metabarcoding with ecological network analysis provides a revolutionary opportunity to construct some of the largest, phylogenetically structured species-interaction networks to date, providing new ways to: (i) monitor biodiversity and ecosystem functioning; (ii) assess the robustness of interacting communities to species loss; and (iii) build ecosystems that are more resilient to environmental change

A molecular imprinted polymer based sensor for measuring phosphate in wastewater samples

Phosphate detection in water samples is still completed using colorimetric standard methods, which have a number of disadvantages, to such as being time consuming, requiring filtration, a number of different reagents, frequent calibration and proper disposal of waste chemicals generated. Hence, a simple cost effective analytical method and instrumentation is highly desirable to aid the optimisation of treatment processes and assist the water industry in their efforts to comply with stringent regulations such as the EU's Water Framework Directive. A sensor based on molecular imprinted polymer (MIP) and a conductance transducer was developed for direct and label-free detection of phosphate in water. The sensor was able to measure the presence of phosphate in wastewater samples with good reproducibility, a linear range of 0.66-8 mg P L-1 and a lower detection limit of 0.16 mg P L-1. The sensor was further tested to measure phosphate concentrations in unfiltered field samples such as domestic wastewater treatment influent and river water and demonstrated a close correlation with reference measurements. The phosphate MIP sensor offers a way forward as either a handheld sensor for use in the field, or as a potential solution for remote, continuous monitoring of phosphate

Block-and-hole graphs: Constructibility and (3,0)(3,0)-sparsity

We show that minimally 3-rigid block-and-hole graphs, with one block or one hole, are characterised as those which are constructible from $K_3$ by vertex splitting, and also, as those having associated looped face graphs which are $(3,0)$-tight. This latter property can be verified in polynomial time by a form of pebble game algorithm. We also indicate connections to the rigidity properties of polyhedral surfaces known as origami and to graph rigidity in $\ell_p^3$ for $p\not=2$.Comment: 17 page

Invisible design: exploring insights and ideas through ambiguous film scenarios

Invisible Design is a technique for generating insights and ideas with workshop participants in the early stages of concept development. It involves the creation of ambiguous films in which characters discuss a technology that is not directly shown. The technique builds on previous work in HCI on scenarios, persona, theatre, film and ambiguity. The Invisible Design approach is illustrated with three examples from unrelated projects; Biometric Daemon, Panini and Smart Money. The paper presents a qualitative analysis of data from a series of workshops where these Invisible Designs were discussed. The analysis outlines responses to the films in terms of; existing problems, concerns with imagined technologies and design speculation. It is argued that Invisible Design can help to create a space for critical and creative dialogue during participatory concept development

The generic rigidity of triangulated spheres with blocks and holes

A simple graph G = (V,E) is 3-rigid if its generic bar-joint frameworks in R^3 are infinitesimally rigid. Block and hole graphs are derived from triangulated spheres by the removal of edges and the addition of minimally rigid subgraphs, known as blocks, in some of the resulting holes. Combinatorial characterisations of minimal 3-rigidity are obtained for these graphs in the case of a single block and finitely many holes or a single hole and finitely many blocks. These results confirm a conjecture of Whiteley from 1988 and special cases of a stronger conjecture of Finbow-Singh and Whiteley from 2013

The rigidity of a partially triangulated torus

A simple graph is 3-rigid if its generic embeddings in R^3 are infinitesimally rigid. Necessary and sufficient conditions are obtained for the minimal 3-rigidity of a simple graph obtained from a triangulated torus by the deletion of edges interior to an embedded triangulated disc

Targeting danger molecules in tendinopathy: the HMGB1/TLR4 axis

Objectives: To seek evidence of the danger molecule, high-mobility group protein B1 (HMGB1) expression in human tendinopathy and thereafter, to explore mechanisms where HMGB1 may regulate inflammatory mediators and matrix regulation in human tendinopathy. Methods: Torn supraspinatus tendon (established pathology) and matched intact subscapularis tendon (representing ‘early pathology’) biopsies were collected from patients undergoing arthroscopic shoulder surgery. Control samples of subscapularis tendon were collected from patients undergoing arthroscopic stabilisation surgery. Markers of inflammation and HMGB1 were quantified by reverse transcriptase PCR (RT-PCR) and immunohistochemistry. Human tendon-derived primary cells were derived from hamstring tendon tissue obtained during hamstring tendon anterior cruciate ligament reconstruction and used through passage 3. In vitro effects of recombinant HMGB1 on tenocyte matrix and inflammatory potential were measured using quantitative RT-PCR, ELISA and immunohistochemistry staining. Results: Tendinopathic tissues demonstrated significantly increased levels of the danger molecule HMGB1 compared with control tissues with early tendinopathy tissue showing the greatest expression. The addition of recombinant human HMGB1 to tenocytes led to significant increase in expression of a number of inflammatory mediators, including interleukin 1 beta (IL-1β), IL-6, IL-33, CCL2 and CXCL12, in vitro. Further analysis demonstrated rhHMGB1 treatment resulted in increased expression of genes involved in matrix remodelling. Significant increases were observed in Col3, Tenascin-C and Decorin. Moreover, blocking HMGB1 signalling via toll-like receptor 4 (TLR4) silencing reversed these key inflammatory and matrix changes. Conclusion: HMGB1 is present in human tendinopathy and can regulate inflammatory cytokines and matrix changes. We propose HMGB1 as a mediator driving the inflammatory/matrix crosstalk and manipulation of the HMGB1/TLR4 axis may offer novel therapeutic approaches targeting inflammatory mechanisms in the management of human tendon disorders