XXIV. On the inverted action of the alburnous vessels of trees. In a letter to the right honourable Sir J oseph B anks , K. B. P. R. S.

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Towards knowing through doing : improving the societal relevance of systematic conservation assessments

Systematic conservation assessments are spatially-explicit techniques for prioritising areas for the implementation of conservation action. There has been considerable reference in the peer-reviewed literature as to the usefulness of these tools, which appear to be primarily used by academics for theoretical research. A literature review and author survey reveals the peer-reviewed literature is largely theoretical, although conservation action results more frequently than reported. The effectiveness of these interventions is generally described as only ‘fairly effective’. This general trend, coupled with previous personal failures in translating systematic conservation assessments into effective conservation action triggered an explicit process of social learning implemented as action research. It examined the workings of the Subtropical Thicket Ecosystem Planning (STEP) project, which included development of a systematic conservation assessment. Systematic conservations assessments simply provide information on where action should be implemented, and so are only useful if situated within broader operational models for conservation planning. Most operational models presented in the peer-reviewed literature are primarily focused upon the testing ecological data, not upon the delivery of conservation action. A new operational model for conservation planning is presented which more accurately reflects the ‘real-world’ process of conservation planning. An implementation strategy is an essential complement to a systematic conservation assessment. It describes how specific, explicitly-stated goals will be achieved, who is accountable for undertaking these activities, and the resources required. As the Implementation Specialist for the STEP Project, I co-lead the collaborative development of an implementation strategy with stakeholders that aimed to mobilise resources towards achieving common goals. Whilst the development and initial uptake of the strategy was good, subsequent implementation has flounder. The reasons for this are explored. The ultimate pragmatic goal of a conservation planning process is the establishment of effective social learning institutions. These develop common visions, mobilise collective action, and adaptively learn and refine their conservation activities. Thicket Forum is one xi such institution established through the STEP Project. My involvement with Thicket Forum since 2004 in implementing an adaptive learning approach facilitates collaboration between land managers, government and research organisations. Systematic conservation assessments evolved in response to the ad hoc way in which protected areas were implemented, leaving unrepresentative, biased protected area networks. Most research is theoretical and without an intimate understanding of the social-ecological system of a planning region, notably opportunities and constraints for implementing conservation action. Highlighting the importance of an approach which is flexible, not only in space, but in time, which can capitalise upon implementation opportunities, is important for stemming the myth that opportunism is the nemesis of systematic conservation assessments. To this end, conservation planners have been slow to include factors influencing effective implementation in systematic conservation assessments. Many studies which identify candidate protected area networks, first, fail to identify the specific instrument(s) to be applied, and second, assume all intact land is available. Having mapped the willingness of land managers in the Albany District, South Africa, to sell their land, it is demonstrated the majority of targets fail to be achieved because land managers will not sell. Knowing this, the current focus of gathering ever-more ecological data is misplaced. Human, social and economic factors influence target achievement, efficiency and spatial configuration of priority areas. Selecting important areas for conservation, particularly at the local-scale, requires the mapping of factors which define opportunities for conservation. Land manager willingness to collaborate and participate, entrepreneurial orientation, conservation knowledge, social capital, and local champions were applied using a method of hierarchical clustering to identify land managers who represent conservation opportunities for private land conservation initiatives

Insect-inspired navigation: Smart tricks from small brains

Small-brained insects are expert at many tasks that are currently difficult for robots, but especially in the speed and robustness of their learning abilities. In contrast to AI methods which generally take long times to train and large amounts of labelled data, insects are rapid learners of visual and olfactory information and are capable of long distance navigation, exploration and spatial learning. What if we could give robots these abilities, by mimicking the sensors, circuits and behaviours of insects? This is the goal of the Brains on Board project (brainsonboard.co.uk). In this talk, we will discuss the Brains on Board project and our work on insect-inspired visual navigation in particular. The use of visual information for navigation is a universal strategy for sighted animals, amongst whom ants are particular experts despite have small brains and low-resolution vision [1]. To understand how they achieve this, we combine behavioural experiments with modelling and robotics to show how ants directly acquire and use task-specific information through specialised sensors, brains and behaviours, enabling complex behaviour to emerge without complex processing. In this spirit, we will show that an agent – insect or robot – can robustly navigate without ever knowing where it is, without specifying when or what it should learn, nor requiring it to recognise specific objects, places routes or maps. This leads to an algorithm in which visual information specifies actions not locations in which route navigation is recast as a search for familiar views allowing routes through visually complex worlds to be encoded by a single layer artificial neural network (ANN) after a single training run with only low resolution vision [2]. As well as meaning that the algorithms are plausible in terms of memory load and computation for a small-brained insect, it also makes them very well-suited to a small, power-efficient, robot. We thus demonstrate that this algorithm, with all computation performed on a small low-power robot, is capable of delivering reliable direction information along outdoor routes, even when scenes contain few local landmarks and have high-levels of noise (from variable lighting and terrain) [3]. Indeed, routes can be precisely recapitulated and we show that the required computation does not increase with the number of training views. Thus the ANN provides a compact representation of the knowledge needed to traverse a route. In fact, rather than the compact representation losing information, there are instances where the use of an ANN ameliorates the problems of sub optimal paths caused by tortuous training routes. Our results suggest the feasibility of familiarity-based navigation for long-range autonomous visual homing. [1] Shettleworth, S. (2010) Clever animals and killjoy explanations in comparative psychology. Trends in Cognitive Sciences 14 (11):477-481 [2] Baddeley, B., Graham, P., Husbands, P., & Philippides, A. (2012). A model of ant route navigation driven by scene familiarity. PLoS computational biology, 8(1), e1002336. [3] Knight, J, Sakhapov, D., Domcsek, A., Dewar, A., Graham, P., Nowotny, T., Philippides, A. (2019) Insect-Inspired Visual Navigation On-Board an Autonomous Robot: Real-World Routes Encoded in a Single Layer Network. Proc. Artificial Life 19. In Press

Vertebrate Hosts as Islands: Dynamics of Selection, Immigration, Loss, Persistence, and Potential Function of Bacteria on Salamander Skin.

Skin bacterial communities can protect amphibians from a fungal pathogen; however, little is known about how these communities are maintained. We used a neutral model of community ecology to identify bacteria that are maintained on salamanders by selection or by dispersal from a bacterial reservoir (soil) and ecological drift. We found that 75% (9/12) of bacteria that were consistent with positive selection, <1% of bacteria that were consistent with random dispersal and none of the bacteria that were consistent under negative selection had a 97% or greater match to antifungal isolates. Additionally we performed an experiment where salamanders were either provided or denied a bacterial reservoir and estimated immigration and loss (emigration and local extinction) rates of bacteria on salamanders in both treatments. Loss was strongly related to bacterial richness, suggesting competition is important for structuring the community. Bacteria closely related to antifungal isolates were more likely to persist on salamanders with or without a bacterial reservoir, suggesting they had a competitive advantage. Furthermore, over-represented and under-represented operational taxonomic units (OTUs) had similar persistence on salamanders when a bacterial reservoir was present. However, under-represented OTUs were less likely to persist in the absence of a bacterial reservoir, suggesting that the over-represented and under-represented bacteria were selected against or for on salamanders through time. Our findings from the neutral model, migration and persistence analyses show that bacteria that exhibit a high similarity to antifungal isolates persist on salamanders, which likely protect hosts against pathogens and improve fitness. This research is one of the first to apply ecological theory to investigate assembly of host associated-bacterial communities, which can provide insights for probiotic bioaugmentation as a conservation strategy against disease

Developmental Regulation of an Adhesin Gene during Cellular Morphogenesis in the Fungal Pathogen Candida albicans

Peer reviewedPublisher PD

Insect-inspired visual navigation on-board an autonomous robot: real-world routes encoded in a single layer network

Insect-Inspired models of visual navigation, that operate by scanning for familiar views of the world, have been shown to be capable of robust route navigation in simulation. These familiarity-based navigation algorithms operate by training an artificial neural network (ANN) with views from a training route, so that it can then output a familiarity score for any new view. In this paper we show that such an algorithm – with all computation performed on a small low-power robot – is capable of delivering reliable direction information along real-world outdoor routes, even when scenes contain few local landmarks and have high-levels of noise (from variable lighting and terrain). Indeed, routes can be precisely recapitulated and we show that the required computation and storage does not increase with the number of training views. Thus the ANN provides a compact representation of the knowledge needed to traverse a route. In fact, rather than losing information, there are instances where the use of an ANN ameliorates the problems of sub optimal paths caused by tortuous training routes. Our results suggest the feasibility of familiarity-based navigation for long-range autonomous visual homing

The phosphoproteome of Arabidopsis plants lacking the oxidative signal-inducible1 (OXI1) protein kinase

The AGC protein kinase OXI1 is a key protein in plant responses to oxidative signals, and is important for two oxidative burst-mediated processes: basal resistance to microbial pathogens and root hair growth. To identify possible components of the OXI1 signalling pathway, phosphoproteomic techniques were used to detect alterations in the abundance of phosphorylated proteins and peptides in an oxi1 null mutant of Arabidopsis thaliana. The relative abundance of phosphorylated proteins was assessed either using two-dimensional gel electrophoresis and staining with the phosphoprotein stain Pro-Q Diamond or by the identification and quantification, by mass spectrometry, of stable-isotope labelled phosphopeptides. A number of proteins show altered phosphorylation in the oxi1 mutant. Five proteins, including a putative F-box and 3-phosphoinositide-dependent kinase 1, show reduced phosphorylation in the oxi1 mutant, and may be direct or indirect targets of OXI1. Four proteins, including ethylene insensitive 2 and phospholipase d-gamma, show increased phosphorylation in the oxi1 mutant. This study has identified a range of candidate proteins from the OXI1 signalling pathway. The diverse activities of these proteins, including protein degradation and hormone signalling, may suggest crosstalk between OXI1 and other signal transduction cascades.</p

Cationic biaryl 1,2,3-triazolyl peptidomimetic amphiphiles: synthesis, antibacterial evaluation and preliminary mechanism of action studies

Synthetic small molecular antimicrobial peptidomimetics represent a promising new class of potential antibiotics due to their membrane-disrupting ability and their decreased propensity for bacterial resistance. A library of 43 mono- and di-cationic biaryl 1,2,3-triazolyl peptidomimetics was designed and synthesized based upon previously established lead biarylpeptidomimetics and a known pharmacophore. A reliable, facile and modular synthetic pathway allowed for the efficient synthesis of multiple unique scaffolds which were subjected to divergent derivatization to furnish the amphiphilic compounds. In vitro testing revealed enhanced antibacterial efficacy against a range of pathogenic bacteria, including bacterial isolates with methicillin, vancomycin, daptomycin, or multi-drug resistance. Preliminary time-kill kinetics and membrane-disruption assays revealed a likely membrane-active mechanism for the tested peptidomimetics. An optimal balance between hydrophobicity and cationic charge was found to be essential for reduced cytotoxicity/haemolysis (i.e. membrane selectivity) and enhanced Gram-negative activity. The cationic biaryl amphiphile 81 was identified as a potent, broad-spectrum peptidomimetic with activity against Gram-positive (methicillin-resistant Staphylococcus aureus - MIC = 2 μg/mL) and Gram-negative (Escherichia coli - MIC = 4 μg/mL) pathogenic bacteria

Cationic biaryl 1,2,3-triazolyl peptidomimetic amphiphiles: synthesis, antibacterial evaluation and preliminary mechanism of action studies

Synthetic small molecular antimicrobial peptidomimetics represent a promising new class of potential antibiotics due to their membrane-disrupting ability and their decreased propensity for bacterial resistance. A library of 43 mono- and di-cationic biaryl 1,2,3-triazolyl peptidomimetics was designed and synthesized based upon previously established lead biarylpeptidomimetics and a known pharmacophore. A reliable, facile and modular synthetic pathway allowed for the efficient synthesis of multiple unique scaffolds which were subjected to divergent derivatization to furnish the amphiphilic compounds. In vitro testing revealed enhanced antibacterial efficacy against a range of pathogenic bacteria, including bacterial isolates with methicillin, vancomycin, daptomycin, or multi-drug resistance. Preliminary time-kill kinetics and membrane-disruption assays revealed a likely membrane-active mechanism for the tested peptidomimetics. An optimal balance between hydrophobicity and cationic charge was found to be essential for reduced cytotoxicity/haemolysis (i.e. membrane selectivity) and enhanced Gram-negative activity. The cationic biaryl amphiphile 81 was identified as a potent, broad-spectrum peptidomimetic with activity against Gram-positive (methicillin-resistant Staphylococcus aureus - MIC = 2 μg/mL) and Gram-negative (Escherichia coli - MIC = 4 μg/mL) pathogenic bacteria. © 2019 Elsevier Masson SA

Science based tools informing coastal management in a changing climate

To better inform decisions associated with coastal management a database of numerical simulations has been generated using publically available data to populate an online decision-support tool (DST). This research is part of the Adaptation and Resilience of Coastal Energy Supply (ARCoES) project that focuses on areas of critical coastal energy infrastructure within the UK, such as nuclear power station locations. This web-based tool has been developed with coastal and energy sector practitioners to produce a system that visualizes plausible future changes in flood hazard to assess when ‘tipping points’ in a location’s management strategy may be required in response to rising sea levels and storms over the next 500 years. Although the main product is focused on vulnerability to flooding, additional research on the natural resilience of shorelines has also been considered in relation to future adaptation strategies. These findings are fed into economic models developed through ARCoES to assess the cost-benefit impacts or real option