The importance of interaction strength for food web dynamics and ecosystem functioning

Global biodiversity is eroding at an alarming rate, through a combination of anthropogenic disturbance and environmental change. Ecological communities are bewildering in their complexity. Experimental ecologists strive to understand the mechanisms that drive the stability and structure of these complex communities in a bid to inform nature conservation and management. Two fields of research have had high profile success at developing theories related to these stabilising structures and testing them through controlled experimentation. Biodiversity-ecosystem functioning (BEF) research has explored the likely consequences of biodiversity loss on the functioning of natural systems and the provision of important ecosystem services. Empirical tests of BEF theory often consist of simplified laboratory and field experiments, carried out on subsets of ecological communities. Such experiments often overlook key information relating to patterns of interactions, important relationships, and fundamental ecosystem properties. The study of multi-species predator-prey interactions has also contributed much to our understanding of how complex systems are structured, particularly through the importance of indirect effects and predator suppression of prey populations. A growing number of studies describe these complex interactions in detailed food webs, which encompass all the interactions in a community. This has led to recent calls for an integration of BEF research with the comprehensive study of food web properties and patterns, to help elucidate the mechanisms that allow complex communities to persist in nature. This thesis adopts such an approach, through experimentation at Lough Hyne marine reserve, in southwest Ireland. Complex communities were allowed to develop naturally in exclusion cages, with only the diversity of top trophic levels controlled. Species removals were carried out and the resulting changes to predator-prey interactions, ecosystem functioning, food web properties, and stability were studied in detail. The findings of these experiments contribute greatly to our understanding of the stability and structure of complex natural communities.

Interaction strengths and net effects in food web models

Understanding how dynamic ecological communities respond to anthropogenic drivers of change such as habitat loss and fragmentation, climate change and the introduction of alien species requires that there is a theoretical framework able to predict community dynamics. At present there is a lack of empirical data that can be used to inform and test predictive models, which means that much of our knowledge regarding the response of ecological communities to perturbations is obtained from theoretical analyses and simulations. This thesis is composed of two strands of research: an empirical experiment conducted to inform the scaling of intraspecific and interspecific interaction strengths in a three species food chain and a series of theoretical analyses on the changes to equilibrium biomass abundances following press perturbations. The empirical experiment is a consequence of the difficulties faced when parameterising the intraspecific interaction strengths in a Lotka-Volterra model. A modification of the dynamic index is used alongside the original dynamic index to estimate intraspecific interactions and interspecific interaction strengths in a three species food. The theoretical analyses focused on the effect of press perturbations to focal species on the equilibrium biomass densities of all species in the community; these perturbations allow for the quantification of a species total net effect. It was found that there is a strong and consistent positive relationship between a species body size and its total net effect for a set of 97 synthetic food webs and also for the Ythan Estuary and Tuesday Lake food webs (empirically described food webs). It is shown that ecological constraints (due to allometric scaling) on the magnitude of entries in the community matrix cause the patterns observed in the inverse community matrix and thus explain the relationship between a species body mass and its total net effect in a community.

An investigation of innovation and knowledge creation in virtual worlds

The Internet and World Wide Web have had, and continue to have, an incredible impact on our civilization. These technologies have radically influenced the way that society is organised and the manner in which people around the world communicate and interact. The structure and function of individual, social, organisational, economic and political life begin to resemble the digital network architectures upon which they are increasingly reliant. It is increasingly difficult to imagine how our ‘offline’ world would look or function without the ‘online’ world; it is becoming less meaningful to distinguish between the ‘actual’ and the ‘virtual’. Thus, the major architectural project of the twenty-first century is to “imagine, build, and enhance an interactive and ever changing cyberspace” (Lévy, 1997, p. 10). Virtual worlds are at the forefront of this evolving digital landscape. Virtual worlds have “critical implications for business, education, social sciences, and our society at large” (Messinger et al., 2009, p. 204). This study focuses on the possibilities of virtual worlds in terms of communication, collaboration, innovation and creativity. The concept of knowledge creation is at the core of this research. The study shows that scholars increasingly recognise that knowledge creation, as a socially enacted process, goes to the very heart of innovation. However, efforts to build upon these insights have struggled to escape the influence of the information processing paradigm of old and have failed to move beyond the persistent but problematic conceptualisation of knowledge creation in terms of tacit and explicit knowledge. Based on these insights, the study leverages extant research to develop the conceptual apparatus necessary to carry out an investigation of innovation and knowledge creation in virtual worlds. The study derives and articulates a set of definitions (of virtual worlds, innovation, knowledge and knowledge creation) to guide research. The study also leverages a number of extant theories in order to develop a preliminary framework to model knowledge creation in virtual worlds. Using a combination of participant observation and six case studies of innovative educational projects in Second Life, the study yields a range of insights into the process of knowledge creation in virtual worlds and into the factors that affect it. The study’s contributions to theory are expressed as a series of propositions and findings and are represented as a revised and empirically grounded theoretical framework of knowledge creation in virtual worlds. These findings highlight the importance of prior related knowledge and intrinsic motivation in terms of shaping and stimulating knowledge creation in virtual worlds. At the same time, they highlight the importance of meta-knowledge (knowledge about knowledge) in terms of guiding the knowledge creation process whilst revealing the diversity of behavioural approaches actually used to create knowledge in virtual worlds and. This theoretical framework is itself one of the chief contributions of the study and the analysis explores how it can be used to guide further research in virtual worlds and on knowledge creation. The study’s contributions to practice are presented as actionable guide to simulate knowledge creation in virtual worlds. This guide utilises a theoretically based classification of four knowledge-creator archetypes (the sage, the lore master, the artisan, and the apprentice) and derives an actionable set of behavioural prescriptions for each archetype. The study concludes with a discussion of the study’s implications in terms of future research.

Investigation of global regulators influencing styrene metabolism and bioplastic synthesis in Pseudomonas putida CA-3

The genetics and biochemistry involved in the biodegradation of styrene and the production of polyhydroxyalkanoates in Pseudomonas putida CA-3 have been well characterised to date. Knowledge of the role played by global regulators in controlling these pathways currently represents a critical knowledge gap in this area. Here we report on our efforts to identify such regulators using mini-Tn5 transposon mutagenesis of the P. putida CA-3 genome. The library generated was subjected to phenotypic screening to identify mutants exhibiting a reduced sensitivity to the effects of carbon catabolite repression of aromatic pathway activity. Our efforts identified a clpX disrupted mutant which exhibited wild-type levels of growth on styrene but significantly reduced growth on phenylacetic acid. RT-PCR analysis of key PACoA catabolon genes necessary for phenylacetic acid metabolism, and SDS-PAGE protein profile analyses suggest that no direct alteration of PACoA pathway transcriptional or translational activity was involved. The influence of global regulators affecting the accumulation of PHAs in P. putida CA-3 was also studied. Phenotypic screening of the mini-Tn5 library revealed a gacS sensor kinase gene disruption resulting in the loss of PHA accumulation capacity in P. putida CA-3. Subsequent SDS-PAGE protein analyses of the wild type and gacS mutant strains identified post-transcriptional control of phaC1 synthase as a key point of control of PHA synthesis in P. putida CA-3. Disruption of the gacS gene in another PHA accumulating organism, P. putida S12, also demonstrated a reduction of PHA accumulation capacity. PHA accumulation was observed to be disrupted in the CA-3 gacS mutant under phosphorus limited growth conditions. Over-expression studies in both wild type CA-3 and gacS mutant demonstrated that rsmY over-expression in gacS disrupted P. putida CA-3 is insufficient to restore PHA accumulation in the cell however in wild type cells, over-expression of rsmY results in an altered PHA monomer compositions.

Flat surfaces of finite type in the 3-sphere

We introduce the notion of flat surfaces of finite type in the 3- sphere, give the algebro-geometric description in terms of spectral curves and polynomial Killing fields, and show that finite type flat surfaces generated by curves on S2 with periodic curvature functions are dense in the space of all flat surfaces generated by curves on S2 with periodic curvature functions.

An investigation into the role of Bcl-3 in toll-like receptor signalling

Through the recognition of potentially harmful stimuli, Toll-like receptors (TLRs) initiate the innate immune response and induce the expression of hundreds of immune and pro-inflammatory genes. TLRs are critical in mounting a defence against invading pathogens however, strict control of TLR signalling is vital to prevent host damage from excessive or prolonged immune activation. In this thesis the role of the IκB protein Bcl (B-cell lymphoma)-3 in the regulation of TLR signalling is investigated. Bcl3-/- mice and cells are hyper responsive to TLR stimulation and are defective in LPS tolerance. Bcl-3 interacts with and blocks the ubiquitination of homodimers of the NF-κB subunit, p50. Through stabilisation of inhibitory p50 homodimers, Bcl-3 negatively regulates NF-κB dependent inflammatory gene transcription following TLR activation. Firstly, we investigated the nature of the interaction between Bcl-3 and p50 and using peptide array technology. Key amino acids required for the formation of the p50:Bcl-3 immunosuppressor complex were identified. Furthermore, we demonstrate for the first time that interaction between Bcl-3 and p50 is necessary and sufficient for the anti-inflammatory properties of Bcl-3. Using the data generated from peptide array analysis we then generated cell permeable peptides designed to mimic Bcl-3 function and stabilise p50 homodimers. These Bcl-3 derived peptides are potent inhibitors of NF-κB dependent transcription activity in vitro and provide a solid basis for the development of novel gene-specific approaches in the treatment of inflammatory diseases. Secondly, we demonstrate that Bcl-3 mediated regulation of TLR signalling is not limited to NF-κB and identify the MAK3K Tumour Progression Locus (Tpl)-2 as a new binding partner of Bcl-3. Our data establishes role for Bcl-3 as a negative regulator of the MAPK-ERK pathway.

Trophic role of small cetaceans and seals in Irish waters

Understanding the role of marine mammals in specific ecosystems and their interactions with fisheries involves, inter alia, an understanding of their diet and dietary requirements. In this thesis, the foraging ecology of seven marine mammal species that regularly occur in Irish waters was investigated by reconstructing diet using hard parts from digestive tracts and scats. Of the species examined, two (striped and Atlantic white-sided dolphin) can be considered offshore species or species inhabiting neritic waters, while five others usually inhabit more coastal areas (white-beaked dolphin, harbour porpoise, harbour seal and grey seal); the last species studied was the bottlenose dolphin whose population structure is more complex, with coastal and offshore populations. A total of 13,028 prey items from at least 81 different species (62 fish species, 14 cephalopods, four crustaceans, and a tunicate) were identified. 28% of the fish species were identified using bones other than otoliths, highlighting the importance of using all identifiable structures to reconstruct diet. Individually, each species of marine mammal presented a high diversity of prey taxa, but the locally abundant Trisopterus spp. were found to be the most important prey item for all species, indicating that Trisopterus spp. is probably a key species in understanding the role of these predators in Irish waters. In the coastal marine mammals, other Gadiformes species (haddock, pollack, saithe, whiting) also contributed substantially to the diet; in contrast, in pelagic or less coastal marine mammals, prey was largely comprised of planktivorous fish, such as Atlantic mackerel, horse mackerel, blue whiting, and mesopelagic prey. Striped dolphins and Atlantic white-sided dolphins are offshore small cetaceans foraging in neritic waters. Differences between the diet of striped dolphins collected in drift nets targeting tuna and stranded on Irish coasts showed a complex foraging behaviour; the diet information shows that although this dolphin forages mainly in oceanic waters it may occasionally forage on the continental shelf, feeding on available prey. The Atlantic white-sided dolphin diet showed that this species prefers to feed over the continental edge, where planktivorous fish are abundant. Some resource partitioning was found in bottlenose dolphins in Irish waters consistent with previous genetic and stable isotope analysis studies. Bottlenose dolphins in Irish waters appears to be generalist feeders consuming more than 30 prey species, however most of the diet comprised a few locally abundant species, especially gadoid fish including haddock/pollack/saithe group and Trisopterus spp., but the contribution of Atlantic hake, conger eels and the pelagic planktivorous horse mackerel were also important. Stomach content information suggests that three different feeding behaviours might occur in bottlenose dolphin populations in Irish waters; firstly a coastal behaviour, with animals feeding on prey that mainly inhabit areas close to the coast; secondly an offshore behaviour where dolphins feed on offshore species such as squid or mesopelagic fish; and a third more complex behaviour that involves movements over the continental shelf and close to the shelf edge. The other three coastal marine mammal species (harbour porpoise, harbour seal and grey seal) were found to be feeding on similar prey and competition for food resources among these sympatric species might occur. Both species of seals were found to have a high overlap (more than 80%) in their diet composition, but while grey seals feed on large fish (>110mm), harbour seals feed mostly on smaller fish (<110mm), suggesting some spatial segregation in foraging. Harbour porpoises and grey seals are potentially competing for the same food resource but some differences in prey species were found and some habitat partitioning might occur. Direct interaction (by catch) between dolphins and fisheries was detected in all species. Most of the prey found in the stomach contents from both stranded and by catch dolphins were smaller sizes than those targeted by commercial fisheries. In fact, the total annual food consumption of the species studied was found to be very small (225,160 tonnes) in comparison to fishery landings for the same area (~2 million tonnes). However, marine mammal species might be indirectly interacting with fisheries, removing forage fish. Incorporating the dietary information obtained from the four coastal species, an ECOPATH food web model was established for the Irish Sea, based on data from 2004. Five trophic levels were found, with bottlenose dolphins and grey and harbour seals occurring at the highest trophic level. A comparison with a previous model based on 1973 data suggests that while the overall Irish Sea ecosystem appears to be “maturing”, some indices indicate that the 2004 fishery was less efficient and was targeting fish at higher trophic levels than in 1973, which is reflected in the mean trophic level of the catch. Depletion or substantial decrease of some of the Irish Sea fish stocks has resulted in a significant decline in landings in this area. The integration of diet information in mass-balance models to construct ecosystem food-webs will help to understand the trophic role of these apex predators within the ecosystem.

Access to modified geiparvarins using Pd(0)-mediated C-C bond forming reactions

Geiparvarin is a natural product which contains both a 3(2H)-furanone and a coumarin moiety in its structure. The aim of this project was to investigate the use of Pd(0)-mediated C–C bondforming reactions to produce structurally modified geiparvarins. Chapter 1 consists of a review of the relevant literature, including that pertaining to the syntheses of selected naturally occurring 3(2H)-furanones. The known syntheses of geiparvarin and closely related analogues are examined, along with the documented biological activity of these compounds. The synthetic routes which allow access to 4-substituted-3(2H)-furanones are also described. Chapter 2 describes in detail the synthesis of a variety of novel structurally modified geiparvarins by two complementary routes, both approaches utilising Pd(0)-mediated crosscoupling reactions, and discusses the characterisation of these compounds. The preparation of 5-ethyl-3(2H)-furanones is described, as is their incorporation into geiparvarin and the corresponding 5″-alkylgeiparvarin analogues via formation and dehydration of intermediate alcohols. Halogenation of 5-ethyl-3(2H)-furanones and the corresponding geiparvarin derivatives is discussed, along with further reactions of the resulting halides. Preparation of 3″-arylgeiparvarins involving both Suzuki–Miyura and Stille reactions, using the appropriate intermediate iodides and bromides, is described. The application of Stille and Heck conditions to give 3″-ethenylgeiparvarin analogues and Sonogashira conditions to produce 3″-ethynylgeiparvarin analogues, using the relevant intermediate iodides, is also extensively outlined. Chapter 3 contains all of the experimental data and details of the synthetic methods employed for the compounds prepared during the course of this research. All novel compounds prepared were fully characterised using NMR spectroscopy, IR spectroscopy, mass spectrometry and elemental analysis; the details of which are included.

Synthesis of 4-substituted-3(2H)-furanones with novel luminescence properties

The objective of this project was to prepare a range of 4-substituted 3-(2H)-furanones, and to investigate the relationship between their molecular structures and photoluminescence properties. The effects of substituents and conjugated linker unit were also investigated. After generation of the key 3(2H)-furanone heterocycle, extension of the conjugated framework at the C-4 position was achieved through Pd(0)-catalysed coupling reactions. Chapter one of the thesis comprises a review of the relavent literature and is split into three sections. These include information about the prevalence of 3-(2H)-furanones as natural products and synthetic routes to 3-(2H)-furanones in general. The synthetic routes are divided according to the synthetic precursor employed. The final section of chapter one outlines the fundamental principles and application of photoluminescence to organic compounds in general. Chapter two contains the results of the research achieved in the course of this work and a discussion of the findings. Two routes were successfully employed to generate 4-unsubstituted 3-(2H)-furanone moieties: (i) base induced cyclisation of hydroxyenones and (ii) isoxazole chemistry. A number of methods which proved ineffective in the production of furanones with the desired substitution pattern are also detailed. The majority of this study was focused on the introduction of substituents at the C-4 position of the 3-(2H)-furanone ring. This was achieved through the use of Sonogashira and Suzuki cross coupling protocols for Pd(0) catalysed C-C bond formation. The further functionalisation of some compounds was performed using transfer hydrogenation and “click chemistry” methodologies. Finally, the photophysical properties of 3-(2H)-furanones prepared in this project are discussed and the effect of substitution patterns in a complementary “push push” and “push pull” manner have also been investigated. All the experimental data and details of the synthetic methods employed, for the compounds prepared during the course of this research is contained in chapter three together with the spectroscopic and analytical properties of the compounds prepared.

An investigation into reactivity and selectivity in cycloadditions of 1,3-dipoles with formamidines

The objective of this research was to investigate the synthesis of nitrile oxides and to study their reactivity in 1,3-dipolar cycloadditions with formamidines. Chapter one looks at the literature surrounding the 1,3-dipolar cycloaddition reaction. It explores the generation of 1,3-dipoles (mainly nitrile oxides) and dipolarophiles (predominantly amidines). It discusses the potential synthetic uses of the 1,3-dipolar cycloadducts. It examines both and inter- and intra-molecular cycloaddition reactions. It recognises the use of the 1,3-dipolar cycloadditions as a successful method in building natural products and oxadiazolines. The decomposition of oxadiazolines as a route to nitriles is also outlined in this chapter. Chapter two discusses the results of this research candidate. The preparation of nitrile oxide precursors - hydroximoyl halides - is outlined at first. The generation of nitrile oxides is then demonstrated, followed by the preparation of furoxans. Methods for preparing the reference materials (nitriles and ureas), which result from decomposition of oxadiazolines, then follow. The preparation of series of Δ2-1,2,4- oxadiazolines via the 1,3-dipolar cycloaddition reaction is illustrated in this chapter. The selectivity of the addition of nitrile oxides to dipolarophiles was tested by competition reactions, which are also described in this chapter. NMR techniques were used in the study of the kinetics of the 1,3-dipolar cycloadditions used for the preparation of a series of Δ2-1,2,4-oxadiazolines, which is addressed in this chapter. Chapter three charts the experimental procedures followed to gain results which are discussed in chapter two. It also outlines all analytical data produced during the course of this research.

Chemistry and synthesis of 3(2H)-furanones and 4,5-dihydro analogues: mechanistic investigations and stereochemical control

The subject matter of this thesis relates to the chemistry of the five-membered oxygen heterocycles – 3(2H)-furanones and their 4, 5-dihydro analogues. Chapter one of the thesis is a review of the relevant chemistry of the compounds: their synthesis and key transformations. In chapter two, new research on 3(2H)-furanones is outlined in two parts. The first describes an investigation into the cyclisation of α'-trialkylsilyloxyenone adducts with arenesulfenyl and selenenyl chlorides into the corresponding sulfur and selenium substituted 3(2H)-furanones without the involvement of a Lewis acid catalyst. The study, largely involving in situ NMR techniques, identified key features associated with the formation and reaction of the chlorosulfide and chloroselenide intermediates, including operation of the Thorpe-Ingold effect. The knowledge gained in this study was applied (the second part) to the synthesis of vinyl substituted furanone systems from α'-trialkylsilyloxydienones where choice of the reaction conditions and electrophilic reagent was a key feature. An important difference in the behaviour of arenesulfenyl and selenenyl halides towards conjugated dienes emerged from this work. This phase of the research concluded with a new synthesis of geiparvarin, a natural product possessing anti-tumour properties.