Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae) is an invasive worldwide pest of many agricultural, horticultural and ornamental crops. They are difficult to control because of their small size and high resistance to chemical insecticides. The aggregation pheromone of this species is currently used for monitoring, but the full potential for use of this and other pheromones has not yet been explored. Two male-specific headspace volatiles have been previously identified: neryl (S)-2-methylbutanoate which acts as an aggregation pheromone and (R)-lavandulyl acetate, for which the role is unclear. The roles of these compounds were studied to understand how they can be used in pest management. Laboratory bioassays showed that the aggregation pheromone, apart from being an attractant, also increased the activity level of adult F. occidentalis. This could be utilized to activate the thrips out of their concealed spaces within the crop and enhance pickup of chemical insecticides. (R)-lavandulyl acetate reduced the walking and take-off activity of adult females but increased the activity level of adult males. The possible role of this compound as a mating pheromone is discussed. The chemical analysis of male-exposed filter paper discs showed the presence of another compound, 7-methyltricosane, which was shown to act as a contact pheromone for species recognition. Adult females respond by raising their abdomen showing mating rejection towards adult males while abdominal wagging sideways was observed in adult males, a behaviour used in aggressive male-male interactions. This is the first identification of a contact pheromone in the order Thysanoptera.

Lignin is a complex phenolic hetropolymer with an established role in structure, support and defence in higher plants. The chemical structure of lignin is as yet undefined but controlled by an enzymatic pathway leading to three monomeric subunits. Lignin accumulates in plants in response to pathogen challenge. A scanning densitrometric assay to detect lignin was developed that was non-invasive, quantitative and quick to perform. The assay was used in conjunction with assessments of phytotoxicity, mycotoxity and pathogen resistance to assess the efficacy of potential biochemical inhibitors of the phenylpropanoid pathway in vivo. With this information, tolerances for biochemical inhibition of the phenylpropanoid pathway were obtained. This allowed further investigation of the basis of genetic and metabolic regulation of one form of one enzyme of the pathway, phenylalanine ammonia lyase, in wheat. Evidence of a potential role for endogenous elicitation in the ligninification pathway was also gained by the use of the assay. Elicitation in terms of the hypersensitive response was also investigated during attempts to purify the fungal elicitor Avr2 using the tovnaXo!Cladosporium fulvum model; however this work was completed by an alternative genetic screen protocol published elsewhere. Control of ligninificiation and the enzymes that produce the polymer is therefore an essential part of the defence response in wheat. This has important implications for genetic modification of the pathway. It was shown in this study that the phenylpropanoid pathway controls one aspect of resistance in wheat and concludes that care must be taken when manipulating the pathway in plants for increased digestibility or ease of pulping. In addition, a separate project was undertaken in order to purify an avirulence protein possessed by the Cladosporiumfulvum fungus. The projects aim was to obtain amino acid sequence(s) of potential interacting proteins that would be used to design primer sequences to provide a genetic sequence of the target avirulence protein Avr2. Although several candidate proteins were obtained and amino acid sequencing attempted; a competing group obtained the genetic sequence of Avr2. The sequence of this clone predicts a protein whose molecular weight and isoelectric point falls within a region of proteins whose isoelectric points and molecular weights show activity in a bioassay for Cf-2 interacting proteins. This data supports the conclusion that the work by Luderer et al (2002) defines the genetic sequence of Avr 2.

The changing landscape of the UK’s dairy farms poses increasing challenges to farm staff in terms of monitoring individuals behaviour within increasing herds, and more intensive conditions. Failure to detect behavioural changes may be costly, both from a welfare and financial perspective, as such alterations may indicate underlying disease or other challenges with corresponding impacts on yield and animal well-being. Social behaviour may provide a useful indicator of normal animal activity, and subsequent changes with health status, particularly if automatically monitored to reduce labour. This thesis applies a local positioning system (LPS) to collect social proximities of dairy cows, to investigate the social structure of a housed herd via social network analysis, and any relationship with traits or health. The LPS was validated by comparing sensor reported, with human observed proximities, and accurately detected proximities at lying, feeding and in direct interactions. Use of this data to construct social networks indicated a highly connected structure, with some substructure becoming evident after filters were applied. An approaching significant effect of parity on sociality was found, but stage of lactation had no effect. Temporally, the network showed some stability but a much greater amount of variation. When divided into ‘functional area’ (feeding, non-feeding and milking), the non-feeding area of the shed yielded the most loosely connected network with likely most interest for further analysis due to its potential basis in choice, as opposed to forced proximity. In these functional area networks, some evidence exists for homophily (association with similar cows – based on parity and days in milk). Finally, sociality was investigated alongside health status, with evidence for a tendency for greater betweenness in lame cows than non-lame. The results suggest that sociality is a highly variable trait, and that further investigation is required to assess its suitability as a disease indicator.

Food and energy security are two key environmental challenges currently faced by mankind. The principles behind organic farming are to promote environmental sustainability; however within the organic standards the use of renewable energy is only a suggested method with which to achieve this. If organic farmers can successfully utilise anaerobic digesters, they could contribute towards the provision of both food and energy security using one holistic system. Within this thesis, the suitability of anaerobic digesters on organic farms was explored using methods from ecological, sociological and environmental sciences. This enabled both the practical and theoretical issues behind the question of whether it is suitable for anaerobic digesters to be used on organic farms to be addressed. Field and laboratory experiments were used to compare the effects digestate and slurry had on earthworms, grass and weeds. Digestate and slurry had species dependent effects on earthworms during both LD50 / LT50 experiments and behavioural bioassays; Lumbricus terrestris survived longer in slurry and showed a behavioural preference towards slurry over digestate, whereas Eisenia fetida showed the opposite responses. Fertiliser application rates over 170 kg N ha-1 were found to be harmful to both species of earthworm. Suppressed germination effects were seen on thistles treated with digestate compared with no treatment (F0.56,19.66 =4.66, P < 0.01), whilst grass fertilised with digestate had a greater total mass than grass fertilised with slurry or left unfertilised (F2,27 =17.92, P < 0.001). Questionnaires and interviews were used to obtain a better understanding of the opinions farmers had about anaerobic digesters. Organic farmers believed renewable energy generation fitted well within organic principles, but using an anaerobic digester on an organic farm was less practical than on a conventional farm. This was due to multiple reasons including lack of information, poor associated finances, and that existing digesters are currently unsuitable for small organic farms. There was also support for anaerobic digesters to be on dairy farms- this was regardless of whether the farm was organic or conventional. Two case-study farms were used to assess the impact an anaerobic digester would have on the farms total GHG emissions. An anaerobic digester on the dairy farm was calculated to reduce GHG emissions by up to 24%, while for the mixed farm, the maximum reduction was by 20%. This was primarily due to the fact that the dairy farm benefitted from a higher volume of feedstock and proposed to use the biogas in a more energy efficient manner by producing electricity rather than vehicle fuel. Due to the high emissions associated with keeping livestock, both case studies needed to import additional feedstock if the farms were to achieve zero net GHG emissions. The answer to whether anaerobic digesters can be suitable for organic farms was judged on how well they complimented or conflicted with IFOAM’s definition of organic farming. Three main aspects of their definition were chosen and evidence from each chapter used to address the main question of the thesis. In conclusion, anaerobic digesters are theoretically suitable for use on organic farms, but are generally more practical for use on conventional farm systems. Across both farm systems the most suitable enterprises to adopt anaerobic digesters are dairy farms. This highlights the need for suitability of new systems to be assessed on a case-by-case scenario when trying to maximise positive impacts from new technologies.