Combining and choosing case base maintenance algorithms

Case-Based Reasoning (CBR) uses past experiences to solve new problems. The quality of the past experiences, which are stored as cases in a case base, is a big factor in the performance of a CBR system. The system's competence may be improved by adding problems to the case base after they have been solved and their solutions verified to be correct. However, from time to time, the case base may have to be refined to reduce redundancy and to get rid of any noisy cases that may have been introduced. Many case base maintenance algorithms have been developed to delete noisy and redundant cases. However, different algorithms work well in different situations and it may be difficult for a knowledge engineer to know which one is the best to use for a particular case base. In this thesis, we investigate ways to combine algorithms to produce better deletion decisions than the decisions made by individual algorithms, and ways to choose which algorithm is best for a given case base at a given time. We analyse five of the most commonly-used maintenance algorithms in detail and show how the different algorithms perform better on different datasets. This motivates us to develop a new approach: maintenance by a committee of experts (MACE). MACE allows us to combine maintenance algorithms to produce a composite algorithm which exploits the merits of each of the algorithms that it contains. By combining different algorithms in different ways we can also define algorithms that have different trade-offs between accuracy and deletion. While MACE allows us to define an infinite number of new composite algorithms, we still face the problem of choosing which algorithm to use. To make this choice, we need to be able to identify properties of a case base that are predictive of which maintenance algorithm is best. We examine a number of measures of dataset complexity for this purpose. These provide a numerical way to describe a case base at a given time. We use the numerical description to develop a meta-case-based classification system. This system uses previous experience about which maintenance algorithm was best to use for other case bases to predict which algorithm to use for a new case base. Finally, we give the knowledge engineer more control over the deletion process by creating incremental versions of the maintenance algorithms. These incremental algorithms suggest one case at a time for deletion rather than a group of cases, which allows the knowledge engineer to decide whether or not each case in turn should be deleted or kept. We also develop incremental versions of the complexity measures, allowing us to create an incremental version of our meta-case-based classification system. Since the case base changes after each deletion, the best algorithm to use may also change. The incremental system allows us to choose which algorithm is the best to use at each point in the deletion process.

Investigation of lantibiotic regulation, immunity and synergy

Due to the increasing incidence of antibiotic resistant strains, the use of novel antimicrobials, such as bacteriocins, has become an ever more likely prospect. Lacticin 3147 (of which there are two components, Ltnα and Ltnβ) and nisin belong to the subgroup of bacteriocins called the lantibiotics, which has attracted much attention in recent years. The lantibiotics are antimicrobial peptides that contain unusual amino acids resulting from a series of enzyme-mediated post translational modifications. Given that there have been relatively few examples of lantibiotic-specific resistance; these antimicrobials appear to represent valid alternatives to classical antibiotics. However, the fact that lantibiotics are naturally only produced in small amounts often hinders their commercialisation. In order to overcome this bottleneck, several approaches can be employed. For example, we can create a situation that reduces the quantity of a lantibiotic required to inhibit a target by combining it with other antimicrobials. Here, following an initial screen involving lacticin 3147 and several classical antibiotics, it was observed between lacticin 3147 and the commercial antibiotics polymyxin B/E function synergistically. This reduced the amounts of the individual antimicrobials required for kill and broadened the spectrum of inhibition of both agents. Upon combination with polymyxins, lacticin 3147, which has been associated with Gram positive targets only, actively targeted Gram negative species such as Escherichia coli and Cronobacter sp. An alternative means of addressing problems associated with lantibiotic yield is to better understand how production is regulated, and ultimately use this information to enhance peptide levels. With this in mind the regulation of lacticin 3147 production from the promoter Pbac was investigated using a green fluorescent protein (GFP) expression reporter system. This revealed that elements within both of the divergent operons of the lacticin 3147 gene cluster are involved in Pbac regulation. That is, LtnR, already established as a negative regulator of itself and the lacticin 3147 associated immunity genes, also acts as an activator of Pbac transcription. In contrast, an enhanced level of expression is observed in the absence of the lacticin 3147 structural genes, ltnA1 and ltnA2, indicating that these genes/gene products are involved in Pbac repression. In fact, through complementation of the ltnA2 gene, it was revealed that this regulation is more likely to be dependent on the presence of the gene transcript rather that the corresponding prepropeptide or modified Ltnβ. It may be that if lacticin 3147 production is successfully enhanced, the ability of the producing cell to protect itself may become an issue. To prepare for such a possibility a bioengineered derivative of the lacticin 3147 immunity protein LtnI (LtnI I81V) which provides enhanced protection was discovered through an in depth investigation involving the site and saturation mutagenesis of this protein. In addition, the creation of truncated forms of LtnI allowed the identification of important and essential regions of this immunity protein. Finally, as mentioned, self-immunity is essential to prevent self-killing. However the discovery of nisin U immunity and regulatory gene homologues (spiFEGRR’K) within the pathogenic strain S. infantarius subsp. infantarius is a cause for concern as it represents an example of immune mimicry, a form of lantibiotic-specific resistance. The ability of spiFEG to confer protection was apparent when they successfully provided protection to nisin A, F, Z, Q and U when expressed heterologously in the nisin sensitive L. lactis HP host. As a consequence of the studies presented in this thesis, it is likely that strategies will emerge that will facilitate the production of greater levels of lacticin 3147 production and lead to enhanced immunity in lactococcal backgrounds. Alternatively the need for enhanced production could be avoided through the use of antimicrobial combinations. In addition, providing awareness of the threats of the emergence of resistance through immune mimicry can allow researchers to develop strategies to prevent this phenomenon from leading to the dissemination of lantibiotic resistance.

Evaluation of rhizobacterial colonisation and the ability to induce Globodera pallida hatch

Three bacterial isolates, SB13 (Acinetobacter sp.), SB14 (Arthrobacter sp.) and SB15 (Bacillus sp.), were previously isolated from the rhizosphere of sugar beet (Beta vulgaris ssp. vulgaris) plants and shown to increase hatch of potato cyst nematodes in vitro. In this study, the three isolates were assayed for rhizosphere competence. Each isolate was applied to seeds at each of four concentrations (105-108 CFU ml−1) and the inoculated seeds were planted in plastic microcosms containing coarse sand. All three isolates were shown to colonise the rhizosphere, although to differing degrees, with the higher inoculation densities providing significantly better colonisation. The isolates increased sugar beet root and shoot dry weight. Isolates SB14 and SB15 were analysed for their ability to induce in vivo hatch of Globodera pallida in non-sterile soil planted with sugar beet. After 4 and 6 weeks, both isolates had induced significantly greater percentage hatch compared to controls.