Genomic variations associated with attenuation in Mycobacterium avium subsp paratuberculosis vaccine strains

BACKGROUND: Mycobacterium avium subspecies paratuberculosis (MAP) whole cell vaccines have been widely used tools in the control of Johne's disease in animals despite being unable to provide complete protection. Current vaccine strains derive from stocks created many decades ago; however their genotypes, underlying mechanisms and relative degree of their attenuation are largely unknown. RESULTS: Using mouse virulence studies we confirm that MAP vaccine strains 316 F, II and 2e have diverse but clearly attenuated survival and persistence characteristics compared with wild type strains. Using a pan genomic microarray we characterise the genomic variations in a panel of vaccine strains sourced from stocks spanning over 40 years of maintenance. We describe multiple genomic variations specific for individual vaccine stocks in both deletion (26-32 Kbp) and tandem duplicated (11-40 Kbp) large variable genomic islands and insertion sequence copy numbers. We show individual differences suitable for diagnostic differentiation between vaccine and wild type genotypes and provide evidence for functionality of some of the deleted MAP-specific genes and their possible relation to attenuation. CONCLUSIONS: This study shows how culture environments have influenced MAP genome diversity resulting in large tandem genomic duplications, deletions and transposable element activity. In combination with classical selective systematic subculture this has led to fixation of specific MAP genomic alterations in some vaccine strain lineages which link the resulting attenuated phenotypes with deficiencies in high reactive oxygen species handling

Improving evolutionary algorithms by MEANS of an adaptive parameter control approach

Evolutionary algorithms (EA) constitute a class of optimization methods that is widely used to solve complex scientific problems. However, EA often converge prematurely over suboptimal solutions, the evolution process is computational expensive, and setting the required EA parameters is quite difficult. We believe that the best way to address these problems is to begin by improving the parameter setting strategy, which will in turn improve the search path of the optimizer, and, we hope, ultimately help prevent premature convergence and relieve the computational burden. The strategy that will achieve this outcome, and the one we adopt in this research, is to ensure that the parameter setting approach takes into account the search path and attempts to drive it in the most advantageous direction. Our objective is therefore to develop an adaptive parameter setting approach capable of controlling all the EA parameters at once. To interpret the search path, we propose to incorporate the concept of exploration and exploitation into the feedback indicator. The first step is to review and study the available genotypic diversity measurements used to characterize the exploration of the optimizer over the search space. We do this by implementing a specifically designed benchmark, and propose three diversity requirements for evaluating the meaningfulness of those measures as population diversity estimators. Results show that none of the published formulations is, in fact, a qualified diversity descriptor. To remedy this, we introduce a new genotypic formulation here, the performance analysis of which shows that it produces better results overall, notwithstanding some serious defects. We initiate a similar study aimed at describing the role of exploitation in the search process, which is to indicate promising regions. However, since exploitation is mainly driven by the individuals’ fitness, we turn our attention toward phenotypic convergence measures. Again, the in-depth analysis reveals that none of the published phenotypic descriptors is capable of portraying the fitness distribution of a population. Consequently, a new phenotypic formulation is developed here, which shows perfect agreement with the expected population behavior. On the strength of these achievements, we devise an optimizer diagnostic tool based on the new genotypic and phenotypic formulations, and illustrate its value by comparing the impacts of various EA parameters. Although the main purpose of this development is to explore the relevance of using both a genotypic and a phenotypic measure to characterize the search process, our diagnostic tool proves to be one of the few tools available to practitioners for interpreting and customizing the way in which optimizers work over real-world problems. With the knowledge gained in our research, the objective of this thesis is finally met, with the proposal of a new adaptive parameter control approach. The system is based on a Bayesian network that enables all the EA parameters to be considered at once. To the authors’ knowledge, this is the first parameter setting proposal devised to do so. The genotypic and phenotypic measures developed are combined in the form of a credit assignment scheme for rewarding parameters by, among other things, promoting maximization of both exploration and exploitation. The proposed adaptive system is evaluated over a recognized benchmark (CEC’05) through the use of a steady-state genetic algorithm (SSGA), and then compared with seven other approaches, like FAUC-RMAB and G-CMA-ES, which are state-of-the-art adaptive methods. Overall, the results demonstrate statistically that the new proposal not only performs as well as G-CMA-ES, but outperforms almost all the other adaptive systems. Nonetheless, this investigation revealed that none of the methods tested is able to locate global optimum over complex multimodal problems. This led us to conclude that synergy and complementarity among the parameters involved is probably missing. Consequently, more research on these topics is advised, with a view to devising enhanced optimizers. We provide numerous recommendations for such research at the end of this thesis

A Review of Flavobacterium Psychrophilum Biology, Clinical Signs, and Bacterial Cold Water Disease Prevention and Treatment

Flavobacterium psychrophilum is a ubiquitous bacterium in the aquatic environment, particularly in freshwater [1]. As the etiological agent of bacterial coldwater disease, it is a serious fish pathogen causing substantial economic losses and rearing difficulties to both commercial and conservation aquaculture [2]. This review paper describes the epidemiology, clinical signs, prevention, and treatment of the fish diseases attributed to this pathogen, which are similar despite the different geographic labels. In addition, the basic biology of F. psychrophilum and the techniques required for successful bacterial culture, isolation, and identification are discussed

Project design of the multicultural education and training structured interview for cultural formulation

The purpose of this project is to outline a validation study demonstrating the utility of the Mulicultural Education and Training Structured Interview for Cultural Formulations (METSICF)

Gene Therapy for Cardiomyopathies

Heart disease remains the prevalent cause of premature death and accounts for a significant proportion of all hospital admissions. Molecular genetics was integrated quite late in cardiology, but introduced new concepts like sarcolemmopathies, cytoskeletalopathies, and channelopathies useful to better understand the pathophysiology of the development of inherited cardiomyopathies (CMs). As our understanding of the cellular and molecular processes involved in the development and progression of heart disease improved, new therapeutic targets were identified, as were novel approaches such as delivery of genes to replace defective or deficient components and thereby restore structure or function in a diseased heart. We discuss gene addition strategies in the context of monogenic disorders. Moreover, a broader nucleic acid-based modulation of cardiac gene expression for the treatment of cardiac diseases might have larger clinical indications. Inadequate gene delivery remains a potential cause of negative trials. However, progress in innovative formulations and clinically relevant ways of administration should lead to significant progress in the future. Cardiac gene therapy will be integrated into the therapeutic armamentarium for CM and heart failure

Oral candidiasis and molecular epidemiology of Candida glabrata

A description of the human infection oral candidiasis, and a study in molecular epidemiology of the yeast fungus Candida glabrata, using multilocus sequence typing (MLST)

Improved methods for the isolation and characterization of Flavobacterium columnare

Columnaris disease, caused by the bacterium Flavobacterium columnare, is an economically significant problem in many warmwater fish species. Difficulties encountered in the isolation and culture of F. columnare have been an impediment to research on the organism and the disease it causes. The goal of this study was to improve the methods for isolation, culture, identification and maintenance of F. columnare. Following the evaluation of different culture media selective cytophaga agar was determined to be the optimum isolation medium, Flavobacterum columnare growth medium proved to be the optimum culture medium, and tryptone yeast extract agar with increased moisture was best for maintenance of cultures. Biochemical characterization of 49 F. columnare isolates was accomplished utilizing the method of Griffin et al. (1992), and the API ZYM system from BioMérieux (Hazelwood Missouri). Using these methods 48 of the 49 strains were presumptively identified as F. columnare. Ten representative F. columnare isolates were further characterized by the API NE system, and all isolates yielded identical phenotypes. Molecular characterization of various strains of F. columnare was accomplished by random amplified polymorphic DNA analysis (reference). Strains evaluated were confirmed as F. columnare by polymerase chain reaction (PCR) using primers and methodology published by Bader et al (2003). The data from RAPD analysis was used to construct three groups based on similarity comparisons. Methods for antimicrobial susceptibility testing by disk diffusion were evaluated on different formulations of dilute Mueller Hinton agar to address the problem of non distinct zones of inhibition, and to reduce the variability of resulting zone data seen when using the published dilute Mueller Hinton formulation (Hawke and Thune 1992). The improved dilute Mueller Hinton medium formulation reduced variability by 40%, increase overall bacterial growth, and also improved the zones of inhibition by producing distinct margins