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

The sedimentology of river confluences

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this record.Channel confluences are key nodes within large river networks, and yet surprisingly little is known about their spatial and temporal evolution. Moreover, because confluences are associated with vertical scour that typically extends to several times the mean channel depth, the deposits associated with such scours should have a high preservation potential within the rock record. Paradoxically, such scours are rarely observed, and their preservation and sedimentological interpretation are poorly understood. The present study details results from a physically‐based morphodynamic model that is applied to simulate the evolution and alluvial architecture of large river junctions. Boundary conditions within the model were defined to approximate the junction of the Ganges and Jamuna rivers, Bangladesh, with the model output being supplemented by geophysical datasets collected at this junction. The numerical simulations reveal several distinct styles of sedimentary fill that are related to the morphodynamic behaviour of bars, confluence scour downstream of braid bars, bend scour and major junction scour. Comparison with existing, largely qualitative, conceptual models reveals that none of these can be applied simply, although elements of each are evident in the deposits generated by the numerical simulation and observed in the geophysical data. The characteristics of the simulated scour deposits are found to vary according to the degree of reworking caused by channel migration, a factor not considered adequately in current conceptual models of confluence sedimentology. The alluvial architecture of major junction scours is thus characterized by the prevalence of erosion surfaces in conjunction with the thickest depositional sets. Confluence scour downstream of braid bar and bend scour sites may preserve some large individual sets, but these locations are typically characterized by lower average set thickness compared to major junction scour and by a lack of large‐scale erosional surfaces. Areas of deposition not related to any of the specific scour types highlighted above record the thinnest depositional sets. This variety in the alluvial architecture of scours may go some way towards explaining the paradox of ancient junction scours, that while abundant large scours are likely in the rock record, they have been reported rarely. The present results outline the likely range of confluence sedimentology and will serve as a new tool for recognizing and interpreting these deposits in the ancient fluvial record.This work was funded by a UK Natural Environment Research Council award to Sambrook Smith (NE/I023228/1), Bull (NE/I023864/1) and Nicholas (NE/I023120/1)

The planform mobility of river channel confluences: Insights from analysis of remotely sensed imagery

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.River channel confluences are widely acknowledged as important geomorphological nodes that control the downstream routing of water and sediment, and which are locations for the preservation of thick fluvial deposits overlying a basal scour. Despite their importance, there has been little study of the stratigraphic characteristics of river junctions, or the role of confluence morphodynamics in influencing stratigraphic character and preservation potential. As a result, although it is known that confluences can migrate through time, models of confluence geomorphology and sedimentology are usually presented from the perspective that the confluence remains at a fixed location. This is problematic for a number of reasons, not least of which is the continuing debate over whether it is possible to discriminate between scour that has been generated by autocyclic processes (such as confluence scour) and that driven by allocyclic controls (such as sea-level change). This paper investigates the spatial mobility of river confluences by using the 40-year record of Landsat Imagery to elucidate the styles, rates of change and areal extent over which large river confluence scours may migrate. On the basis of these observations, a new classification of the types of confluence scour is proposed and applied to the Amazon and Ganges-Brahmaputra-Meghna (GBM) basins. This analysis demonstrates that the drivers of confluence mobility are broadly the same as those that drive channel change more generally. Thus in the GBM basin, a high sediment supply, large variability in monsoonal driven discharge and easily erodible bank materials result in a catchment where over 80% of large confluences are mobile over this 40-year window; conversely this figure is < 40% for the Amazon basin. These results highlight that: i) the potential areal extent of confluence scours is much greater than previously assumed, with the location of some confluences on the Jamuna (Brahmaputra) River migrating over a distance of 20 times the tributary channel width; ii) extensive migration in the confluence location is more common than currently assumed, and iii) confluence mobility is often tied to the lithological and hydrological characteristics of the drainage basins that determine sediment yield.This work was funded by NERC grant NE/I023228/1 to Sambrook Smith, Bull, Nicholas and Best

The Phenotype-Fitness Map in Experimental Evolution of Phages

Evolutionary biologists commonly interpret adaptations of organisms by reference to a phenotype-fitness map, a model of how different states of a phenotype affect fitness. Notwithstanding the popularity of this approach, it remains difficult to directly test these mappings, both because the map often describes only a small subset of phenotypes contributing to total fitness and because direct measures of fitness are difficult to obtain and compare to the map. Both limitations can be overcome for bacterial viruses (phages) grown in the experimental condition of unlimited hosts. A complete accounting of fitness requires 3 easily measured phenotypes, and total fitness is also directly measurable for arbitrary genotypes. Yet despite the presumed transparency of this system, directly estimated fitnesses often differ from fitnesses calculated from the phenotype-fitness map. This study attempts to resolve these discrepancies, both by developing a more exact analytical phenotype-fitness map and by exploring the empirical foundations of direct fitness estimates. We derive an equation (the phenotype-fitness map) for exponential phage growth that allows an arbitrary distribution of lysis times and burst sizes. We also show that direct estimates of fitness are, in many cases, plausibly in error because the population has not attained stable age distribution and thus violates the model underlying the phenotype-fitness map. In conjunction with data provided here, the new understanding appears to resolve a discrepancy between the reported fitness of phage T7 and the substantially lower value calculated from its phenotype-fitness map