Growth Phase-Dependent Regulation of Vsr Endonuclease May Contribute to 5-Methylcytosine Mutational Hot Spots in Escherichia coli

Using rabbit polyclonal antibodies, we have shown that the Dcm cytosine methylase of Escherichia coli is maintained at a constant level during cell growth, while Vsr endonuclease levels are growth phase dependent. Decreased production of Vsr relative to Dcm during the log phase may contribute substantially to the mutability of 5-methylcytosine.     

Marine incursions,cryptic species and ecological diversification in Amazonia: the biogeographic history of the croaker genus Plagioscion (Sciaenidae)

Aim We propose a phylogenetic hypothesis for the marine‐derived sciaenid genus Plagioscion in the context of geomorphology and adaptation to freshwaters of South America, and assess the extent to which contemporary freshwater hydrochemical gradients influence diversification within a widely distributed Plagioscion species, Plagioscion squamosissimus. Location Amazon Basin and South America. Methods Using nuclear and mitochondrial DNA sequence data, phylogenetic analyses were conducted on the five nominal Plagioscion species, together with representatives from Pachyurus and Pachypops, using character and model‐based methods. Genealogical relationships and population genetic structure of 152 P. squamosissimus specimens sampled from the five major rivers and three hydrochemical settings/‘colours’ (i.e. white, black and clear water) of the Amazon Basin were assessed. Results Phylogenetic analyses support the monophyly of Plagioscion in South America and identify two putative cryptic species of Plagioscion. Divergence estimates suggest that the Plagioscion ancestor invaded South America via a northern route during the late Oligocene to early Miocene. Within P. squamosissimus a strong association of haplotype and water colour was observed, together with significant population structure detected between water colours. Main conclusions Our analyses of Plagioscion are consistent with a biogeographic scenario of early Miocene marine incursions into South America. Based on our phylogenetic results, the fossil record, geomorphological history and distributional data of extant Plagioscion species, we propose that marine incursions into western Venezuela between the late Oligocene and early Miocene were responsible for the adaptation to freshwaters in Plagioscion species. Following the termination of the marine incursions during the late Miocene and the establishment of the modern Amazon River, Plagioscion experienced a rapid diversification. Plagioscion squamosissimus arose during that time. The formation of the Amazon River probably facilitated population and range expansions for this species. Further, the large‐scale hydrochemical gradients within the Amazon Basin appear to be acting as ecological barriers maintaining population discontinuities in P. squamosissimus even in the face of gene flow. Our results highlight the importance of divergent natural selection through time in the generation and maintenance of sciaenid diversity in Amazonia.     

False Memory ≠ False Memory: DRM Errors Are Unrelated to the Misinformation Effect

The DRM method has proved to be a popular and powerful, if controversial, way to study ‘false memories’. One reason for the controversy is that the extent to which the DRM effect generalises to other kinds of memory error has been neither satisfactorily established nor subject to much empirical attention. In the present paper we contribute data to this ongoing debate. One hundred and twenty participants took part in a standard misinformation effect experiment, in which they watched some CCTV footage, were exposed to misleading post-event information about events depicted in the footage, and then completed free recall and recognition tests. Participants also completed a DRM test as an ostensibly unrelated filler task. Despite obtaining robust misinformation and DRM effects, there were no correlations between a broad range of misinformation and DRM effect measures (mean r  = −.01). This was not due to reliability issues with our measures or a lack of power. Thus DRM ‘false memories’ and misinformation effect ‘false memories’ do not appear to be equivalent.     

Non-linear dynamics of a pelagic ecosystem model with multiple predator and prey types

Using numerical techniques, we explored the dynamics of a one-dimensional,six-component nutrient–phytoplankton–zooplankton(NPZ) model in which zooplankton grazed on a mixed prey field.Five alternative functional forms were implemented to describezooplankton grazing, and the form for predation on mesozooplanktonwas prescribed by a product of a specific predation rate (h)and the mesozooplankton concentration raised to a power (q),which we varied between one and two. With all five grazing functions,Hopf bifurcations, where the form of the solution transitionedbetween steady equilibrium and periodic limit cycles, persistedacross the q–h parameter space. Regardless of the valuesof h and q, with some forms of the grazing function, we wereunable to find steady equilibrium solutions that simultaneouslycomprised non-zero concentrations for all six model components.Extensions of Michaelis–Menten-based single resource grazingformulations to multiple resources resulted in periodic solutionsfor a large portion of the q–h space. Conversely, extensionsof the sigmoidal grazing formulation to multiple resources resultedin steady solutions for a large portion of q–h parameterspace. Our results demonstrate the consequences of the functionalform of biological processes on the form of the model solutions.Both the steady or oscillatory nature of state variable concentrationsand the likelihood of their elimination are important considerationsfor ecosystem-modelling studies, particularly when attemptingto model an ecosystem in which multiple phytoplankton and zooplanktoncomponents are thought to persist simultaneously for at leasta portion of the seasonal cycle.