Comparative genomic assessment of Multi-Locus Sequence Typing: rapid accumulation of genomic heterogeneity among clonal isolates of <Emphasis Type="Italic">Campylobacter jejuni</Emphasis>

Background  

Multi-Locus Sequence Typing (MLST) has emerged as a leading molecular typing method owing to its high ability to discriminate among bacterial isolates, the relative ease with which data acquisition and analysis can be standardized, and the high portability of the resulting sequence data. While MLST has been successfully applied to the study of the population structure for a number of different bacterial species, it has also provided compelling evidence for high rates of recombination in some species. We have analyzed a set of Campylobacter jejuni strains using MLST and Comparative Genomic Hybridization (CGH) on a full-genome microarray in order to determine whether recombination and high levels of genomic mosaicism adversely affect the inference of strain relationships based on the analysis of a restricted number of genetic loci.     

A second gene at the tomato Cf-4 locus confers resistance to cladosporium fulvum through recognition of a novel avirulence determinant

The tomato Cf-4 and Cf-9 genes confer resistance to the leaf mould pathogen Cladosporium fulvum and map at a complex locus on the short arm of chromosome 1. It was previously shown that the gene encoding Cf-4, which recognizes the Avr4 avirulence determinant, is one of five tandemly duplicated homologous genes (Hcr9-4s) at this locus. Cf-4 was identified by molecular analysis of rare Cf-4/Cf-9 disease-sensitive recombinants and by complementation analysis. The analysis did not exclude the possibility that an additional gene(s) located distal to Cf-4 may also confer resistance to C. fulvum. We demonstrate that a number of Dissociation-tagged Cf-4 mutants, identified on the basis of their insensitivity to Avr4, are still resistant to infection by C. fulvum race 5. Molecular analysis of 16 Cf-4 mutants, most of which have small chromosomal deletions in this region, suggested the additional resistance specificity is encoded by Hcr9-4E. Hcr9-4E recognizes a novel C. fulvum avirulence determinant that we have designated Avr4E.     

Lateral induction by juxtacrine signaling is a new mechanism for pattern formation

Many signaling molecules in epithelia are now known to function in a membrane-bound form, binding to receptors on immediately neighbouring cells. This "juxtacrine" mode of communication has been well studied in the case of lateral inhibition, where ligand binding at the cell surface downregulates ligand and receptor expression, and is known to generate spatial patterns with a wavelength of exactly two cells. However, recent evidence shows that a number of juxtacrine signals can lead to the opposite phenomenon of lateral induction. Here, we use mathematical modeling to show that such positive feedback, in combination with juxtacrine communication, provides a novel mechanism for the generation of spatial patterns, with wavelengths that vary with parameters and can be many cell lengths.     

Effects of Holliday junction position on Xer-mediated recombination in vitro.

Site-specific recombination mediated by XerC and XerD functions in the segregation of circular replicons in Escherichia coli. A key feature of most models of recombination for the family of recombinases to which XerC and XerD belong is that a Holliday junction forms at the position of the first pair of recombinase-mediated strand exchanges and then branch migrates 6-8 bp to the position of the second pair of strand exchanges. We have tested this hypothesis for Xer recombination by studying the effects of junction position on XerC-mediated strand exchange in vitro. Recombination of synthetic Holliday junction substrates in which junction mobility was constrained to a region extending over or removed away from the normal cleavage and exchange point was analysed. All substrates undergo strand cleavage at the normal position. We infer that the Holliday junction need not be at this position during strand cleavage and exchange. With substrates in which the Holliday junction is constrained to a region away from the XerC-mediated cleavage point, strand exchange generates products with the predicted mispaired bases.     

Conspicuous Coloration in Males of the Damselfly Nehalennia irene (Zygoptera: Coenagrionidae): Do Males Signal Their Unprofitability to Other Males?

In damselflies, sexual colour dimorphism is commonly explained as a consequence of selection on traits that increase male attractiveness to females. However, while many species in the damselfly family Coenagrionidae (Insecta: Odonata) are sexually dimorphic, the males do not engage in displays, and male competition for mates resembles a “scramble”. An alternative explanation for the sexual differences in coloration within these species is that sexual dimorphism has evolved as a sex-related warning signal, with males signalling their uprofitability as mates to other males, thereby avoiding harassment from conspecifics. We evaluated an underlying assumption of the theory that male-male harassment rate is influenced by colour by comparing harassment of males of the species Nehalennia irene that had been painted to make them appear: (i) similar to an unaltered male (blue), (ii) different from a male (orange) and (iii) more similar to a female (black). When caged together we found that blue-painted males experienced significantly lower harassment than black-painted males. When unpainted males were caged with each type of painted male we found that blue-painted males and the unpainted males housed in the same cages experienced lower rates of harassment than males housed in cages where some males were painted black, suggesting that a single, reliable signal of unprofitability may benefit the individuals that carry it. While our results do not in themselves demonstrate that sexual colour dimorphism originally evolved as an intra-specific warning signal, they do show that harassment is influenced by coloration, and that such selection could conceivably maintain male coloration as a warning signal.     

Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions

Background  

The pan-genome of a bacterial species consists of a core and an accessory gene pool. The accessory genome is thought to be an important source of genetic variability in bacterial populations and is gained through lateral gene transfer, allowing subpopulations of bacteria to better adapt to specific niches. Low-cost and high-throughput sequencing platforms have created an exponential increase in genome sequence data and an opportunity to study the pan-genomes of many bacterial species. In this study, we describe a new online pan-genome sequence analysis program, Panseq.     

Models of epidermal wound healing

The spreading of cells across the surface of an epidermal wound enables epidermal migration to be studied independently of the wound contraction that occurs in deeper wounds. In particular, the stimulus for the increase in epidermal mitosis during would healing is uncertain. Our modelling suggests that biochemical regulation of mitosis is fundamental to the process, and that a single chemical with a simple regulatory effect can account for the healing of circular epidermal wounds. The model results compare well with experimental data.     

Social Eavesdropping: A Game-Theoretic Analysis

Here we extend the classic Hawk-Dove model of animal conflict to allow for continuous variation in fighting strengths. Whereas the winner of a fight is chosen at random in the discrete game, in our continuous game, the winner of any fight is the stronger individual, and costs are higher for more evenly matched opponents. We identify the evolutionary stable strength threshold beyond which an animal should be prepared to engage in aggressive behaviour and show that this threshold increases with variance in fighting strength when the costs of aggression are insensitive to the level of strength asymmetry, but decreases with variance when the costs are sensitive to the level of asymmetry. In contrast to the classic discrete game, population-wide aggressive behaviour occurs only when the costs of fighting are zero. It is now known that animals can eavesdrop on the outcome of contests between neighbours and modify their behaviour towards observed winners and losers. We therefore further extend our model to allow for social eavesdropping within networks comprising three individuals. Whereas earlier work showed that eavesdropping increases the frequency of mutually aggressive contests in the discrete game by enhancing the value of victory, here we show that aggression thresholds in the continuous game are always higher with eavesdropping than without it: for sufficiently weak animals, avoiding the costs of challenging an observed winner over-rides the potential benefit of winning, so that eavesdropping reduces the frequency of aggressive encounters. Thus, even though strength is not directly observable, information is extracted from the variation in fighting ability that the classic Hawk-Dove game ignores.