Breeding phenology,variation in reproductive effort and offspring size in a tropical population of the woodlouse Porcellionides pruinosus

Summary Most species of woodlice in temperate habitats have discrete breeding seasons. It is hypothesised that breeding synchronises with favourable environmental conditions to maximise offspring growth and survivorship (Willows 1984). We measured the breeding phenology of a species introduced to a tropical environment, primarily to consider the assumption that life histories in the tropics will differ fundamentally from those in temperate habitats. In addition to breeding phenology we considered variation in reproductive effort between individual females and the division of this effort between the size and number of young.A continuous breeding phenology was observed in a synanthropic population of Porcellionides pruinosus within the tropics. Reproductive effort varied between months, showed a weak relationship with female size and was independent of female fecundity. Female sizefecundity relationships varied between samples and when the proportion of reproductive females was high size-fecundity slopes were steeper than at other times. Mean offspring size varied between months and there was a wide range in offspring size within broods. Offspring size was not related to female body mass, reproductive effort or fecundity; consequently brood mass increased linearly with an increase in fecundity. Increased reproductive effort goes into more rather than larger offspring.We propose that the continuous breeding in this population was the result of the constant presence of an environmental cue to reproduction evolved in temperate habitats. Continuous breeding is not necessarily equivocal to high individual reproductive success even though overall population growth may be rapid. However, variation in reproductive effort suggests that individuals respond to current environmental conditions on short time scales.     

Phenotypic variation in the breeding phenology of the woodlouse Armadillidium vulgare

Summary The breeding phenology of temperate wood-lice is strongly seasonal, the result of physiological constraints and precise environmental cues for reproduction. The adaptive value of such mechanisms is that the release of offspring coincides with favourable conditions for growth and survival (Willows 1984). We recorded the breeding phenology of Armadillidium vulgare (Latreille) on two grassland sites in Great Britain and found between-site and between-year variation in the onset of reproduction, the duration of reproductive activity, the release of offspring, the size of reproductive females and the number of broods per female. Between 82.7 and 97.7% of gravid females sampled were semelparous at 23 months, with the remainder iteroparous, producing a second brood after 35 months. On one site (Weeting Health) improved growth conditions during 1984 allowed some females (19.3% of gravid females sampled in that year) to produce a brood after 11 months. There was also an increase in the number of 3-year-old females found to be gravid. An experimental manipulation of the same habitat confirmed that such changes in life history tactics could be phenotypic responses. The observed phenotypic variation was sufficient to produce a range of life history tactics within a population. Mixtures of life history tactics within a population may be typical of invasive species and populations at the edge of the species range. Our results support the idea that phenotypic plasticity can be an appropriate tactic to maximise fitness in a fluctuating environment (Caswell 1983, 1989).     

Revisiting the use of Iprodione and Trichoderma in the integrated management of onion white rot

The biocontrol properties of Trichoderma species are well documented, but their effectiveness in antagonism of the problematic Sclerotium cepivorum, the causal agent of white rot in Allium species, appears limited with reports of significant control only relating to deliberately-mutated strains of Trichoderma. Our previous studies have indicated the possibility of using selected naturally-occurring strains of the antagonist in the suppression of other diseases; now in vitro and controlled environment in vivo studies have indicated that a degree of control of Onion White Rot is possible, and that the selected antagonist strains can be used in integrated treatments with Iprodione to good effect. The possible value of such treatments is considered in light of other approaches to the suppression of this continuing problem.     

Substrate specificity and proposed structure of the proofreading complex of T7 DNA polymerase

Faithful replication of genomic DNA by high-fidelity DNA polymerases is crucial for the survival of most living organisms. While high-fidelity DNA polymerases favor canonical base pairs over mismatches by a factor of ∼1 × 10⁵, fidelity is further enhanced several orders of magnitude by a 3′–5′ proofreading exonuclease that selectively removes mispaired bases in the primer strand. Despite the importance of proofreading to maintaining genome stability, it remains much less studied than the fidelity mechanisms employed at the polymerase active site. Here we characterize the substrate specificity for the proofreading exonuclease of a high-fidelity DNA polymerase by investigating the proofreading kinetics on various DNA substrates. The contribution of the exonuclease to net fidelity is a function of the kinetic partitioning between extension and excision. We show that while proofreading of a terminal mismatch is efficient, proofreading a mismatch buried by one or two correct bases is even more efficient. Because the polymerase stalls after incorporation of a mismatch and after incorporation of one or two correct bases on top of a mismatch, the net contribution of the exonuclease is a function of multiple opportunities to correct mistakes. We also characterize the exonuclease stereospecificity using phosphorothioate-modified DNA, provide a homology model for the DNA primer strand in the exonuclease active site, and propose a dynamic structural model for the transfer of DNA from the polymerase to the exonuclease active site based on MD simulations.     

Conformational dynamics during misincorporation and mismatch extension defined using a DNA polymerase with a fluorescent artificial amino acid

High-fidelity DNA polymerases select the correct nucleotide over the structurally similar incorrect nucleotides with extremely high specificity while maintaining fast rates of incorporation. Previous analysis revealed the conformational dynamics and complete kinetic pathway governing correct nucleotide incorporation using a high-fidelity DNA polymerase variant containing a fluorescent unnatural amino acid. Here we extend this analysis to investigate the kinetics of nucleotide misincorporation and mismatch extension. We report the specificity constants for all possible misincorporations and characterize the conformational dynamics of the enzyme during misincorporation and mismatch extension. We present free energy profiles based on the kinetic measurements and discuss the effect of different steps on specificity. During mismatch incorporation and subsequent extension with the correct nucleotide, the rates of the conformational change and chemistry are both greatly reduced. The nucleotide dissociation rate, however, increases to exceed the rate of chemistry. To investigate the structural basis for discrimination against mismatched nucleotides, we performed all atom molecular dynamics simulations on complexes with either the correct or mismatched nucleotide bound at the polymerase active site. The simulations suggest that the closed form of the enzyme with a mismatch bound is greatly destabilized due to weaker interactions with active site residues, nonideal base pairing, and a large increase in the distance from the 3ʹ-OH group of the primer strand to the α-phosphate of the incoming nucleotide, explaining the reduced rates of misincorporation. The observed kinetic and structural mechanisms governing nucleotide misincorporation reveal the general principles likely applicable to other high-fidelity DNA polymerases.     

A web server to locate periodicities in a sequence

Summary : FT is a tool written in C++, which implements the Fourier analysis method to locate periodicities in aminoacid or DNA sequences. It is provided for free public use on a WWW server with a Java interface. Availability : The server address is http://o2.db. uoa.gr/FT Contact : shamodr@atlas.uoa.gr