Pacific Coral-reef Fishes: The Implications of Behaviour and Ecology of Larvae for Biodiversity and Conservation, and a Reassessment of the Open Population Paradigm

The two-phase life history of most marine fishes and invertebrates has enormous implications for dispersal, population connectivity, and resource management. Pelagic dispersal larvae of marine animals traditionally thought to ensure that populations are widespread, that chances of local extinction are low, and that marine protected areas (MPA) can easily function to replenish both their own populations and those of unprotected areas. Traditionally, dispersal is considered to depend primarily on two variables: pelagic larva duration and far-field currents. These conclusions arise from the open population paradigm and are usually accompanied by a simplifying assumption: larvae are distributed passively by far-field currents. Unfortunately, they ignore the complex reality of circulation and hydrological connectivity of reefs, and do not consider newly-demonstrated behavioural capabilities of coral-reef fish larvae. Far-field circulation varies with depth and often excludes water bodies where propagules are released, and this has important implications for predicting trajectories of even passive larvae. However, larvae are not passive: late-stage larvae of coral-reef fishes can swim faster than currents for long periods, can probably detect reefs at some distance, and can actively find them. This behaviour is flexible, which greatly complicates modelling of larval fish trajectories. Populations at ecological (as opposed to evolutionary) scales are probably less open and more subdivided than previously assumed. All this means that dispersal predictions based solely on far-field water circulation are probably wrong. An emerging view of larval-fish dispersal is articulated that takes these new data and perspectives into account. This emerging view shows that re-evaluation of traditional views in several areas is required, including the contribution of larval-fish biology and dispersal to biodiversity patterns, the way reef fishes are managed, and the way in which MPA are thought to operate. At evolutionary and zoogeographic scales, reef-fish populations are best considered to be open.     

A theoretical framework of ecological phase transitions for characterizing tree-grass dynamics

This paper describes a theoretical framework of ecological phase transitions for modeling tree-grass dynamics and analyzing the shifts or phase transitions from one vegetation structure to another in the southern Texas landscape. This framework implements the integration of percolation theory, fractal geometry and phase transition theory as a method for modeling the spatial patterns of tree-grass dynamics, and nonlinear Markov non-equilibrium thermodynamic stability theory as a method for characterizing temporal tree-grass dynamics and phase transition. An historical sequence of aerial photographs at a Prosopis - thornscrub savanna parkland site in southern Texas was used to determine the parameters of the models. The preliminary analytical result accords well with current understanding and field survey of vegetation dynamics in the southern Texas landscape. The potential of such approaches and other relevant theories such as self-organized criticality and synergetics to vegetation dynamics is also discussed.     

Effects of resource supplies on the structure and function of microbial communities

The supplies of nutrients, and their elemental stoichiometry, can have significant impacts upon the structure and function of microbial communities. This review focuses on the effects of nutrient supplies on the biodegradation of organic matter, and on the dynamics of host-pathogen interactions. Analyses of data from the literature suggest significant effects of nitrogen:phosphorus supply ratios on the microbial decomposition of organic matter, and it is argued that these stoichiometric effects may have important implications for the fate and fluxes of carbon in natural ecosystems. In addition, it is shown that the supplies of nitrogen and phosphorus to the host can strongly influence the outcome of infections in both terrestrial and aquatic plants, suggesting that resource availability and resource supply ratios potentially may have significant effects on the health of many plant communities. This revised version was published online in August 2006 with corrections to the Cover Date.     

Dynamics of green fluorescent protein mutant2 in solution, on spin-coated glasses, and encapsulated in wet silica gels

Single-molecule experiments are performed by investigating spectroscopic properties of molecules either diffusing in and out of the observation volume or fixed in space by different immobilization procedures. To evaluate the effect of immobilization methods on the structural and dynamic properties of proteins, a highly fluorescent mutant of the green fluorescent protein, GFPmut2, was spectroscopically characterized in bulk solutions, dispersed on etched glasses, and encapsulated in wet, nanoporous silica gels. The emission spectrum, the fluorescence lifetimes, the anisotropy, and the rotational correlation time of GFPmut2, encapsulated in silica gels, are very similar to those obtained in solution. This finding indicates that the gel matrix does not alter the protein conformation and dynamics. In contrast, the fluorescence lifetimes of GFPmut2 on glasses are two-to fourfold higher and the fluorescence anisotropy decays yield almost no phase shifts. This indicates that the interaction of the protein with the bare glass surface induces a significant structural perturbation and severely restricts the rotational motion. Single molecules of GFPmut2 on glasses or in silica gels, identified by confocal image analysis, show a significant stability to illumination with bleaching times of the order of 90 and 60 sec, respectively. Overall, these data indicate that silica gels represent an ideal matrix for following biologically relevant events at a single molecule level.     

Molecular dynamics of the FixJ receiver domain: movement of the beta4-alpha4 loop correlates with the in and out flip of Phe101

FixJ is a two-domain response regulator involved in nitrogen fixation in Sinorhizobium meliloti. Recent X-ray characterization of both the native (unphosphorylated) and the active (phosphorylated) states of the protein identify conformational changes of the beta4-alpha4 loop and the conserved residue Phe101 as the key switches in activation. These structures also allowed investigation of the transition between conformations of this two-component regulatory receiver domain by molecular dynamics simulations. The path for the conformational change was studied with a distance constraint directing the system from one state to the other. The simulations provide evidence for a correlation between the conformation of the beta4-alpha4 loop and the orientation of the residue Phe101. A model presenting the sequence of events during the activation/deactivation process is discussed.     

Charge states rather than propensity for beta-structure determine enhanced fibrillogenesis in wild-type Alzheimer's beta-amyloid peptide compared to E22Q Dutch mutant

The activity of the Alzheimer's amyloid beta-peptide is a sensitive function of the peptide's sequence. Increased fibril elongation rate of the E22Q Dutch mutant of the Alzheimer's amyloid beta-peptide relative to that of the wild-type peptide has been observed. The increased activity has been attributed to a larger propensity for the formation of beta structure in the monomeric E22Q mutant peptide in solution relative to the WT peptide. That hypothesis is tested using four nanosecond timescale simulations of the WT and Dutch mutant forms of the Abeta(10-35)-peptide in aqueous solution. The simulation results indicate that the propensity for formation of beta-structure is no greater in the E22Q mutant peptide than in the WT peptide. A significant measure of "flickering" of helical structure in the central hydrophobic cluster region of both the WT and mutant peptides is observed. The simulation results argue against the hypothesis that the Dutch mutation leads to a higher probability of formation of beta-structure in the monomeric peptide in aqueous solution. We propose that the greater stability of the solvated WT peptide relative to the E22Q mutant peptide leads to decreased fibril elongation rate in the former. Stability difference is due to the differing charge state of the two peptides. The other proposal leads to the prediction that the fibril elongation rates for the WT and the mutant E22Q should be similar under acid conditions.     

Clonal mixing in the soldier-producing aphid Pemphigus spyrothecae (Hemiptera: Aphididae)

Illuminating the genetic relationships within soldier-producing aphid colonies is an essential element of any attempt to explain the evolution of the altruistic soldier caste. Pemphigus spyrothecae is a soldier-producing aphid that induces galls on the leaf petioles of its host (trees of the genus Populus). At least a quarter of the aphids within the clonally produced gall population are morphologically and behaviourally distinct first-instar soldiers that defend the gall population from predation. Using field trapping and microsatellites, we investigated the degree of clonal mixing within natural gall populations. Field trapping in the UK showed that all the migrants of P. spyrothecae and of two other Pemphigus species were wingless first-instar soldiers. The average degree of mixing estimated from trapping P. spyrothecae migrants was 0.68% (range = 0-15%). Microsatellite genotyping of 277 aphids from 13 galls collected in Italy revealed an average mixing level of 10.4% (range = 0-59%). Six galls contained more than one clone (range = 2-5 clones). Non-kin aphids were not restricted to the soldier caste but were evenly distributed across instars. An additional gall, from which 527 occupants were genotyped, contained 12 non-kin aphids distributed among nine clones, showing that clonal diversity can be high even when mixing is very low. These observations suggest that although soldiers migrate regularly and can moult and reproduce within foreign galls, clonal mixing in this species is generally low and is unlikely to provide a barrier to the evolution of investment by the aphid clones in an altruistic soldier caste.     

Insights into recently fragmented vole populations from combined genetic and demographic data

We combined demographic and genetic data to evaluate the effects of habitat fragmentation on the population structure of the California red-backed vole (Clethrionomys californicus). We analysed variation in the mitochondrial DNA (mtDNA) control region and five nuclear microsatellite loci in small samples collected from two forest fragments and an unfragmented control site in 1990-91. We intensively sampled the same forest fragments and two different control sites in 1998 and 1999. Vole abundances fluctuated greatly at sizes below 50 individuals per fragment. Fragment populations had significantly lower mtDNA allelic diversity than controls, but not nuclear heterozygosity or numbers of alleles. The use of only trapping and/or mtDNA marker data would imply that fragment populations are at least partially isolated and vulnerable to inbreeding depression. In contrast, the abundance estimates combined with microsatellite data show that small fragment populations must be linked to nearby forests by high rates of migration. These results provide evidence for the usefulness of combining genetic and demographic data to understand nonequilibrium population structure in recently fragmented habitats.     

Response of SCP-2L domain of human MFE-2 to ligand removal: binding site closure and burial of peroxisomal targeting signal

In the study of the structure and function relationship of human MFE-2, we have investigated the dynamics of human MFE-2SCP-2L (hSCP-2L) and its response to ligand removal. A comparison was made with homologous rabbit SCP-2. Breathing and a closing motion are found, identifiable with an adjustment in size and a closing off of the binding pocket. Crucial residues for structural integrity have been identified. Particularly mobile areas of the protein are loop 1 that is connecting helices A and C in space, and helix D, next to the entrance of the pocket. In hSCP-2L, the binding pocket gets occupied by Phe93, which is making a tight hydrophobic contact with Trp36. In addition, it is found that the C-terminal peroxisomal targeting signal (PTS1) that is solvent exposed in the complexed structure becomes buried when no ligand is present. Moreover, an anti-correlation exists between burial of PTS1 and the size of the binding pocket. The results are in accordance with plant nsLTPs, where a similar accommodation of binding pocket size was found after ligand binding/removal. Furthermore, the calculations support the suggestion of a ligand-assisted targeting mechanism.