Evolution of the gall wasp-host plant association

Gall wasps, or cynipids, form the second largest radiation of galling insects with more than 1300 described species. According to current views, the first cynipids were phytophagous and developed in herb stems of the Asteraceae without modifying plant growth or development. The first galls were supposedly multichambered stem swellings, and subsequent trends involved increase in gall complexity and reduction in the number of larval chambers. Gall wasps also have many of the features believed to be characteristic for phytophagous insects radiating in parallel with their host plants. We tested these hypotheses by mapping characters onto a recent estimate of higher cynipid relationships from a morphology-based analysis of exemplar taxa, controlling for phylogenetic uncertainty using bootstrapping. Characters were also mapped onto a metatree including all gall wasps, assembled from phylogenetic analyses as well as recent classifications. The results contradict many of the current hypotheses. The first cynipids with extant descendants were not Asteraceae stem feeders but induced distinct single-chambered galls in reproductive organs of herbaceous Papaveraceae, or possibly Lamiaceae. There has been a general trend toward more complex galls but the herb-stem feeders evolved from ancestors inducing distinct galls and their larval chambers are best understood as cryptic galls. Woody hosts have been colonized only three times, making the apparently irreversible transition from herbs to woody hosts one of the most conservative features of the gall wasp-host plant association. The evolution of host plant preferences is characterized by colonization of preexisting host-plant lineages rather than by parallel cladogenesis. Cynipids are mono- or oligophagous and host-plant choice is strongly phylogenetically conserved. Yet, the few major host shifts have involved remarkably distantly related plants. Many shifts have been onto plant species already exploited by other gall wasps, suggesting that interspecific parasitism among cynipids facilitates colonization of novel host plants.     

Structural basis for sequential displacement of Ca(2+) by Yb(3+) in a protozoan EF-hand calcium binding protein

We have studied the displacement of Ca(2+)by the trivalent lanthanide ions (Yb(3+)) in a protozoan (Entamoeba histolytica) Ca(2+)-binding protein (EhCaBP), by NMR and thermodynamics. We have demonstrated, for the first time, how one can use in a combined fashion the utility of NMR and thermodynamics to have an insight to the relative binding specificities/affinity between Ca(2+) and Yb(3+). As revealed by the titration experiments, Yb(3+) displaces Ca(2+) from the four metal binding sites present in EhCaBP in a sequential manner. The study provides a structural origin for such a sequential Ca(2+) displacement by Yb(3+) in EhCaBP.     

Amide proton temperature coefficients as hydrogen bond indicators in proteins

Correlations between amide proton temperature coefficients (_HN/T) and hydrogen bonds were investigated for a data set of 793 amides derived from 14 proteins. For amide protons showing temperature gradients more positive than –4.6 ppb/K there is a hydrogen bond predictivity value exceeding 85%. It increases to over 93% for amides within the range between –4 and –1 ppb/K. Detailed analysis shows an inverse proportionality between amide proton temperature coefficients and hydrogen bond lengths. Furthermore, for hydrogen bonds of similar bond lengths, values of temperature gradients in -helices are on average 1 ppb/K more negative than in -sheets. In consequence, a number of amide protons in -helices involved in hydrogen bonds shorter than 2 Å show _HN/T < –4.6 ppb/K. Due to longer hydrogen bonds, 90% of amides in 3₁₀ helices and 98% in -turns have temperature coefficients more positive than –4.6ppb/K. Ring current effect also significantly influences temperature coefficients of amide protons. In seven out of eight cases non-hydrogen bonded amides strongly deshielded by neighboring aromatic rings show temperature coefficients more positive than –2 ppb/K. In general, amide proton temperature gradients do not change with pH unless they correspond to conformational changes. Three examples of pH dependent equilibrium showing hydrogen bond formation at higher pH were found. In conclusion, amide proton temperature coefficients offer an attractive and simple way to confirm existence of hydrogen bonds in NMR determined structures.     

Coral mortality and interaction with algae in relation to sedimentation

The impact of sedimentation on coral–algal interactions was studied by monitoring tissue mortality and radial growth in two coral species, Colpophyllia natans and Siderastrea siderea, over a continuum of sediment input intensities. This study sets out to investigate (1) whether sedimentation can facilitate algal overgrowth of corals and (2) whether this was a significant cause of coral mortality. Over a 15-month period, 198 coral colonies were tagged and photographed at six sites along two replicate gradients of sediment input, spanning high inputs near river mouths to low inputs at exposed headlands. Photographs were taken so that they covered the interface between colonies and algae. Radial growth was measured along colony edges in contact with algae and unaffected by tissue loss from causes other than competition with algae. To establish whether algal overgrowth was a significant cause of coral mortality, tissue mortality on the colony surface area visible in the photographs was related to different causes, including sediment smothering, disease, and algal overgrowth. Radial growth became negative with increasing proximity to river mouths in C. natans and remained negative or close to zero throughout the gradients in S. siderea, overall suggesting that sedimentation can facilitate algal overgrowth on corals. However, the analysis of tissue mortality revealed that algal overgrowth was a relatively minor cause of tissue loss. In contrast, the most important cause of coral mortality in relation to sedimentation was from sediment smothering, probably during intense episodes of deposition associated with heavy rainfall. We conclude that sedimentation may lead to reef degradation by causing coral mortality through sediment smothering and burial, and then by suppressing the regrowth of surviving adult colonies through increased competition with algae.     

Adaptive peak shifts in a heterogenous environment

The problem of moving from one coadapted gene complex to a better one can be divided into two steps: first the advantageous combination has to appear and then it has to take over the population. Selection can have contrasting effects on the two stages. When selection is weak intermediate forms are frequent, and the advantageous combination appears easily. Spreading of that advantageous combination, on the other hand, tends to be hard, as recombination acts to break it. The opposite is true when selection is strong. Spreading is easier, but if selection is also strong against the intermediate forms, the appearance of the beneficial combination becomes an extremely rare event.This inherent contrast in the optimal conditions for the two stages raises the possibility that proximity of areas differing in the intensity of selection may significantly shorten the expected waiting time for a peak shift. We studied this phenomenon in a haploid two-locus diallelic model of two neighboring subpopulations. Our results show that limited migration between the two areas might shorten the waiting time for a peak shift by orders of magnitude in comparison with either complete isolation or complete mixing. Implications for peripheral evolution and speciation are discussed.     

Unblocked statistical-coil tetrapeptides in aqueous solution: quantum-chemical computation of the carbon-13 NMR chemical shifts

We recently reported a theoretical characterization of representative ensembles of statistical-coil conformations for tetrapeptides with unblocked termini in aqueous solution, at pH 7. The results showed good agreement between the computed Boltzmann-averaged and experimentally-determined values for both the vicinal coupling constants ³J_NH and the -proton chemical shifts. Here, we carry out a cluster analysis of the ensembles of conformations generated in that study, and use them to compute the Boltzmann-averaged values of the quantum-chemical ¹³C chemical shifts for different amino acids in the unblocked tetrapeptides GGXA (where X stands for Phe, Arg, His, Glu, Ile, Lys, Gln, Tyr, Leu, Thr, Ala, Gly and Val). The values of the ¹³C chemical shifts in these thirteen amino acids (for which experimental data are available) were computed by using Density Functional Theory with a 6–311+G(2d,p) basis set. Good agreement is found in terms of both the correlation coefficient (R) and standard deviations of the difference between the computed Bolztmann-averaged and the NMR-determined values for the ¹³C chemical shifts. These results suggest that it may be possible to build a reliable theoretically-derived database of chemical shifts for statistical-coil residues. The results of the current study contribute to our understanding of the relations between chemical shifts, dihedral angles and vicinal coupling constants, ³J_NH. In addition, they can shed light as to how the statistical-coilconformation is related to the conformational preference of more structured states, such as the -helical conformation.