Symmetrical stabilization of bound Ca2+ ions in a cooperative pair of EF-hands through hydrogen bonding of coordinating water molecules in calbindin D(9k)

Water molecules are found to complete the Ca2+ coordination sphere when a protein fails to provide enough ligating oxygens. Hydrogen bonding of these water molecules to the protein backbone or side chains may contribute favorably to the Ca2+ affinity, as suggested in an earlier study of two calbindin D(9k) mutants [E60D and E60Q; Linse et al. (1994) Biochemistry 33, 12478-12486]. To investigate the generality of this conclusion, another side chain, Gln 22, which hydrogen bonds to a Ca2+-coordinating water molecule in calbindin D(9k), was mutated. Two calbindin D(9k) mutants, (Q22E+P43M) and (Q22N+P43M), were constructed to examine the interaction between Gln 22 and the water molecule in the C-terminal calcium binding site II. Shortening of the side chain, as in (Q22N+P43M), reduces the affinity of binding two calcium ions by a factor of 18 at low ionic strength, whereas introduction of a negative charge, as in (Q22E+P43M), leads to a 12-fold reduction. In 0.15 M KCl, a 7-fold reduction in affinity was observed for both mutants. The cooperativity of Ca2+ binding increases for (Q22E+P43M), while it decreases for (Q22N+P43M). The rates of Ca2+ dissociation are 5.5-fold higher for the double mutants than for P43M at low ionic strength. For both mutants, reduced strength of hydrogen bonding to calcium-coordinating water molecules is a likely explanation for the observed effects on Ca2+ affinity and dissociation. In the apo forms, the (Q22E+P43M) mutant has lower stability toward urea denaturation than (Q22N+P43M) and P43M. 2D (1)H NMR and crystallographic experiments suggest that the structure of (Q22E+P43M) and (Q22N+P43M) is unchanged relative to P43M, except for local perturbations in the loop regions.     

Cell Size and Growth Rate Are Modulated by TORC2-Dependent Signals

1. Download high-res image (81KB)
2. Download full-size image

     

Calibration-in-time versus calibration-in-space (transfer function) to quantitatively infer July air temperature using biological indicators (chironomids) preserved in lake sediments

Calibration-in-space (i.e. modern taxonomic assemblages of biota from many lakes located along a wide temperature gradient calibrated against meteorological data) is generally used to derive species-specific optima and tolerances. This results in transfer functions which then are applied to subfossil assemblages to quantitatively reconstruct environmental variables such as air/water temperature. Developing such transfer functions is time- and money-consuming, thus many biota-inferred temperature records are either based on transfer functions from other regions which might not take into account local characteristics or are only used qualitatively. In varved Lake Silvaplana (Engadine, Switzerland), another way of obtaining quantitative climate reconstructions from taxonomical assemblages preserved in lake sediments was assessed for the past 1000 years. A calibration-in-time (i.e. taxonomic-assemblage-of-biota time series calibrated against meteorological data covering the same time period) was developed for chironomids (non-biting midges) using a weighted-average-partial-least-square (WAPLS) model and compared with a calibration-in-space model. The calibration-in-time had a weaker correlation coefficient (r² = 0.71) than the calibration-in-space (r² = 0.86), but the error of prediction (RMSEP = 0.58 °C) and the maximum bias (Max Bias = 0.73 °C) outperformed the statistics of the calibration-in-space (RMSEP = 1.5 °C; Max Bias = 1.72). This result is probably due to the smaller temperature gradient of the calibration-in-time (6.5 °C) than the calibration-in-space (11.5 °C). For the last 150 years, the Pearson correlation coefficient was significant between the two reconstructions (r_Pearson = 0.52; p < 0.01) suggesting that both models recorded a similar pattern of temperature changes. On the millennium time-scale, both models showed a warm “Medieval Climate Anomaly”, a cold “Little Ice Age” and a warming through the present with significant correlations (rPearson corrected for autocorrelation (corr) = 0.61, p < 0.01) until ca. 1780 AD and between ca. 1937 and 2000 AD (r_{Pearson corr} = 0.90, p < 0.01). The reconstructions using both models significantly diverged between ca. 1780 and 1937 AD (r_{Pearson corr} = ?0.47, p < 0.01). The results of both reconstruction methods were compared with four independent local and regional records of early instrumental and documentary data during the period of divergence. Both reconstructions showed similarities with the early instrumental/documentary records, thus it was inconclusive which of the reconstruction models provides the better estimates. However, these results suggest that a calibration-in-time can be used to reconstruct climate over the last 1000 years when no calibration-in-space is available.     

Functional anatomy of scent glands in Paranemastoma quadripunctatum (Opiliones,Dyspnoi, Nemastomatidae)

The morphological organization and functional anatomy of prosomal defensive (scent) glands in Paranemastoma quadripunctatum, a representative of the dyspnoid harvestmen, was investigated by means of histological semithin sections, software‐based 3D‐reconstruction and scanning electron microscopy. Scent glands comprise large, hollow sacs on either side of the prosoma, each of these opening to the outside via one orifice (ozopore) immediately above coxa I. In contrast to the situation known from laniatorean, cyphophthalmid and some eupnoid Opiliones, ozopores are not exposed but hidden in a depression (atrium), formed by a dorsal integumental fold of the carapace and the dorsal parts of coxae I. Glandular sacs are connected to ozopores via a short duct which is equipped with a specific closing mechanism in its distal part: A layer of modified epidermal cells forms a kind of pad‐like tissue, surrounding the duct like a valve. Several muscles attached to the anterior parts of the glandular reservoir and to the epithelial pad may be associated with ozopore‐opening. The actual mechanism of secretion discharge seems to be highly unusual and may be hypothesized on the basis of corroborating data from behavioral observations, scent gland anatomy and secretion chemistry as follows: Enteric fluid is considered to be directed towards the ozopores via cuticular grooves in the surface of the coxapophyses of legs I. Then, the fluid is sucked into the anterior part of the scent gland reservoirs by the action of dorsal dilator muscles that widen the reservoir and produce a short‐term negative pressure. After dilution/solution of the naphthoquinone‐rich scent gland contents, a secretion‐loaded fluid is thought to be discharged with the help of transversal compressor muscles. This is the first detailed study on the functional anatomy of scent glands and the mechanisms of secretion discharge in the Dyspnoi. J. Morphol. 2011. © 2011 Wiley‐Liss, Inc.     

A Dated Phylogeny Complements Macroecological Analysis to Explain the Diversity Patterns in Geonoma (Arecaceae)

Integrating phylogenetic data into macroecological studies of biodiversity patterns may complement the information provided by present‐day spatial patterns. In the present study, we used range map data for all Geonoma (Arecaceae) species to assess whether Geonoma species composition forms spatially coherent floristic clusters. We then evaluated the extent to which the spatial variation in species composition reflects present‐day environmental variation vs. nonenvironmental spatial effects, as expected if the pattern reflects historical biogeography. We also examined the degree of geographic structure in the Geonoma phylogeny. Finally, we used a dated phylogeny to assess whether species richness within the floristic clusters was constrained by a specific historical biogeographic driver, namely time‐for‐diversification. A cluster analysis identified six spatially coherent floristic clusters, four of which were used to reveal a significant geographic phylogenetic structure. Variation partitioning analysis showed that 56 percent of the variation in species composition could be explained by spatial variables alone, consistent with historical factors having played a major role in generating the Geonoma diversity pattern. To test for a time‐for‐diversification effect, we correlated four different species richness measures with the diversification time of the earliest large lineage that is characteristic of each cluster. In support of this hypothesis, we found that geographic areas with higher richness contained older radiations. We conclude that current geographic diversity patterns in Geonoma reflect the present‐day climate, but to a larger extent are related to nonenvironmental spatial constraints linked to colonization time, dispersal limitation, and geological history, followed by within‐area evolutionary diversification. Abstract in Spanish is available at http://www.blackwell‐synergy.com/loi/btp .     

Multiscale landscape genomic models to detect signatures of selection in the alpine plant Biscutella laevigata

Plant species are known to adapt locally to their environment, particularly in mountainous areas where conditions can vary drastically over short distances. The climate of such landscapes being largely influenced by topography, using fine‐scale models to evaluate environmental heterogeneity may help detecting adaptation to micro‐habitats. Here, we applied a multiscale landscape genomic approach to detect evidence of local adaptation in the alpine plant Biscutella laevigata. The two gene pools identified, experiencing limited gene flow along a 1‐km ridge, were different in regard to several habitat features derived from a very high resolution (VHR) digital elevation model (DEM). A correlative approach detected signatures of selection along environmental gradients such as altitude, wind exposure, and solar radiation, indicating adaptive pressures likely driven by fine‐scale topography. Using a large panel of DEM‐derived variables as ecologically relevant proxies, our results highlighted the critical role of spatial resolution. These high‐resolution multiscale variables indeed indicate that the robustness of associations between genetic loci and environmental features depends on spatial parameters that are poorly documented. We argue that the scale issue is critical in landscape genomics and that multiscale ecological variables are key to improve our understanding of local adaptation in highly heterogeneous landscapes.     

Genetic population structure, queen supersedure and social polymorphism in a social Hymenoptera

In social insects, the emergence of multiple queening is linked to changes in a suite of traits such as the reproductive life span of queens, mating patterns and population structure. We investigated queen turnover, colony longevity, spatial distribution patterns and genetic differentiation in a population of the socially polymorphic ant Formica fusca. Genetic differentiation between the social forms was absent, and mating patterns were similar in the two forms. The spatial distribution of single- and multi-queen colonies indicated an absence of colony reproduction by budding in both colony types. However, the rate of queen supersedure was high in multi-queen colonies and absent in single-queen ones. The social structure of colonies remained stable across years, but colony mortality did not differ between the two social forms. These results imply that differences between social types may appear and persist also in sympatry, and that these differences may occur in some traits, but not others, despite the presence of homogenizing gene flow.