Optimization of speed and accuracy of decoding in translation

The speed and accuracy of protein synthesis are fundamental parameters for understanding the fitness of living cells, the quality control of translation, and the evolution of ribosomes. In this study, we analyse the speed and accuracy of the decoding step under conditions reproducing the high speed of translation in vivo. We show that error frequency is close to 10⁻³, consistent with the values measured in vivo. Selectivity is predominantly due to the differences in k_cat values for cognate and near-cognate reactions, whereas the intrinsic affinity differences are not used for tRNA discrimination. Thus, the ribosome seems to be optimized towards high speed of translation at the cost of fidelity. Competition with near- and non-cognate ternary complexes reduces the rate of GTP hydrolysis in the cognate ternary complex, but does not appreciably affect the rate-limiting tRNA accommodation step. The GTP hydrolysis step is crucial for the optimization of both the speed and accuracy, which explains the necessity for the trade-off between the two fundamental parameters of translation.     

Consequences of floral visits by ants and invasive honeybees to the hummingbird‐pollinated,Caribbean cactus Melocactus intortus

The pink, tubular, nectariferous flowers of Melocactus intortus (Cactaceae) in Puerto Rico are visited by native hummingbirds (Anthracothorax dominicus), but also by invasive honeybees (Apis mellifera) and ants (Solenopsis sp.). We sought to determine if the bees and ants significantly alter the pollination of M. intortus by measuring pollinator effectiveness. Using traditional estimates of effectiveness (visitation rate and seed set), our results show that hummingbirds were the most effective pollinators as expected. Bees and ants were less effective, and their contributions were one‐fourth to one‐tenth of that observed for hummingbirds. We then modified this measure of effectiveness by adding two components, fitness of progeny and temporal availability of visitors, both of which refine estimates of flower visitor effectiveness. With these new estimations, we found that the effectiveness values of all three animal visitors decreased; however, the role of hummingbirds as the principal pollinator was maintained, whereas the effectiveness values of bees and ants approached zero. By these new measures of overall pollinator effectiveness, the invasive honeybees and ants have little effect on the reproductive success of M. intortus.     

Site fidelity in predictable and unpredictable habitats

Summary Site fidelity, the tendency to return to a previously occupied location, has been observed in numerous species belonging to at least three phyla. In this paper I develop a general model using dynamic programming to investigate conditions under which fidelity to a previously occupied territory will be advantageous. The results predict that site fidelity should be inversely related to heterogeneity in territory quality and the animal's lifespan and positively related to the cost of changing territories, age and probability of mortality in the habitat. The predictability of reproductive outcome (defined as the probability that next period's outcome will be the same as this period's outcome) also affects site fidelity. In predictable habitats, changing territories may be favoured after a bad previous outcome. In contrast, settlement should be independent of the previous outcome in unpredictable habitats. Individuals should also be site-faithful in unpredictable habitats, as long as the mean territory quality is equal among available territories. I also investigate the success of two potential decision rules (always stay and win-stay: lose-switch) relative to the optimal settlement strategy. The results show that these rules may perform as well as the optimal strategy under certain conditions. The always stay strategy does well in unpredictable habitats, when the mean quality within a territory is equal among territories. In contrast, the win-stay: lose-switch strategy performs best in predictable habitats.     

Defining null expectations for animal site fidelity

Site fidelity—the tendency to return to previously visited locations—is widespread across taxa. Returns may be driven by several mechanisms, including memory, habitat selection, or chance; however, pattern-based definitions group different generating mechanisms under the same label of ‘site fidelity’, often assuming memory as the main driver. We propose an operational definition of site fidelity as patterns of return that deviate from a null expectation derived from a memory-free movement model. First, using agent-based simulations, we show that without memory, intrinsic movement characteristics and extrinsic landscape characteristics are key determinants of return patterns and that even random movements may generate substantial probabilities of return. Second, we illustrate how to implement our framework empirically to establish ecologically meaningful, system-specific null expectations for site fidelity. Our approach provides a conceptual and operational framework to test hypotheses on site fidelity across systems and scales.     

Temporal pattern of resource use and variation in diets of individual grasshoppers (Orthoptera: Acrididae)

Patterns of resource fidelity, switching, and variation in individual diet were examined in the polyphagous grasshopper Taeniopoda equesforaging in experimental cages over an 11-day period. Ten novel dicots were provided in the cages, but grasshoppers fed primarily on kale (Brassica oleraceavar. acephala),lobelia (Lobelia erinus),pansy (Viola x wittrockiana),and dry bermuda grass (Cynodon dactylon).Grasshoppers showed significant fidelity to a single plant within a meal but tended to eat less of the same plant in the next meal and, in the case of pansy, on the next day. Grasshoppers switched nonrandomly, suggesting that compensatory feeding on complementary resources may have occurred. There was no evidence that behavioral interactions among individuals increased switching rate or lowered fidelity. Overall patterns of resource use varied significantly among grasshoppers during the study, despite frequent switching among resources and a significant tendency to aggregate while feeding. All individuals were polyphagous but differed in relative consumption of available plants. The results suggest that individual grasshoppers express different feeding patterns that are consistent over time and that variation in diet among individual observed in the field may be more than simple sampling error.     

Consecutive incorporation of fluorophore-labeled nucleotides by mammalian DNA polymerase β

In the present study, we investigated mammalian polymerases that consecutively incorporate various fluorophore-labeled nucleotides. We found that rat DNA polymerase β (pol β) consecutively incorporated fluorophore-labeled nucleotides to a greater extent than four bacterial polymerases, Sequenase Version 2.0, Vent_R (exo-), DNA polymerase IIIα and the Klenow fragment, and the mammalian polymerases DNA polymerase α and human DNA polymerase δ, under mesophilic conditions. Furthermore, we investigated the kinetics of correct or mismatched incorporation with labeled nucleotides during synthesis by rat pol β. The kinetic parameters K_m and k_cat were measured and used for evaluating: (i) the discrimination against correct pair incorporation of labeled nucleotides relative to unlabeled nucleotides; and (ii) the fidelity for all nucleotide combinations of mismatched pairs in the presence of labeled or unlabeled nucleotides. We also investigated the effect of fluorophore-labeled nucleotides on terminal deoxynucleotidyl transferase activity of rat pol β. We have demonstrated for the first time that mammalian pol β can consecutively incorporate various fluorophore-labeled dNTPs. These findings suggest that pol β is useful for high-density labeling of DNA probes and single-molecule sequencing for high-speed genome analysis.     

SPATIAL FLOWER PARAMETERS AND INSECT SPATIAL VISION

The present article reviews recent and older literature on the spatial parameters that flowers display, as well as on the capacities of anthophilous insects to perceive and use these parameters for optimizing their foraging success. Although co-evolution of plants and pollinators has frequently been discussed with respect to floral colours and insect colour vision, it has rarely been assessed with respect to insect spatial vision and spatial floral cues, such as shape, pattern, size, contrast, symmetry, spatial frequency, contour density and orientation of contours. This review is an attempt to fill this gap. From experimental findings and observations on both flowers and insects, we arrive at the conclusion that all of the spatial and spatio-temporal parameters that flowers offer are relevant to the foraging task and are tuned to the insect's visual capacities and visually guided behaviour. We try, in addition, to indicate that temporal cues are closely related to spatial cues, and must therefore be included when flower–pollinator interactions are examined. We include results that show that colour vision and spatial vision have diverged over the course of evolution, particularly regarding the processing of spatio-temporal information, but that colour vision plays a role in the processing of spatial cues that are independent of temporal parameters. By presenting this review we hope to contribute to closer collaboration among scientists working in the vast fields of botany, ecology, evolution, ethology and sensory physiology.     

Flowering phenology, fruiting success and progressive deterioration of pollination in an early-flowering geophyte

Spatio-temporal patterns of snowmelt and flowering times affect fruiting success in Erythronium grandiflorum Pursh (Liliaceae) in subalpine western Colorado, USA. From 1990 to 1995, I measured the consistency across years of snowmelt patterns and flowering times along a permanent transect. In most years since 1993, I have monitored fruit set in temporal cohorts (early- to late-flowering groups of plants) at one site. To assess ‘pollination limitation’, I have also conducted supplemental hand-pollination experiments at various times through the blooming season. The onset of blooming is determined by snowmelt, with the earliest years starting a month before the latest years owing to variation in winter snowpack accumulation. Fruit set is diminished or prevented entirely by killing frosts in some years, most frequently but not exclusively for the earlier cohorts. When frosts do not limit fruit set, pollination limitation is frequent, especially in the earlier cohorts. Pollination limitation is strongest for middle cohorts: it tends to be negated by frost in early cohorts and ameliorated by continuing emergence of bumble-bee queens in later cohorts. This lily appears to be poorly synchronized with its pollinators. Across the years of the study, pollination limitation appears to be increasing, perhaps because the synchronization is getting worse.     

Contrasting floral biology of Artabotrys species (Annonaceae): Implications for the evolution of pollinator trapping

Artabotrys comprises a species-poor early divergent grade (EDG) and a main species-rich clade (“main Artabotrys clade,” MAC). All members of the MAC exhibit a remarkably well-conserved floral Bauplan characterized by a tightly enclosed floral chamber with an elaborate rim between the inner petal blade and claw. Conversely, EDG resembles the sister genus Xylopia in lacking the inner petal rim, with one species (Artabotrys brachypetalus) bearing petals that lack the distinction between blade and claw altogether. The floral phenology and pollination ecology of two exemplar species—Artabotrys brachypetalus from the EDG and Artabotrys blumei from the MAC—are compared, including assessment of effective pollinators and their activity patterns, scent chemistry and thermogenesis. Our study revealed that Artabotrys blumei exhibits abbreviated anthesis (c. 27 hr), with a floral phenology and morphology that are clearly consistent with pollinator trapping, and may be pollinated by small beetles. Artabotrys brachypetalus has a typical anthetic duration (c. 45 hr), lacks a pollinator trapping mechanism, and is pollinated by honey bees and curculionid beetles. The “xylopioid” traits of the EDG are likely to be plesiomorphic, whereas the tightly enclosed floral chamber is likely to be apomorphic for the MAC and functionally significant in trapping pollinators.