Significant impact of divalent metal ions on the fidelity,sugar selectivity,and drug incorporation efficiency of human PrimPol

Human PrimPol is a recently discovered bifunctional enzyme that displays DNA template-directed primase and polymerase activities. PrimPol has been implicated in nuclear and mitochondrial DNA replication fork progression and restart as well as DNA lesion bypass. Published evidence suggests that PrimPol is a Mn²⁺-dependent enzyme as it shows significantly improved primase and polymerase activities when binding Mn²⁺, rather than Mg²⁺, as a divalent metal ion cofactor. Consistently, our fluorescence anisotropy assays determined that PrimPol binds to a primer/template DNA substrate with affinities of 29 and 979 nM in the presence of Mn²⁺ and Mg²⁺, respectively. Our pre-steady-state kinetic analysis revealed that PrimPol incorporates correct dNTPs with 100-fold higher efficiency with Mn²⁺ than with Mg²⁺. Notably, the substitution fidelity of PrimPol in the presence of Mn²⁺ was determined to be in the range of 3.4 × 10⁻² to 3.8 × 10⁻¹, indicating that PrimPol is an error-prone polymerase. Furthermore, we kinetically determined the sugar selectivity of PrimPol to be 57–1800 with Mn²⁺ and 150–4500 with Mg²⁺, and found that PrimPol was able to incorporate the triphosphates of two anticancer drugs (cytarabine and gemcitabine), but not two antiviral drugs (emtricitabine and lamivudine).     

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.     

HAUL-OUT PATTERNS, SITE FIDELITY AND ACTIVITY BUDGETS OF MALE HOOKER'S SEA LIONS (PHOCARCTOS HOOKERI) ON THE NEW ZEALAND MAINLAND

Diurnal and seasonal haul-out patterns, site fidelity and activity budgets of individually identified Hooker's sea lions were studied for two years at Papanui Beach, Otago Peninsula, New Zealand.
Fourteen male sea lions were identified. Lengths ranged from 1.65 m–2.28 m and estimated ages from 2-11 yr. The population consisted of four sexually and socially mature (potentially breeding), eight sexually mature but socially immature and two immature males. Most haul-outs (95.6%) were by nine identifiable individuals (Residents) returning on a regular basis, suggesting a high degree of site specificity. Emigration and recruitment were low in relation to the length of the study. Daily arrivals (mean = 0844 h, SD = 1.49) and departures (mean = 1802 h, SD = 1.18) indicate nocturnal feeding. During March 1986 sea lions spent 43.8% of each day ashore (= 78% of daylight hours). Numbers of sea lions hauled out declined in both breeding seasons; in 1986/87 this was due to a decrease in haul-out frequency of resident animals. All but one of these sea lions returned after the breeding season.
Sea lions preferentially selected the middle and the extreme ends of the beach as haul-out sites. During winter use was made of the grass dunes as haul-out areas.
There were significant differences in the frequencies of behavioral activities between summer and winter; more time was allocated to resting in summer.     

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.     

Home‐site fidelity and homing behavior of the big‐headed turtle Platysternon megacephalum

Site fidelity refers to the restriction of dispersal distance of an animal and its tendency to return to a stationary site. To our knowledge, the homing ability of freshwater turtles and their fidelity is reportedly very low in Asia. We examined mark–recapture data spanning a 4‐year period in Diaoluoshan National Nature Reserve, Hainan Province, China, to investigate the site fidelity and homing behavior of big‐headed turtles Platysternon megacephalum. A total of 11 big‐headed turtles were captured, and all individuals were used in this mark–recapture study. The site fidelity results showed that the adult big‐headed turtles (n = 4) had a 71.43% recapture rate in the original site after their release at the same site, whereas the juveniles (n = 1) showed lower recapture rates (0%). Moreover, the homing behavior results showed that the adults (n = 5) had an 83.33% homing rate after displacement. Adult big‐headed turtles were able to return to their initial capture sites (home) from 150 to 2,400 m away and precisely to their home sites from either upstream or downstream of their capture sites or even from other streams. However, none of the juveniles (n = 4) returned home, despite only being displaced 25–150 m away. These results indicated that the adult big‐headed turtles showed high fidelity to their home site and strong homing ability. In contrast, the juvenile turtles may show an opposite trend but further research is needed.     

Spatial distribution of nests constrains the strength of sexual selection in a warbler

In socially monogamous species, extra‐pair paternity may increase the strength of intersexual selection by allowing males with preferred phenotypes to monopolize matings. Several studies have found relationships between male signals and extra‐pair mating, but many others fail to explain variation in extra‐pair mating success. A greater appreciation for the role that ecological contingencies play in structuring behavioural processes may help to reconcile contradictory results. We studied extra‐pair mating in a spatial context in the common yellowthroat (Geothlypis trichas), a territorial wood warbler. Over the course of 6 years, we observed 158 breeding attempts by 99 males, resulting in a total of 369 nests and 520 sampled nestlings. The spatial distribution of territories varied greatly, with males having between 0 and 10 close neighbours and between three and 39 neighbouring nestlings close enough to represent extra‐pair siring opportunities. Both within‐pair and extra‐pair reproductive success increased with breeding density, but the opportunity for sexual selection and strength of selection varied with density. Total variance in reproductive success was highest at low density and was mostly explained by variation in within‐pair success. In contrast, at high density, both within‐pair and extra‐pair successes contributed substantially to variance in reproductive success. The relationships between plumage and extra‐pair mating also varied by density; plumage was under strong sexual selection via extra‐pair mating success at high density, but no selection was detected at low density. Thus, ecological factors that structure social interactions can drive patterns of sexual selection by facilitating or constraining the expression of mating preferences.     

Contribuzione alla flora algologica del mare Adriatico

The specific species-rich high-altitude vegetation of the class Carici rupestris-Kobresietea bellardii Ohba 1974 (CK), with the occurrence of many arctic-alpine and endemic species, was chosen for a case study. The analyses were based on a dataset of 37,204 phytosociological relevés from the Slovak Vegetation Database. The traditional classification of the class CK, based on cluster analyses, was reproduced satisfactorily by means of formalised classification, based on the formal definitions created by the Cocktail method together with the frequency-positive fidelity index affiliation. Unequivocal assignment criteria for all eight associations of both alliances [Oxytropido-Elynion Br.-Bl. (1948) 1949 and Festucion versicoloris Krajina 1933] of the class CK were formulated. The formal delimitations followed the traditional ones very well. It was demonstrated that the results of applying the formal definitions created on the basis of a large, geographically stratified dataset capturing the occurrence of all vegetation types in Slovakia were highly similar in comparison with the traditional classification based on the results of cluster analysis. The reliability and the pros and cons of the expert system are also discussed.