Clutch size and the costs of incubation in the house wren

Trade-offs in the allocation of finite resources among differentstages of a breeding attempt as well as between different reproductiveevents should shape the evolution of life-history traits. Toinvestigate the effects of incubation effort on within-broodand between-brood trade-offs in house wrens (Troglodytes aedon),we manipulated the clutch size that females incubated. We isolatedeffects of incubation by reversing the manipulation at hatchingto allow all parents to provision their natural brood sizes.Females that incubated enlarged clutches had longer incubationperiods than control females, both early and late in the season,suggesting that the experimental treatment increased incubationeffort. Contrary to predictions, however, increased incubationeffort did not adversely affect the allocation of effort tonestling provisioning. Rather, in the early season, but notin the late season, females that incubated enlarged clutchesappeared to allocate more effort to nestling provisioning, producingheavier and larger fledglings than control females. Althoughfemales with enlarged early-season clutches consequently lostmore mass than control females, this was likely an adaptiveresponse to reduce wing loading in anticipation of high provisioningdemands. There were no treatment-related differences in fledglingmass or size, or in female mass loss, in the late season. Thus,elevated incubation demands negatively affected a fitness-relatedtrait (duration of incubation) that may constrain clutch sizebut not the allocation of resources to subsequent stages ofthe same breeding event or to subsequent breeding events. Wesuggest that environmental conditions may mediate clutch-sizeeffects on trade-offs in allocation of resources between incubationand nestling provisioning.     

Effect of abscisic acid pretreatments on stomatal reopening in Vicia faba

After a pretreatment of 2 h exposure to a solution containing 2 × 10⁻⁴ M ABA, reopening of stomata occurred in epidermal strips of Vicia faba L. cv. Cavalier on an ABA-free incubation solution. After pretreatment with exogenous ABA stomatal apertures were greater when higher levels of KCl were incorporated into the solution used for reopening. Prolonged exposure to exogenous ABA (14 h) did not prevent stomatal reopening upon transfer to ABA-free solutions. However, for both ABA and ABA-free pretreatments, prolonged incubation (1 day after removal of epidermis) resulted in enhanced stomatal apertures when the epidermal strips were exposed to light. This effect was lost 2 days after removal of the epidermis and opening did not occur after 3 days. Epidermal strips containing endogenous ABA were obtained from wilted leaves. Reopening was greatly reduced by the endogenous ABA treatment, and variation of KCl concentration in the incubation solution had little effect on stomatal aperture. It is postulated that during wilting endogenous ABA becomes reversibly bound without loss of activity for a longer period than is obtained using exogenous ABA. The presence of other unidentified compounds may be involved in this process.     

Partner-specific prediction of RNA-binding residues in proteins: A critical assessment

RNA-protein interactions play essential roles in regulating gene expression. While some RNA-protein interactions are “specific”, that is, the RNA-binding proteins preferentially bind to particular RNA sequence or structural motifs, others are “non-RNA specific.” Deciphering the protein-RNA recognition code is essential for comprehending the functional implications of these interactions and for developing new therapies for many diseases. Because of the high cost of experimental determination of protein-RNA interfaces, there is a need for computational methods to identify RNA-binding residues in proteins. While most of the existing computational methods for predicting RNA-binding residues in RNA-binding proteins are oblivious to the characteristics of the partner RNA, there is growing interest in methods for partner-specific prediction of RNA binding sites in proteins. In this work, we assess the performance of two recently published partner-specific protein-RNA interface prediction tools, PS-PRIP, and PRIdictor, along with our own new tools. Specifically, we introduce a novel metric, RNA-specificity metric (RSM), for quantifying the RNA-specificity of the RNA binding residues predicted by such tools. Our results show that the RNA-binding residues predicted by previously published methods are oblivious to the characteristics of the putative RNA binding partner. Moreover, when evaluated using partner-agnostic metrics, RNA partner-specific methods are outperformed by the state-of-the-art partner-agnostic methods. We conjecture that either (a) the protein-RNA complexes in PDB are not representative of the protein-RNA interactions in nature, or (b) the current methods for partner-specific prediction of RNA-binding residues in proteins fail to account for the differences in RNA partner-specific versus partner-agnostic protein-RNA interactions, or both.     

Impacts of forest fragmentation on orchid bee (Hymenoptera: Apidae: Euglossini) communities in the Chocó biodiversity hotspot of northwest Ecuador

Habitat loss is a major driver of bee declines worldwide, and is of key relevance in the tropics given high deforestation rates, but we continue to have a poor understanding of the impact of land-cover change on tropical bee communities. Orchid bees (Apidae: Euglossini) are critical long-distance pollinators and may be highly susceptible to forest fragmentation given their reliance on forest habitat. Previous studies on the impact of forest fragmentation on euglossines have been geographically limited, have largely ignored β-diversity, and have not compared fragments with continuous forest. To contribute to addressing these gaps, we sampled male euglossine bees in 18 forest fragments (area range: 2.5–33 ha) and at eight locations within a large (3500 ha) continuous forest in the Chocó biodiversity hotspot of Ecuador during the dry season in 2014. We assessed how euglossine abundance, richness, and evenness related to fragment area, isolation, and edge:area ratio. We also compared fragments to continuous forest, in terms of α- and β-diversity. In fragments, a single species (Euglossa tridentata) comprised 78% of captures, and we found no significant effect of fragment area, isolation, or edge on abundance, richness, or evenness among fragments. Forest fragments and continuous forest differed in both community composition and evenness, but not in abundance or species richness. Spatial turnover (β-diversity) showed a non-significant trend toward changing more rapidly in continuous forest relative to fragments. These results underscore the conservation value of continuous forest for orchid bee diversity.     

Mean Recency Period for Estimation of HIV-1 Incidence with the BED-Capture EIA and Bio-Rad Avidity in Persons Diagnosed in the United States with Subtype B

HIV incidence estimates are used to monitor HIV-1 infection in the United States. Use of laboratory biomarkers that distinguish recent from longstanding infection to quantify HIV incidence rely on having accurate knowledge of the average time that individuals spend in a transient state of recent infection between seroconversion and reaching a specified biomarker cutoff value. This paper describes five estimation procedures from two general statistical approaches, a survival time approach and an approach that fits binomial models of the probability of being classified as recently infected, as a function of time since seroconversion. We compare these procedures for estimating the mean duration of recent infection (MDRI) for two biomarkers used by the U.S. National HIV Surveillance System for determination of HIV incidence, the Aware BED EIA HIV-1 incidence test (BED) and the avidity-based, modified Bio-Rad HIV-1/HIV-2 plus O ELISA (BRAI) assay. Collectively, 953 specimens from 220 HIV-1 subtype B seroconverters, taken from 5 cohorts, were tested with a biomarker assay. Estimates of MDRI using the non-parametric survival approach were 198.4 days (SD 13.0) for BED and 239.6 days (SD 13.9) for BRAI using cutoff values of 0.8 normalized optical density and 30%, respectively. The probability of remaining in the recent state as a function of time since seroconversion, based upon this revised statistical approach, can be applied in the calculation of annual incidence in the United States.