Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition

Riboswitches are conserved functional domains in mRNA that mostly exist in bacteria. They regulate gene expression in response to varying concentrations of metabolites or metal ions. Recently, the NMT1 RNA motif has been identified to selectively bind xanthine and uric acid, respectively, both are involved in the metabolic pathway of purine degradation. Here, we report a crystal structure of this RNA bound to xanthine. Overall, the riboswitch exhibits a rod-like, continuously stacked fold composed of three stems and two internal junctions. The binding-pocket is determined by the highly conserved junctional sequence J1 between stem P1 and P2a, and engages a long-distance Watson–Crick base pair to junction J2. Xanthine inserts between a G–U pair from the major groove side and is sandwiched between base triples. Strikingly, a Mg²⁺ ion is inner-sphere coordinated to O6 of xanthine and a non-bridging oxygen of a backbone phosphate. Two further hydrated Mg²⁺ ions participate in extensive interactions between xanthine and the pocket. Our structure model is verified by ligand binding analysis to selected riboswitch mutants using isothermal titration calorimetry, and by fluorescence spectroscopic analysis of RNA folding using 2-aminopurine-modified variants. Together, our study highlights the principles of metal ion-mediated ligand recognition by the xanthine riboswitch.     

Males of a single-brooded tropical bird species do not show increases in testosterone during social challenges

The challenge hypothesis poses that in socially monogamous vertebrates, males increase circulating testosterone in response to aggressive challenges to promote intense and persistent aggression. However, in bird species that raise only a single brood during short breeding seasons as well as those with essential male parental care, males lack the well-documented testosterone response to social challenges. We tested male behavioral and hormonal responses to social challenges in a neotropical bird species, the buff-breasted wren (Thryothorus leucotis), which is single-brooded with extensive male parental care, but in contrast to most species studied to date, has a long breeding season. We presented live female, male, and paired decoys with song playback for 30 min during pre-breeding and breeding periods. Males responded aggressively to all intruders, but male decoys elicited somewhat weaker responses overall. Responses to female decoys were most intense during pre-breeding, whereas pair decoys elicited stronger responses at breeding. Plasma testosterone concentrations did not differ between challenged and unchallenged males, or among males exposed to different decoys or during different seasons. Plasma corticosterone in pre-breeding males was higher in challenged than unchallenged males and varied positively with the duration of social challenge. Circulating dehydroepiandrosterone concentrations were similar in challenged and unchallenged males, but correlated positively with the proportion of time males spent in close proximity to the decoy. Both testosterone and corticosterone results support recent findings, suggesting that brood number and essential male care, but not breeding-season length, may be important determinants of male hormonal responsiveness during aggressive interactions.     

Micropatterning for quantitative analysis of protein-protein interactions in living cells

We present a method to identify and characterize interactions between a fluorophore-labeled protein ('prey') and a membrane protein ('bait') in live mammalian cells. Cells are plated on micropatterned surfaces functionalized with antibodies to the bait extracellular domain. Bait-prey interactions are assayed through the redistribution of the fluorescent prey. We used the method to characterize the interaction between human CD4, the major co-receptor in T-cell activation, and human Lck, the protein tyrosine kinase essential for early T-cell signaling. We measured equilibrium associations by quantifying Lck redistribution to CD4 micropatterns and studied interaction dynamics by photobleaching experiments and single-molecule imaging. In addition to the known zinc clasp structure, the Lck membrane anchor in particular had a major impact on the Lck-CD4 interaction, mediating direct binding and further stabilizing the interaction of other Lck domains. In total, membrane anchorage increased the interaction lifetime by two orders of magnitude.     

Hybridization and crossability in Caiophora (Loasaceae subfam. Loasoideae): Are interfertile species and inbred populations results of a recent radiation?

Interspecific hybridization is considered a possible mechanism of plant diversification. The Andes are a hotspot of biodiversity, but hybridization in Andean taxa has so far not been investigated intensively. The current study investigates crossability in Caiophora (Loasaceae subfam. Loasoideae) by experimental interspecific hybridization of seven different species. Hand pollination was undertaken, developing fruits counted, thousand (seed) grain weights, and seed viability were examined. Cross pollination led to some fruit set in 36 of the 37 different combinations. Overall fruit set was virtually identical irrespective of the combination of parental plants. Mean germination rates were much higher in hybrid seeds, indicating a marked heterosis effect and the possible presence of an inbreeding depression in the source populations: In experimental hybridization the divergent taxa of Caiophora behave like isolated, inbred populations of a single species. Allopatry and different habitat preferences seem to be the key factors keeping the (interfertile) taxa of Caiophora apart in the apparent absence of both postmating isolating mechanisms and obvious isolating mechanisms in phenology and floral biology. Interspecific hybrids reported from the wild appear to be the result of secondary contact due to human impact.     

Validation of the International Classification of Functioning, Disability and Health (ICF) Core Set for rheumatoid arthritis from the patient perspective using focus groups

Functioning is recognized as an important study outcome in rheumatoid arthritis (RA). The Comprehensive ICF Core Set for RA is an application of the International Classification of Functioning, Disability and Health (ICF) of the World Health Organisation with the purpose of representing the typical spectrum of functioning of patients with RA. To strengthen the patient perspective, persons with RA were explicitly involved in the validation of the Comprehensive ICF Core Set for RA using qualitative methodology. The objective of the study was twofold: to come forward with a proposal for the most appropriate methodology to validate Comprehensive ICF Core Sets from the patient perspective; and to add evidence to the validation of the Comprehensive ICF Core Set for RA from the perspective of patients. The specific aims were to explore the aspects of functioning and health important to patients with RA using two different focus group approaches (open approach and ICF-based approach) and to examine to what extent these aspects are represented by the current version of the Comprehensive ICF Core Set for RA. The sampling of patients followed the maximum variation strategy. Sample size was determined by saturation. The focus groups were digitally recorded and transcribed verbatim. The meaning condensation procedure was used for the data analysis. After qualitative data analysis, the resulting concepts were linked to ICF categories according to established linking rules. Forty-nine patients participated in ten focus groups (five in each approach). Of the 76 ICF categories contained in the Comprehensive ICF Core Set for RA, 65 were reported by the patients based on the open approach and 71 based on the ICF-based approach. Sixty-six additional categories (open approach, 41; ICF-based approach, 57) that are not covered in the Comprehensive ICF Core Set for RA were raised. The existing version of the Comprehensive ICF Core Set for RA could be confirmed almost entirely by the two different focus group approaches applied. Focus groups are a highly useful qualitative method to validate the Comprehensive ICF Core Set for RA from the patient perspective. The ICF-based approach seems to be the most appropriate technique.     

Assessment of trends in predation pressure on insects across temperate forest microhabitats

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Hormone levels predict individual differences in reproductive success in a passerine bird

Hormones mediate major physiological and behavioural components of the reproductive phenotype of individuals. To understand basic evolutionary processes in the hormonal regulation of reproductive traits, we need to know whether, and during which reproductive phases, individual variation in hormone concentrations relates to fitness in natural populations. We related circulating concentrations of prolactin and corticosterone to parental behaviour and reproductive success during both the pre-breeding and the chick-rearing stages in both individuals of pairs of free-living house sparrows, Passer domesticus. Prolactin and baseline corticosterone concentrations in pre-breeding females, and prolactin concentrations in pre-breeding males, predicted total number of fledglings. When the strong effect of lay date on total fledgling number was corrected for, only pre-breeding baseline corticosterone, but not prolactin, was negatively correlated with the reproductive success of females. During the breeding season, nestling provisioning rates of both sexes were negatively correlated with stress-induced corticosterone levels. Lastly, individuals of both sexes with low baseline corticosterone before and high baseline corticosterone during breeding raised the most offspring, suggesting that either the plasticity of this trait contributes to reproductive success or that high parental effort leads to increased hormone concentrations. Thus hormone concentrations both before and during breeding, as well as their seasonal dynamics, predict reproductive success, suggesting that individual variation in absolute concentrations and in plasticity is functionally significant, and, if heritable, may be a target of selection.     

Evaluation of different Bacillus strains in respect of their ability to produce Surfactin in a model fermentation process with integrated foam fractionation

Biosurfactants increasingly gain attention due to the manifold of possible applications and production on the basis of renewable resources. Owing to its various characteristics, Surfactin is one of the most studied biosurfactants. Since its discovery, several Surfactin producers have been identified, but their capacity to produce Surfactin has not been evaluated in a comparison. Six different Bacillus strains were analyzed regarding their ability to produce Surfactin in model fermentations with integrated foam fractionation, for in situ product enrichment and removal. Three of the investigated strains are commonly used in Surfactin production (ATCC 21332, DSM 3256, DSM 3258), whereas two Bacillus strains are described for the first time (DSM 1090, LM43a50°C) as Surfactin producers. Additionally, the Bacillus subtilis type strain DSM 10^T was included in the evaluation. Interestingly, all strains, except DSM 3256, featured high values for Surfactin recovered from foam in comparison to other studies, ranging between 0.4 and 1.05 g. The fermentation process was characterized by calculating procedural parameters like substrate yield Y _X/S, product yield Y _P/X, specific growth rate μ, specific productivity q _Surfactin, volumetric productivity q _Surfactin, Surfactin and bacterial enrichment as well as Surfactin recovery. The strains differ most in specific and volumetric productivity; nevertheless, it is evident that it is not possible to name a Bacillus strain that is the most appropriate for the production of Surfactin under these conditions. In contrast, it becomes apparent that the choice of a specific strain should depend on the applied fermentation conditions.     

Correction to: Linear relation between leaf xylem water potential and transpiration in pearl millet during soil drying

Plant and Soil - In the original version of this article, equations 4 and 9 unfortunately contained errors