The first specimen of Archaeopteryx from the Upper Jurassic Mörnsheim Formation of Germany

From an initial isolated position as the oldest evolutionary prototype of a bird, Archaeopteryx has, as a result of recent fossil discoveries, become embedded in a rich phylogenetic context of both more and less crownward stem-group birds. This has prompted debate over whether Archaeopteryx is simply a convergently bird-like non-avialan theropod. Here we show, using the first synchrotron microtomographic examination of the genus, that the eighth or Daiting specimen of Archaeopteryx possesses a character suite that robustly constrains it as a basal avialan (primitive bird). The specimen, which comes from the Mörnsheim Formation and is thus younger than the other specimens from the underlying Solnhofen Formation, is distinctive enough to merit designation as a new species, Archaeopteryx albersdoerferi sp. nov., but is recovered in close phylogenetic proximity to Archaeopteryx lithographica. Skeletal innovations of the Daiting specimen, such as fusion and pneumatization of the cranial bones, well vascularized pectoral girdle and wing elements, and a reinforced configuration of carpals and metacarpals, suggest that it may have had more characters seen in flying birds than the older Archaeopteryx lithographica. These innovations appear to be convergent on those of more crownward avialans, suggesting that Bavarian archaeopterygids independently acquired increasingly bird-like traits over time. Such mosaic evolution and iterative exploration of adaptive space may be typical for major functional transitions like the origin of flight.     

Inter‐individual variation in colour patterns in noctuid moths characterizes long‐distance dispersers and agricultural pests

A high capacity for long‐distance dispersal is a key to success for species confronted with environmental heterogeneity, habitat modification, fragmentation and loss. However, dispersal capacity is difficult to quantify and therefore poorly known in most taxa. Here, we report on a test for an association of variation in dispersal capacity with variable colouration of noctuid moths. First, using data from 12 experienced lepidopterologists, we showed that despite variation among experts in average assessments, different species are consistently classified as having non‐variable, variable or highly variable colour patterns when assessed by different experts. We then compared the incidence of non‐resident species with high inter‐individual variation in colour patterns recorded on the isolated island Utklippan (n = 47), with that in a species pool of potential long‐distance dispersers from the nearest mainland (n = 295). Species with high inter‐individual colour pattern variation were over‐represented on the island compared with species having non‐variable colouration. This finding constitutes rare evidence from the wild of long‐distance dispersal, measured on a spatial scale relevant for moths when tracking habitats in fragmented and changing landscapes or when keeping pace with environmental challenges associated with climate change. Finally, we showed that Swedish noctuid moths classified as agricultural pests (n = 28) had more variable colour patterns compared with non‐pests (n = 368). The majority of agricultural pests were also recorded on the isolated island, an outcome that is indicative of pest species having high dispersal capacity. Data on colour pattern variation may thus offer a simple and cost‐effective proxy to estimate dispersal capacity and can also help identify potential pest species. Our findings are potentially useful when modelling and predicting population and range dynamics of species in spatiotemporally heterogeneous environments, with direct implications for conservation biology and pest management.     

Long‐term rearing affects pheromone‐mediated flight behaviour of the Indian meal moth,Plodia interpunctella

The pest Plodia interpunctella (Hübner) is reared in many research laboratories. In a culture established in 1996, attraction of males to the female‐produced sex pheromone in flight tunnel assays gradually decreased after ≈15 years of rearing. A new culture was established to enable comparison with the old culture regarding traits associated with mate finding. Female calling activity, pheromone titre and male antennal response to pheromone components did not differ between cultures. In contrast, very few males from the old culture reached the pheromone source in flight tunnel assays compared with 61%–81% of males from the other culture. Our results highlight the importance of maintaining viable insect cultures for research purposes and suggest frequent evaluation of traits involved in chemical communication in such cultures to ensure reliable results in experiments.     

A nationwide school fruit and vegetable policy and childhood and adolescent overweight: A quasi-natural experimental study

BackgroundSchool free fruit and vegetable (FFV) policies are used to promote healthy dietary habits and tackle obesity; however, our understanding of their effects on weight outcomes is limited. We assess the effect of a nationwide FFV policy on childhood and adolescent weight status and explore heterogeneity by sex and socioeconomic position.Methods and findingsThis study used a quasi-natural experimental design. Between 2007 and 2014, Norwegian combined schools (grades 1–10, age 6 to 16 years) were obligated to provide FFVs while elementary schools (grades 1–7) were not. We used 4 nationwide studies (n = 11,215 children) from the Norwegian Growth Cohort with longitudinal or cross-sectional anthropometric data up to age 8.5 and 13 years to capture variation in FFV exposure. Outcomes were body mass index standard deviation score (BMI_SDS), overweight and obesity (OW/OB), waist circumference (WC), and weight to height ratio (WtHR) at age 8.5 years, and BMI_SDS and OW/OB at age 13 years. Analyses included longitudinal models of the pre- and post-exposure trajectories to estimate the policy effect. The participation rate in each cohort was >80%, and in most analyses <4% were excluded due to missing data. Estimates were adjusted for region, population density, and parental education. In pooled models additionally adjusted for pre-exposure BMI_SDS, there was little evidence of any benefit or unintended consequence from 1–2.5 years of exposure to the FFV policy on BMI_SDS, OW/OB, WC, or WtHR in either sex. For example, boys exposed to the FFV policy had a 0.05 higher BMI_SDS (95% CI: −0.04, 0.14), a 1.20-fold higher odds of OW/OB (95% CI: 0.86, 1.66) and a 0.3 cm bigger WC (95% CI: −0.3, 0.8); while exposed girls had a 0.04 higher BMI_SDS (95% CI: −0.04, 0.13), a 1.03 fold higher odds of OW/OB (95% CI: 0.75, 1.39), and a 0-cm difference in WC (95% CI: −0.6, 0.6). There was evidence of heterogeneity in the policy effect estimates at 8.5 years across cohorts and socioeconomic position; however, these results were inconsistent with other comparisons. Analysis at age 13 years, after 4 years of policy exposure, also showed little evidence of an effect on BMI_SDS or OW/OB. The main limitations of this study are the potential for residual confounding and exposure misclassification, despite efforts to minimize their impact on conclusions.ConclusionsIn this study we observed little evidence that the Norwegian nationwide FFV policy had any notable beneficial effect or unintended consequence on weight status among Norwegian children and adolescents.

Bente Øvrebø and colleagues assess whether a nationwide free school fruit and vegetable policy was associated with weight outcomes in children and early adolescents in Norway.     

Partitioning additive genetic variance into genomic and remaining polygenic components for complex traits in dairy cattle

ABSTRACT: BACKGROUND: Low cost genotyping of individuals using high density genomic markers were recently introduced as genomic selection in genetic improvement programs in dairy cattle. Most implementations of genomic selection only use marker information, in the models used for prediction of genetic merit. However, in other species it has been shown that only a fraction of the total genetic variance can be explained by markers. Using 5217 bulls in the Nordic Holstein population that were genotyped and had genetic evaluations based on progeny, we partitioned the total additive genetic variance into a genomic component explained by markers and a remaining component explained by familial relationships. The traits analyzed were production and fitness related traits in dairy cattle. Furthermore, we estimated the genomic variance that can be attributed to individual chromosomes and we illustrate methods that can predict the amount of additive genetic variance that can be explained by sets of markers with different density. RESULTS: The amount of additive genetic variance that can be explained by markers was estimated by an analysis of the matrix of genomic relationships. For the traits in the analysis, most of the additive genetic variance can be explained by 44 K informative SNP markers. The same amount of variance can be attributed to individual chromosomes but surprisingly the relation between chromosomal variance and chromosome length was weak. In models including both genomic (marker) and familial (pedigree) effects most (on average 77.2%) of total additive genetic variance was explained by genomic effects while the remaining was explained by familial relationships. CONCLUSIONS: Most of the additive genetic variance for the traits in the Nordic Holstein population can be explained using 44 K informative SNP markers. By analyzing the genomic relationship matrix it is possible to predict the amount of additive genetic variance that can be explained by a reduced (or increased) set of markers. For the population analyzed the improvement of genomic prediction by increasing marker density beyond 44 K is limited.     

Probing a polar cluster in the retinal binding pocket of bacteriorhodopsin by a chemical design approach

Bacteriorhodopsin has a polar cluster of amino acids surrounding the retinal molecule, which is responsible for light harvesting to fuel proton pumping. From our previous studies, we have shown that threonine 90 is the pivotal amino acid in this polar cluster, both functionally and structurally. In an attempt to perform a phenotype rescue, we have chemically designed a retinal analogue molecule to compensate the drastic effects of the T90A mutation in bacteriorhodopsin. This analogue substitutes the methyl group at position C(13) of the retinal hydrocarbon chain by and ethyl group (20-methyl retinal). We have analyzed the effect of reconstituting the wild-type and the T90A mutant apoproteins with all-trans-retinal and its 20-methyl derivative (hereafter, 13-ethyl retinal). Biophysical characterization indicates that recovering the steric interaction between the residue 90 and retinal, eases the accommodation of the chromophore, however it is not enough for a complete phenotype rescue. The characterization of these chemically engineered chromoproteins provides further insight into the role of the hydrogen bond network and the steric interactions involving the retinal binding pocket in bacteriorhodopsin and other microbial sensory rhodopsins.     

Influence of chronic and acute spinal cord injury on skeletal muscle Na+-K+-ATPase and phospholemman expression in humans

Na(+)-K(+)-ATPase is an integral membrane protein crucial for the maintenance of ion homeostasis and skeletal muscle contractibility. Skeletal muscle Na(+)-K(+)-ATPase content displays remarkable plasticity in response to long-term increase in physiological demand, such as exercise training. However, the adaptations in Na(+)-K(+)-ATPase function in response to a suddenly decreased and/or habitually low level of physical activity, especially after a spinal cord injury (SCI), are incompletely known. We tested the hypothesis that skeletal muscle content of Na(+)-K(+)-ATPase and the associated regulatory proteins from the FXYD family is altered in SCI patients in a manner dependent on the severity of the spinal cord lesion and postinjury level of physical activity. Three different groups were studied: 1) six subjects with chronic complete cervical SCI, 2) seven subjects with acute, complete cervical SCI, and 3) six subjects with acute, incomplete cervical SCI. The individuals in groups 2 and 3 were studied at months 1, 3, and 12 postinjury, whereas individuals with chronic SCI were compared with an able-bodied control group. Chronic complete SCI was associated with a marked decrease in [(3)H]ouabain binding site concentration in skeletal muscle as well as reduced protein content of the α(1)-, α(2)-, and β(1)-subunit of the Na(+)-K(+)-ATPase. In line with this finding, expression of the Na(+)-K(+)-ATPase α(1)- and α(2)-subunits progressively decreased during the first year after complete but not after incomplete SCI. The expression of the regulatory protein phospholemman (PLM or FXYD1) was attenuated after complete, but not incomplete, cervical SCI. In contrast, FXYD5 was substantially upregulated in patients with complete SCI. In conclusion, the severity of the spinal cord lesion and the level of postinjury physical activity in patients with SCI are important factors controlling the expression of Na(+)-K(+)-ATPase and its regulatory proteins PLM and FXYD5.     

Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis

The ability to redesign enzymes to catalyze noncognate chemical transformations would have wide-ranging applications. We developed a computational method for repurposing the reactivity of metalloenzyme active site functional groups to catalyze new reactions. Using this method, we engineered a zinc-containing mouse adenosine deaminase to catalyze the hydrolysis of a model organophosphate with a catalytic efficiency (k(cat)/K(m)) of ~10(4) M(-1) s(-1) after directed evolution. In the high-resolution crystal structure of the enzyme, all but one of the designed residues adopt the designed conformation. The designed enzyme efficiently catalyzes the hydrolysis of the R(P) isomer of a coumarinyl analog of the nerve agent cyclosarin, and it shows marked substrate selectivity for coumarinyl leaving groups. Computational redesign of native enzyme active sites complements directed evolution methods and offers a general approach for exploring their untapped catalytic potential for new reactivities.