Geometric morphometric and phylogenetic analyses of Arizona Sky Island populations of Scaphinotus petersi Roeschke (Coleoptera: Carabidae)

Scaphinotus petersi Roeschke, 1907 (Carabidae) is a ground beetle endemic to Sky Islands in south‐eastern Arizona. Previous taxonomic studies described several subspecies with morphological differences inhabiting geographically isolated mountain ranges. We combined molecular sequence data and morphometric data, especially head and pronotum shape analyses, to examine the variation and divergence in subspecies and isolated montane populations. In this study, we employ a combination of distance morphometrics as well as geometric morphometrics to quantify the level of morphological variation, and to test the hypothesis that geographically distinct populations of S. petersi are phenotypically distinct. Results suggest that these isolated populations have diverged morphologically and genetically. Phylogenetic analyses identified two monophyletic lineages within the species that correspond generally to pronotum shape. We observed significant morphological variation among most montane populations in of S. petersi, with the pronotum shape as the clearest delimiting trait. © 2015 The Linnean Society of London     

Predicting genetic values: a kernel-based best linear unbiased prediction with genomic data

Genomic data provide a valuable source of information for modeling covariance structures, allowing a more accurate prediction of total genetic values (GVs). We apply the kriging concept, originally developed in the geostatistical context for predictions in the low-dimensional space, to the high-dimensional space spanned by genomic single nucleotide polymorphism (SNP) vectors and study its properties in different gene-action scenarios. Two different kriging methods ["universal kriging" (UK) and "simple kriging" (SK)] are presented. As a novelty, we suggest use of the family of Matérn covariance functions to model the covariance structure of SNP vectors. A genomic best linear unbiased prediction (GBLUP) is applied as a reference method. The three approaches are compared in a whole-genome simulation study considering additive, additive-dominance, and epistatic gene-action models. Predictive performance is measured in terms of correlation between true and predicted GVs and average true GVs of the individuals ranked best by prediction. We show that UK outperforms GBLUP in the presence of dominance and epistatic effects. In a limiting case, it is shown that the genomic covariance structure proposed by VanRaden (2008) can be considered as a covariance function with corresponding quadratic variogram. We also prove theoretically that if a specific linear relationship exists between covariance matrices for two linear mixed models, the GVs resulting from BLUP are linked by a scaling factor. Finally, the relation of kriging to other models is discussed and further options for modeling the covariance structure, which might be more appropriate in the genomic context, are suggested.     

Demographic components of gene frequency change in free-ranging macaques on Cayo Santiago

Gene frequency profiles from January 1973 to January 1977 for three polymorphic loci were examined in Cayo Santiago rhesus social groups. The effects of demographic components (i.e., births, deaths, immigrations, emigrations, and group fission and fusion) on total change in gene frequencies are assessed. Allelic frequencies at the carbonic anhydrase II, 6-phosphogluconate dehydrogenase, and transferrin loci were analyzed in four social groups. In the two groups that underwent fission and fusion during the study period, the timing of these processes was related to the largest short-term changes in gene frequences. However, immigration and emigration had the greatest effect on total change in gene frequency in all groups during the study period. The relative importance of births and deaths in producing gene frequency change varied among the social groups. These results suggest that the relative importance of the demographic components of gene frequency change in primate populations is determined by behavioral patterns and ecological conditions specific to the population considered.     

The evolution and age of populations of Scaphinotus petersi Roeschke on Arizona Sky Islands (Coleoptera, Carabidae, Cychrini)

Populations of the ground beetle Scaphinotus petersi are isolated in subalpine conifer forest habitats on mountain ranges or Sky Islands in southeastern Arizona. Previous work on this species has suggested these populations have been isolated since the last post-glacial maximum times as warming caused this cool adapted species to retreat to high elevations. To test this hypothesis, we inferred the phylogeny from mitochondrial DNA sequence data from several Arizona Sky Island populations of Scaphinotus petersi and estimated the divergence time of the currently isolated populations. We found two major clades of Scaphinotus petersi, an eastern clade and a western group. Our results indicated most mountain ranges form clades except the Huachucas, which are polyphyletic and the Santa Catalinas, which are paraphyletic. We estimated the Pinaleño population is much older than the last glacial maximum, but the Huachuca and Pinal populations may have been fragmented from the Santa Catalina population since the post-glacial maximum times.     

Reconstruction of surfaces from mixed hydrocarbon and PEG components in water: responsive surfaces aid fouling release

Coatings derived from surface active block copolymers (SABCs) having a combination of hydrophobic aliphatic (linear hydrocarbon or propylene oxide-derived groups) and hydrophilic poly(ethlyene glycol) (PEG) side chains have been developed. The coatings demonstrate superior performance against protein adsorption as well as resistance to biofouling, providing an alternative to coatings containing fluorinated side chains as the hydrophobe, thus reducing the potential environmental impact. The surfaces were examined using dynamic water contact angle, captive air-bubble contact angle, atomic force microscopy, X-ray photoelectron spectroscopy, and near-edge X-ray absorption fine structure analysis. The PS(8K)-b-P(E/B)(25K)-b-PI(10K) triblock copolymer precursor (K3) initially dominated the dry surface. In contrast to previous studies with mixed fluorinated/PEG surfaces, these new materials displayed significant surface changes after exposure to water that allowed fouling resistant behavior. PEG groups buried several nanometers below the surface in the dry state were able to occupy the coating surface after placement in water. The resulting surface exhibits a very low contact angle and good antifouling properties that are very different from those of K3. The surfaces are strongly resistant to protein adsorption using bovine serum albumin as a standard protein challenge. Biofouling assays with sporelings of the green alga Ulva and cells of the diatom Navicula showed the level of adhesion was significantly reduced relative to that of a PDMS standard and that of the triblock copolymer precursor of the SABCs.     

Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster

Predicting organismal phenotypes from genotype data is important for plant and animal breeding, medicine, and evolutionary biology. Genomic-based phenotype prediction has been applied for single-nucleotide polymorphism (SNP) genotyping platforms, but not using complete genome sequences. Here, we report genomic prediction for starvation stress resistance and startle response in Drosophila melanogaster, using ～2.5 million SNPs determined by sequencing the Drosophila Genetic Reference Panel population of inbred lines. We constructed a genomic relationship matrix from the SNP data and used it in a genomic best linear unbiased prediction (GBLUP) model. We assessed predictive ability as the correlation between predicted genetic values and observed phenotypes by cross-validation, and found a predictive ability of 0.239±0.008 (0.230±0.012) for starvation resistance (startle response). The predictive ability of BayesB, a Bayesian method with internal SNP selection, was not greater than GBLUP. Selection of the 5% SNPs with either the highest absolute effect or variance explained did not improve predictive ability. Predictive ability decreased only when fewer than 150,000 SNPs were used to construct the genomic relationship matrix. We hypothesize that predictive power in this population stems from the SNP-based modeling of the subtle relationship structure caused by long-range linkage disequilibrium and not from population structure or SNPs in linkage disequilibrium with causal variants. We discuss the implications of these results for genomic prediction in other organisms.     

Neonatal Fc receptor blockade by Fc engineering ameliorates arthritis in a murine model

Multiple autoimmune diseases are characterized by the involvement of autoreactive Abs in pathogenesis. Problems associated with existing therapeutics such as the delivery of intravenous immunoglobulin have led to interest in developing alternative approaches using recombinant or synthetic methods. Toward this aim, in the current study, we demonstrate that the use of Fc-engineered Abs (Abs that enhance IgG degradation [Abdegs]) to block neonatal FcR (FcRn) through high-affinity, Fc region binding is an effective strategy for the treatment of Ab-mediated disease. Specifically, Abdegs can be used at low, single doses to treat disease in the K/B×N serum transfer model of arthritis using BALB/c mice as recipients. Similar therapeutic effects are induced by 25- to 50-fold higher doses of i.v. Ig. Importantly, we show that FcRn blockade is a primary contributing factor toward the observed reduction in disease severity. The levels of albumin, which is also recycled by FcRn, are not affected by Abdeg delivery. Consequently, Abdegs do not alter FcRn expression levels or subcellular trafficking behavior. The engineering of Ab Fc regions to generate potent FcRn blockers therefore holds promise for the therapy of Ab-mediated autoimmunity.     

3D Single Molecule Tracking with Multifocal Plane Microscopy Reveals Rapid Intercellular Transferrin Transport at Epithelial Cell Barriers

The study of intracellular transport pathways at epithelial cell barriers that line diverse tissue sites is fundamental to understanding tissue homeostasis. A major impediment to investigating such processes at the subcellular level has been the lack of imaging approaches that support fast three-dimensional (3D) tracking of cellular dynamics in thick cellular specimens. Here, we report significant advances in multifocal plane microscopy and demonstrate 3D single molecule tracking of rapid protein dynamics in a 10 micron thick live epithelial cell monolayer. We have investigated the transferrin receptor (TfR) pathway, which is not only essential for iron delivery but is also of importance for targeted drug delivery across cellular barriers at specific body sites, such as the brain that is impermeable to blood-borne substances. Using multifocal plane microscopy, we have discovered a cellular process of intercellular transfer involving rapid exchange of Tf molecules between two adjacent cells in the monolayer. Furthermore, 3D tracking of Tf molecules at the lateral plasma membrane has led to the identification of different modes of endocytosis and exocytosis, which exhibit distinct temporal and intracellular spatial trajectories. These results reveal the complexity of the 3D trafficking pathways in epithelial cell barriers. The methods and approaches reported here can enable the study of fast 3D cellular dynamics in other cell systems and models, and underscore the importance of developing advanced imaging technologies to study such processes.     

An Estimate of the Average Number of Recessive Lethal Mutations Carried by Humans

The effects of inbreeding on human health depend critically on the number and severity of recessive, deleterious mutations carried by individuals. In humans, existing estimates of these quantities are based on comparisons between consanguineous and nonconsanguineous couples, an approach that confounds socioeconomic and genetic effects of inbreeding. To overcome this limitation, we focused on a founder population that practices a communal lifestyle, for which there is almost complete Mendelian disease ascertainment and a known pedigree. Focusing on recessive lethal diseases and simulating allele transmissions, we estimated that each haploid set of human autosomes carries on average 0.29 (95% credible interval [0.10, 0.84]) recessive alleles that lead to complete sterility or death by reproductive age when homozygous. Comparison to existing estimates in humans suggests that a substantial fraction of the total burden imposed by recessive deleterious variants is due to single mutations that lead to sterility or death between birth and reproductive age. In turn, comparison to estimates from other eukaryotes points to a surprising constancy of the average number of recessive lethal mutations across organisms with markedly different genome sizes.     

Effects of surface-active block copolymers with oxyethylene and fluoroalkyl side chains on the antifouling performance of silicone-based films

Block copolymers made from a poly(dimethyl siloxane) (Si) and a poly(meth)acrylate carrying oxyethylene (EG) or fluoroalkyl (AF) side chains were synthesized and incorporated as surface-active components into a silicone matrix to produce cross-linked films with different surface hydrophilicity/phobicity. Near-edge X-ray absorption fine structure (NEXAFS) studies showed that film surfaces containing Si-EG were largely populated by the siloxane, with the oxyethylene chains present only to a minor extent. In contrast, the fluorinated block was selectively segregated to the polymer–air interface in films containing Si-AF as probed by NEXAFS and X-ray photoelectron spectroscopy (XPS) analyses. Such differences in surface composition were reflected in the biological performance of the coatings. While the films with Si-EG showed a higher removal of both Ulva linza sporelings and Balanus amphitrite juveniles than the silicone control, those with Si-AF exhibited excellent antifouling properties, preventing the settlement of cyprids of B. amphitrite.