Tissue microarrays as a platform for proteomic investigation

Tissue microarrays have become an essential tool in translational pathology. They are used to confirm results from other experimental platforms, such as expression microarrays, as well as a primary tool to explore the expression profile of proteins by immunohistochemical analysis. Tissue microarrays are routinely used molecular epidemiology, drug development and determining the diagnostic, prognostic and predictive value of new biomarkers. By applying traditional protein based assays, as well as novel assays to the platform, tissue microarrays have gained a new utility as a proteomic tool for both basic science as well as clinical investigation. This article will explore the new approaches that are being applied to tissue microarrays to, characterize the human proteome, and new technologies that allow tissue microarrays to function as a protein array. The U.S. Government's right to retain a non-exclusive, royalty-free license in and to any copyright is acknowledged     

Patterns,causes and consequences of defensive microbiome dynamics across multiple scales

The microbiome can significantly impact host phenotypes and serve as an additional source of heritable genetic variation. While patterns across eukaryotes are consistent with a role for symbiotic microbes in host macroevolution, few studies have examined symbiont‐driven host evolution or the ecological implications of a dynamic microbiome across temporal, spatial or ecological scales. The pea aphid, Acyrthosiphon pisum, and its eight heritable bacterial endosymbionts have served as a model for studies on symbiosis and its potential contributions to host ecology and evolution. But we know little about the natural dynamics or ecological impacts of the heritable microbiome of this cosmopolitan insect pest. Here we report seasonal shifts in the frequencies of heritable defensive bacteria from natural pea aphid populations across two host races and geographic regions. Microbiome dynamics were consistent with symbiont responses to host‐level selection and findings from one population suggested symbiont‐driven adaptation to seasonally changing parasitoid pressures. Conversely, symbiont levels were negatively correlated with enemy‐driven mortality when measured across host races, suggesting important ecological impacts of host race microbiome divergence. Rapid drops in symbiont frequencies following seasonal peaks suggest microbiome instability in several populations, with potentially large costs of ‘superinfection’ under certain environmental conditions. In summary, the realization of several laboratory‐derived, a priori expectations suggests important natural impacts of defensive symbionts in host‐enemy eco‐evolutionary feedbacks. Yet negative findings and unanticipated correlations suggest complexities within this system may limit or obscure symbiont‐driven contemporary evolution, a finding of broad significance given the widespread nature of defensive microbes across plants and animals.     

De Novo Mutations in SIK1 Cause a Spectrum of Developmental Epilepsies

Developmental epilepsies are age-dependent seizure disorders for which genetic causes have been increasingly identified. Here we report six unrelated individuals with mutations in salt-inducible kinase 1 (SIK1) in a series of 101 persons with early myoclonic encephalopathy, Ohtahara syndrome, and infantile spasms. Individuals with SIK1 mutations had short survival in cases with neonatal epilepsy onset, and an autism plus developmental syndrome after infantile spasms in others. All six mutations occurred outside the kinase domain of SIK1 and each of the mutants displayed autophosphorylation and kinase activity toward HDAC5. Three mutations generated truncated forms of SIK1 that were resistant to degradation and also showed changes in sub-cellular localization compared to wild-type SIK1. We also report the human neuropathologic examination of SIK1-related developmental epilepsy, with normal neuronal morphology and lamination but abnormal SIK1 protein cellular localization. Therefore, these results expand the genetic etiologies of developmental epilepsies by demonstrating SIK1 mutations as a cause of severe developmental epilepsy.     

Subject-specific finite element model of the pelvis: development, validation and sensitivity studies

A better understanding of the three-dimensional mechanics of the pelvis, at the patient-specific level, may lead to improved treatment modalities. Although finite element (FE) models of the pelvis have been developed, validation by direct comparison with subject-specific strains has not been performed, and previous models used simplifying assumptions regarding geometry and material properties. The objectives of this study were to develop and validate a realistic FE model of the pelvis using subject-specific estimates of bone geometry, location-dependent cortical thickness and trabecular bone elastic modulus, and to assess the sensitivity of FE strain predictions to assumptions regarding cortical bone thickness as well as bone and cartilage material properties. A FE model of a cadaveric pelvis was created using subject-specific computed tomography image data. Acetabular loading was applied to the same pelvis using a prosthetic femoral stem in a fashion that could be easily duplicated in the computational model. Cortical bone strains were monitored with rosette strain gauges in ten locations on the left hemipelvis. FE strain predictions were compared directly with experimental results for validation. Overall, baseline FE predictions were strongly correlated with experimental results (r2=0.824), with a best-fit line that was not statistically different than the line y=x (experimental strains = FE predicted strains). Changes to cortical bone thickness and elastic modulus had the largest effect on cortical bone strains. The FE model was less sensitive to changes in all other parameters. The methods developed and validated in this study will be useful for creating and analyzing patient-specific FE models to better understand the biomechanics of the pelvis.     

Rampant horizontal transfer and duplication of rubisco genes in eubacteria and plastids

Previous work has shown that molecular phylogenies of plastids, cyanobacteria, and proteobacteria based on the rubisco (ribulose-1,5- bisphosphate carboxylase/oxygenase) genes rbcL and rbcS are incongruent with molecular phylogenies based on other genes and are also incompatible with structural and biochemical information. Although it has been much speculated that this is the consequence of a single horizontal gene transfer (of a proteobacterial or mitochondrial rubisco operon into plastids of rhodophytic and chromophytic algae), neither this hypothesis nor the alternative hypothesis of ancient gene duplication have been examined in detail. We have conducted phylogenetic analyses of all available bacterial rbcL sequences, and representative plastid sequences, in order to explore these alternative hypothesis and fully examine the complexity of rubisco gene evolution. The rbcL phylogeny reveals a surprising number of gene relationships that are fundamentally incongruent with organismal relationships as inferred from multiple lines of other molecular evidence. On the order of six horizontal gene transfers are implied by the form I (L8S8) rbcL phylogeny, two between cyanobacteria and proteobacteria, one between proteobacteria and plastids, and three within proteobacteria. Alternatively, a single ancient duplication of the form I rubisco operon, followed by repeated and pervasive differential loss of one operon or the other, would account for much of this incongruity. In all probability, the rubisco operon has undergone multiple events of both horizontal gene transfer and gene duplication in different lineages.      

Using remote sensing image texture to study habitat use patterns: a case study using the polymorphic white-throated sparrow (Zonotrichia albicollis)

Aim Ecological factors that vary along spatial scales can greatly influence the outcome of evolution. However, often it is difficult for researchers to identify significant ecological variables that might be associated with the geographical distribution of phenotypes and genotypes in nature. In this paper, we use remote sensing image texture analyses to investigate breeding territories of the white‐throated sparrow (Zonotrichia albicollis), a polymorphic passerine species that has been shown to segregate spatially according to morph. Our aim was to examine how an integrative measure of landscape feature, such as image texture, could be used to distinguish subtle differences in habitat use and, presumably, habitat selection. Location A population of white‐throated sparrows located 1.5 miles east of the Cranberry Lake Biological Station in the Adirondack Mountains of St Lawrence County, New York, was used in this study; the study site itself was approximately 1 km². Methods We analysed 27 territories (16 white males; 11 tan males) to determine if image texture can be used to distinguish differences in vegetation and structure in territories of the two colour morphs. First (variance)‐ and second (homogeneity)‐order image texture measurements with three different window sizes were derived using the green, red, and near infrared bands of Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) data. Texture was then placed into t‐tests to determine statistical differences between the territories of the two male morphs. Results Significant differences between the territories of the two morphs were found in both variance and homogeneity texture measures in the red and green ASTER bands in all three window sizes. There were no differences with any near infrared texture measures. Main conclusions Examination of first‐ and second‐order statistical measures indicated that the territories of tan males have significantly more spectral variance than the territories of white males, while white males’ territories are significantly more homogeneous. These findings are consistent with the previous finding of the morphs settling in ‘high’ and ‘low’ neighbour density habitats that differ with respect to the amount of useable area on their borders. Previous study has also suggested that white and tan male territories differ according to overall landscape structure, not vegetation composition. Therefore, we suggest that red and green spectra may be more useful when examining differences in territory structure and possibly territory quality of similar edge‐type species. Our results suggest that image texture is a useful tool for ecological and evolutionary modelling of the distributions of phenotypes/genotypes across landscapes.     

Partial incubation during egg laying reduces eggshell microbial loads in a temperate‐breeding passerine

Incubation prior to clutch completion may be adaptive if it maintains egg viability by inhibiting eggshell microbial growth, thus reducing the likelihood that the embryo becomes infected. To test this hypothesis, we examined the effect of partial incubation during egg laying on eggshell microbial loads in eastern bluebirds Sialia sialis breeding at a temperate‐zone site. We sampled eggshell microbes prior to and following four days of exposure to either partial incubation during the laying period or ambient environmental conditions without incubation (experimental eggs). Microbial colony counts declined significantly for eggs left in the nest during the laying period but did not vary significantly for eggs exposed to ambient conditions. Initial microbial loads were more similar to those previously reported from tropical than temperate environments, and microbes from potentially pathogenic groups were detected on 88% of first‐laid eggs on the day of laying. Egg viability was maintained when eggs were held indoors for four days without incubation but declined sharply thereafter. Our results suggest that partial incubation during egg laying may enhance egg viability in eastern bluebirds by reducing eggshell microbial loads; these effects appear stronger than those usually reported from the temperate zone.