Talkin' 'bout my generation: environmental variability and cohort effects

In variable environments, it is probable that environmental conditions in the past can influence demographic performance now. Cohort effects occur when these delayed life-history effects are synchronized among groups of individuals in a population. Here we show how plasticity in density-dependent demographic traits throughout the life cycle can lead to cohort effects and that there can be substantial population dynamic consequences of these effects. We show experimentally that density and food conditions early in development can influence subsequent juvenile life-history traits. We also show that conditions early in development can interact with conditions at maturity to shape future adult performance. In fact, conditions such as food availability and density at maturity, like conditions early in development, can generate cohort effects in mature stages. Based on these data, and on current theory about the effects of plasticity generated by historical environments, we make predictions about the consequences of such changes on density-dependent demography and on mite population dynamics. We use a stochastic cohort effects model to generate a range of population dynamics. In accordance with the theory, we find the predicted changes in the strength of density dependence and associated changes in population dynamics and population variability.     

Identification of allosteric peptide agonists of CXCR4

The chemokine receptor CXCR4 is a co-receptor for T-tropic strains of HIV-1. A number of small molecule antagonists of CXCR4 are in development but all are likely to lead to adverse effects due to the physiological function of CXCR4. To prevent these complications, allosteric agonists may be therapeutically useful as adjuvant therapy in combination with small molecule antagonists. A synthetic cDNA library coding for 160,000 different SDF-based peptides was screened for CXCR4 agonist activity in a yeast strain expressing a functional receptor. Peptides that activated CXCR4 in an autocrine manner induced colony formation. Two peptides, designated RSVM and ASLW, were identified as novel agonists that are insensitive to the CXCR4 antagonist AMD3100. In chemotaxis assays using the acute lymphoblastic leukemia cell line CCRF-CEM, RSVM behaves as a partial agonist and ASLW as a superagonist. The superagonist activity of ASLW may be related to its inability to induce receptor internalization. In CCRF-CEM cells, the two peptides are also not inhibited by another CXCR4 antagonist, T140, or the neutralizing monoclonal antibodies 12G5 and 44717.111. These results suggest that alternative agonist-binding sites are present on CXCR4 that could be screened to develop molecules for therapeutic use.     

Finding the tree of life: matching phylogenetic trees to the fossil record through the 20th century

Phylogenies, or evolutionary trees, are fundamental to biology. Systematists have laboured since the time of Darwin to discover the tree of life. Recent developments in systematics, such as cladistics and molecular sequencing, have led practitioners to believe that their phylogenies are more testable now than equivalent efforts from the 1960s or earlier. Whole trees, and nodes within trees, may be assessed for their robustness. However, these quantitative approaches cannot be used to demonstrate that one tree is more likely to be correct than another. Congruence assessments may help. Comparison of a sample of 1000 published trees with an essentially independent standard (dates of origin of groups in geological time) shows that the order of branching has improved slightly, but the disparity between estimated times of origination from phylogeny and stratigraphy has, if anything, become worse. Controlled comparisons of phylogenies of four major groups (Agnatha, Sarcopterygii, Sauria and Mammalia) do not show uniform improvement, or decline, of fit to stratigraphy through the twentieth century. Nor do morphological or molecular trees differ uniformly in their performance.     

A genus-level supertree of the Dinosauria

One of the ultimate aims of systematics is the reconstruction of the tree of life. This is a huge undertaking that is inhibited by the existence of a computational limit to the inclusiveness of phylogenetic analyses. Supertree methods have been developed to overcome, or at least to go around this problem by combining smaller, partially overlapping cladograms. Here, we present a very inclusive generic-level supertree of Dinosauria (covering a total of 277 genera), which is remarkably well resolved and provides some clarity in many contentious areas of dinosaur systematics.     

A NEW LYGINOPTERID POLLEN ORGAN WITH ALVEOLATE POLLEN EXINES

A new lyginopterid pollen organ is described based upon specimens occurring in a single coal ball from the Providence, Kentucky locality. Seven to nine beaked sporangia are fused together at their proximal ends forming a common synangial chamber; synangia are joined together in clusters of two or three. In situ prepollen is similar to Cyclogranisporites and Verrucosisporites sporae dispersae. The thick exine has a lamellate nexine and a prominent alveolate sexine.     

Anthropogenically-Mediated Density Dependence in a Declining Farmland Bird

Land management intrinsically influences the distribution of animals and can consequently alter the potential for density-dependent processes to act within populations. For declining species, high densities of breeding territories are typically considered to represent productive populations. However, as density-dependent effects of food limitation or predator pressure may occur (especially when species are dependent upon separate nesting and foraging habitats), high territory density may limit per-capita productivity. Here, we use a declining but widespread European farmland bird, the yellowhammer Emberiza citrinella L., as a model system to test whether higher territory densities result in lower fledging success, parental provisioning rates or nestling growth rates compared to lower densities. Organic landscapes held higher territory densities, but nests on organic farms fledged fewer nestlings, translating to a 5 times higher rate of population shrinkage on organic farms compared to conventional. In addition, when parental provisioning behaviour was not restricted by predation risk (i.e., at times of low corvid activity), nestling provisioning rates were higher at lower territory densities, resulting in a much greater increase in nestling mass in low density areas, suggesting that food limitation occurred at high densities. These findings in turn suggest an ecological trap, whereby preferred nesting habitat does not provide sufficient food for rearing nestlings at high population density, creating a population sink. Habitat management for farmland birds should focus not simply on creating a high nesting density, but also on ensuring heterogeneous habitats to provide food resources in close proximity to nesting birds, even if this occurs through potentially restricting overall nest density but increasing population-level breeding success.     

The utilization of a Saccharomyces cerevisiae HUG1P-GFP promoter-reporter construct for the selective detection of DNA damage

In this study, we report the creation and characterization of a yeast-based promoter-reporter construct for the detection of genotoxic compounds within a cell's local environment. We have synthesized a fusion containing the HUG1 promoter and GFP and incorporated this cassette into the yeast genome creating a stable, sensitive genotoxicity indicator. To quantify biosensor performance, HUG1P-GFP cells were exposed to multiple doses of a wide variety of genotoxins, including alkylating agents, an oxidative agent, a ribonucleotide reductase inhibitor, a UV mimetic agent, an agent that causes double strand breaks, a topoisomerase I inhibitor, and ionizing radiation, all of which triggered a detectable and reproducible level of GFP production by the HUG1P-GFP strain. Furthermore, GFP was not induced by general cell stresses including starvation, heat shock, and acidic pH. These results suggest this system will be a valuable supplement to traditional genotoxicity assays.     

Hyperglycemia and loss of ovarian hormones mediate atheroma formation through endothelial layer disruption and increased permeability

The overall goal of this project was to examine the interactions of hyperglycemia and loss of ovarian hormones on the artery wall in a type I diabetic mouse model. Intact or ovariectomized (OVX) female BALB/C mice were fed a high-cholesterol diet. Half the animals were treated with steptozotocin to induce insulin-deficient diabetes mellitus, generating four treatment groups: control, intact; control, ovariectomized; diabetic, intact; diabetic, ovariectomized (DOVX). We examined arterial structure and function and found that 1) diabetes and ovariectomy additively increased endothelial layer permeability, 2) arterial stiffening was increased in DOVX, 3) DOVX synergistically increased atheroma formation, and 4) ultrastructural evaluation revealed that the basal lamina was often multilayered and formed convoluted aggregates separating endothelium from the internal elastic lamina in diabetic, but not control arteries or arteries from OVX mice. Endothelium overlying these regions formed thin cytoplasmic extensions between these aggregates and was often separated from the basal lamina by electron lucent spaces. Our studies showed that diabetes and loss of ovarian function have additive and synergistic effects to worsen arterial pathophysiology by disrupting the arterial endothelial layer with increased permeability and increased atheroma formation.     

Turning the other cheek: the viewpoint dependence of facial expression after-effects

How do we visually encode facial expressions? Is this done by viewpoint-dependent mechanisms representing facial expressions as two-dimensional templates or do we build more complex viewpoint independent three-dimensional representations? Recent facial adaptation techniques offer a powerful way to address these questions. Prolonged viewing of a stimulus (adaptation) changes the perception of subsequently viewed stimuli (an after-effect). Adaptation to a particular attribute is believed to target those neural mechanisms encoding that attribute. We gathered images of facial expressions taken simultaneously from five different viewpoints evenly spread from the three-quarter leftward to the three-quarter rightward facing view. We measured the strength of expression after-effects as a function of the difference between adaptation and test viewpoints. Our data show that, although there is a decrease in after-effect over test viewpoint, there remains a substantial after-effect when adapt and test are at differing three-quarter views. We take these results to indicate that neural systems encoding facial expressions contain a mixture of viewpoint-dependent and viewpoint-independent elements. This accords with evidence from single cell recording studies in macaque and is consonant with a view in which viewpoint-independent expression encoding arises from a combination of view-dependent expression-sensitive responses.