Purification and assay protocols for obtaining highly active Jumonji C demethylases

Jumonji C (JmjC) lysine demethylases (KDMs) are Fe(II)-dependent hydroxylases that catalyze the oxidative demethylation of methyllysine residues in histones and nonhistone proteins. These enzymes play vital roles in regulating cellular processes such as gene expression, cell cycle progression, and stem cell self-renewal and differentiation. Despite their biological importance, recombinant forms of JmjC KDMs generally display low enzymatic activity and have remained challenging to isolate in a highly active form. Here we present a simple affinity purification scheme for Strep(II)-tagged JmjC KDMs that minimizes contamination by transition state metal ions, yielding highly active and pure enzyme. We also describe an optimized continuous fluorescent assay for KDMs that detects formaldehyde production during demethylation via a coupled reaction using formaldehyde dehydrogenase. Purification and kinetic analysis of the human KDMs JMJD2A and JMJD2D using these methods yielded activities substantially higher than those previously reported for these enzymes, which are comparable to that of the flavin-dependent KDM LSD1. In addition, we show that JMJD2A exhibited a lower catalytic efficiency toward a histone peptide bearing a chemically installed trimethyllysine analog compared with a bona fide trimethylated substrate. The methodology described here is broadly applicable to other JmjC KDMs, facilitating their biochemical characterization and high-throughput screening applications.     

Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase

JMJD2A is a JmjC histone demethylase (HDM) that catalyzes the demethylation of di- and trimethylated Lys9 and Lys36 in histone H3 (H3K9me2/3 and H3K36me2/3). Here we present the crystal structures of the JMJD2A catalytic domain in complex with H3K9me3, H3K36me2 and H3K36me3 peptides. The structures reveal that histone substrates are recognized through a network of backbone hydrogen bonds and hydrophobic interactions that deposit the trimethyllysine into the active site. The trimethylated epsilon-ammonium cation is coordinated within a methylammonium-binding pocket through carbon-oxygen (CH...O) hydrogen bonds that position one of the zeta-methyl groups adjacent to the Fe(II) center for hydroxylation and demethylation. Mutations of the residues comprising this pocket abrogate demethylation by JMJD2A, with the exception of an S288A substitution, which augments activity, particularly toward H3K9me2. We propose that this residue modulates the methylation-state specificities of JMJD2 enzymes and other trimethyllysine-specific JmjC HDMs.     

Thyroid receptor ligands. Part 5: novel bicyclic agonist ligands selective for the thyroid hormone receptor beta

Based on the examination of the crystal structure of rat TRbeta complexed with 3,5,3'-triiodo-l-thyronine (2) a novel TRbeta-selective indole derivative 6b was prepared and tested in vitro. This compound was found to be 14 times selective for TRbeta over TRalpha in binding and its beta-selectivity could be rationalized through the comparison of the X-ray crystallographic structures of 6b complexed with TRalpha and TRbeta.     

IL-7 and IL-8 inhibit gamete interaction in the zona-free hamster egg sperm penetration assay

Current thought in reproductive endocrinology suggests hat endometriosis-associated subfertility may be the result of an adverse influence of activated immunocompetent cells on fertilization and embryo development. Inflammatory ediators such as interleukin-1 and tumour necrosis actor have been implicated in the pathophysiology of this process. The purpose of this study was to assess the effect of two recently characterized cytokines, interleukin-7 (IL-7 ) and interleukin-8 (IL-8), on gamete interaction in the perm penetration assay (SPA). Donor sperm were preincubated or 4 h with 0.5, 5, 50, or 500 ng ml(-1) of human ecombinant IL-7 or IL-8. Sperm penetration was determined by an experienced gametologist by the presence of decondensed sperm heads or pronuclei formation. A dose-dependent inhibition of gamete interaction was observed following coincubation with either IL-7 or IL-8. These data offer the possibility that IL-7 and IL-8 may play a role in the pathogenesis of immunocompetent cell-associated subfertility.     

The Southern Megalopolis: Using the Past to Predict the Future of Urban Sprawl in the Southeast U.S

The future health of ecosystems is arguably as dependent on urban sprawl as it is on human-caused climatic warming. Urban sprawl strongly impacts the urban ecosystems it creates and the natural and agro-ecosystems that it displaces and fragments. Here, we project urban sprawl changes for the next 50 years for the fast-growing Southeast U.S. Previous studies have focused on modeling population density, but the urban extent is arguably as important as population density per se in terms of its ecological and conservation impacts. We develop simulations using the SLEUTH urban growth model that complement population-driven models but focus on spatial pattern and extent. To better capture the reach of low-density suburban development, we extend the capabilities of SLEUTH by incorporating street-network information. Our simulations point to a future in which the extent of urbanization in the Southeast is projected to increase by 101% to 192%. Our results highlight areas where ecosystem fragmentation is likely, and serve as a benchmark to explore the challenging tradeoffs between ecosystem health, economic growth and cultural desires.     

Guidelines for a priori grouping of species in hierarchical community models

Recent methodological advances permit the estimation of species richness and occurrences for rare species by linking species‐level occurrence models at the community level. The value of such methods is underscored by the ability to examine the influence of landscape heterogeneity on species assemblages at large spatial scales. A salient advantage of community‐level approaches is that parameter estimates for data‐poor species are more precise as the estimation process “borrows” from data‐rich species. However, this analytical benefit raises a question about the degree to which inferences are dependent on the implicit assumption of relatedness among species. Here, we assess the sensitivity of community/group‐level metrics, and individual‐level species inferences given various classification schemes for grouping species assemblages using multispecies occurrence models. We explore the implications of these groupings on parameter estimates for avian communities in two ecosystems: tropical forests in Puerto Rico and temperate forests in northeastern United States. We report on the classification performance and extent of variability in occurrence probabilities and species richness estimates that can be observed depending on the classification scheme used. We found estimates of species richness to be most precise and to have the best predictive performance when all of the data were grouped at a single community level. Community/group‐level parameters appear to be heavily influenced by the grouping criteria, but were not driven strictly by total number of detections for species. We found different grouping schemes can provide an opportunity to identify unique assemblage responses that would not have been found if all of the species were analyzed together. We suggest three guidelines: (1) classification schemes should be determined based on study objectives; (2) model selection should be used to quantitatively compare different classification approaches; and (3) sensitivity of results to different classification approaches should be assessed. These guidelines should help researchers apply hierarchical community models in the most effective manner.     

The ecological cost of morphological specialization: feeding by a fossorial lizard

Summary Head size and shape of reptiles may reflect selection for multiple uses. For example, sexual selection for large head size may enhance feeding efficiency. In contrast, morphological characteristics of the heads of fossorial reptiles suggests that fossoriality may have evolved at the expense of reduced effectiveness in feeding. Our research focused on the question: Does a fossorial lizard feed less effectively than a non-fossorial lizard? To answer this question, we measured the time, number of bites, and oxygen consumption by sand-swimming (Chalcides ocellatus) and epigeal (Eumeces inexpectatus) skinks feeding on crickets. These lizard species were similar in mass, but different in body form: Chalcides had longer bodies and smaller heads than Eumeces. For lizards of the same mass, Chalcides were unable to eat prey as large as those eaten by Eumeces, Chalcides took longer to eat prey of the same size than did Eumeces, and the aerobic energy cost of eating crickets of the same relative size (cricket mass/lizard mass) tended to be greater for Chalcides than for Eumeces. The ecologically relevant costs of feeding appear to be the upper limit to the size of prey and the time of feeding. Both costs would restrict the energy intake per unit time of Chalcides. Moreover, given the same energy requirements and prey community, Chalcides would have to feed more often and would take longer to feed than would Eumeces. Both factors would increase the exposure of Chalcides to predators relative to that of Eumeces. To reduce the risk of predation, Chalcides would have to reduce energy intake or fulfill its energy requirements with relatively small prey, or both. These conclusions are potentially confounded in two ways. The first is that male Eumeces have relatively large heads as a result of sexual selection. Thus, the differences we observed between Chalcides and Eumeces (most of our specimens were males) could have been the result of reduced costs of feeding for Eumeces due to sexual selection and not the result of enhanced costs of feeding for Chalcides. A more likely explanation is that differences in the costs of feeding observed between these species reflect adaptations for fossoriality by Chalcides and sexual selection on Eumeces. Our results may also be confounded because we compared laboratory reared Chalcides with field captured Eumeces. Any deterimental effects of captivity on the vigor of Chalcides would increase their costs of feeding relative to those of Eumeces. Although short-term captivity is not associated with changes in the metabolic capcity of lizards, effects of long-term captivitiy are unknown.