Calmodulin mutations associated with recurrent cardiac arrest in infants

BACKGROUND

Life-threatening disorders of heart rhythm may arise during infancy and can result in the sudden and tragic death of a child. We performed exome sequencing on 2 unrelated infants presenting with recurrent cardiac arrest to discover a genetic cause.

METHODS AND RESULTS

We ascertained 2 unrelated infants (probands) with recurrent cardiac arrest and dramatically prolonged QTc interval who were both born to healthy parents. The 2 parent-child trios were investigated with the use of exome sequencing to search for de novo genetic variants. We then performed follow-up candidate gene screening on an independent cohort of 82 subjects with congenital long-QT syndrome without an identified genetic cause. Biochemical studies were performed to determine the functional consequences of mutations discovered in 2 genes encoding calmodulin. We discovered 3 heterozygous de novo mutations in either CALM1 or CALM2, 2 of the 3 human genes encoding calmodulin, in the 2 probands and in 2 additional subjects with recurrent cardiac arrest. All mutation carriers were infants who exhibited life-threatening ventricular arrhythmias combined variably with epilepsy and delayed neurodevelopment. Mutations altered residues in or adjacent to critical calcium binding loops in the calmodulin carboxyl-terminal domain. Recombinant mutant calmodulins exhibited several-fold reductions in calcium binding affinity.

CONCLUSIONS

Human calmodulin mutations disrupt calcium ion binding to the protein and are associated with a life-threatening condition in early infancy. Defects in calmodulin function will disrupt important calcium signaling events in heart, affecting membrane ion channels, a plausible molecular mechanism for potentially deadly disturbances in heart rhythm during infancy.

No need for disease: testing extinction hypotheses for the thylacine using multi-species metamodels

Population viability analysis (PVA) is widely used to assess the extinction risk of threatened species and to evaluate different management strategies. However, conventional PVA neglects important biotic interactions and therefore can fail to identify important threatening processes. We designed a new PVA approach that includes species interactions explicitly by networking species models within a single 'metamodel'. We demonstrate the utility of PVA metamodels by employing them to reinterpret the extinction of the carnivorous, marsupial thylacine Thylacinus cynocephalus in Tasmania. In particular, we test the claim that well-documented impacts of European settlement cannot account for this extinction and that an unknown disease must have been an additional and necessary cause. We first constructed a classical, single-species PVA model for thylacines, which was then extended by incorporation within a dynamic predator-herbivore-vegetation metamodel that accounted for the influence of Europeans on the thylacine's prey base. Given obvious parameter uncertainties, we explored both modelling approaches with rigorous sensitivity analyses. Single-species PVA models were unable to recreate the thylacine's extinction unless a high human harvest, small starting population size or low maximum population growth rate was assumed, even if disease effects were included from 1906 to 1909. In contrast, we readily recreated the thylacine's demise using disease-free multi-species metamodels that simulated declines in native prey populations (particularly due to competition with introduced sheep). Dynamic, multi-species metamodels provide a simple, flexible framework for studying current species declines and historical extinctions caused by complex, interacting factors.

Regional population structuring and conservation units in the platypus (Ornithorhynchus anatinus)

The platypus (Ornithorhynchus anatinus) has a wide distribution in Australia, encompassing the southern island of Tasmania and a broad latitudinal range of the mainland from the temperate south to the tropical north. We used 12 microsatellite markers from 235 individuals sampled from 13 river systems to examine patterns of genetic differentiation and gene flow throughout the species’ range. Using a Bayesian approach we identified three large-scale groupings that correspond closely to geographically distinct regions of the species’ distribution: the tropical northern mainland, the subtropical and temperate southern mainland, and Tasmania. Six additional clusters were found within the regional groups, three in the northern, two in the southern mainland regions, and the last in Tasmania. These clusters coincided with major river drainages. Genetic differentiation was generally high, with pairwise Fst values ranging from 0.065 to 0.368 for regions and 0.037 to 0.479 for clusters. We found no evidence of contemporary gene flow among the three clusters in the north, but some migration may occur between the larger clusters in the south. Due to the high genetic structuring and lack of gene flow between these three regional populations of the platypus we recommend their treatment as evolutionarily significant units (ESUs) within the platypus species. We have also detailed several smaller management units (MUs) existing within our study area based on subregional clusters and geographically significant features.

Prescribed fire in eucalypt woodlands: immediate effects on a microbat community of northern Australia

Context Fire is a major ecological factor in many landscapes. Prescribed fires are often used in the management of vegetation for ecological values, wildlife habitat and reduction of risk of wildfire. However, debate continues over whether active fire management is beneficial to flora and fauna. Although bats comprise ~20% of the world’s extant mammal fauna, they have been largely ignored in studies investigating ecosystem response to fire, especially in Australia. Aims In the present study, we aim to investigate the immediate responses of microbats to prescribed fires in a tropical eucalypt woodland.Methods We used a replicated paired experimental design, consisting of burned and unburned treatment and control sites, to investigate how bat activity and community structure change following a prescribed fire. Key results Total bat activity increased significantly following fire. Fire also resulted in changes in the bat species assemblage. Changes in community structure were driven by the following five species: Saccolaimus spp., Chalinolobus nigrogriseus, Chaerephon jobensis, Rhinolophus megaphyllus and unidentified Species c35. Activity of C. nigrogriseus, Saccolaimus spp., C. jobensis and Species c35 increased in the burned sites, whereas changes in the activity of R. megaphyllus were uncorrelated with the effects of fire. Conclusions The effect of fire on these species is consistent with flight patterns and habitat use; species with higher wing aspect ratios, such as Saccolaimus spp., which are capable of fast flight but with limited manoeuvrability, became more active in the open conditions created by fire. Implications The results of the present study suggest that prescribed fire as an environmental management tool may be beneficial to bats, at least in the short term, because it increases habitat suitability for a wider range of species.

Environmental temperature affects prevalence of blood parasites of birds on an elevation gradient: implications for disease in a warming climate

Background

The rising global temperature is predicted to expand the distribution of vector-borne diseases both in latitude and altitude. Many host communities could be affected by increased prevalence of disease, heightening the risk of extinction for many already threatened species. To understand how host communities could be affected by changing parasite distributions, we need information on the distribution of parasites in relation to variables like temperature and rainfall that are predicted to be affected by climate change.

Methodology/Principal Findings

We determined relations between prevalence of blood parasites, temperature, and seasonal rainfall in a bird community of the Australian Wet Tropics along an elevation gradient. We used PCR screening to investigate the prevalence and lineage diversity of four genera of blood parasites (Plasmodium, Haemoproteus, Leucocytozoon and Trypanosoma) in 403 birds. The overall prevalence of the four genera of blood parasites was 32.3%, with Haemoproteus the predominant genus. A total of 48 unique lineages were detected. Independent of elevation, parasite prevalence was positively and strongly associated with annual temperature. Parasite prevalence was elevated during the dry season.

Conclusions/Significance

Low temperatures of the higher elevations can help to reduce both the development of avian haematozoa and the abundance of parasite vectors, and hence parasite prevalence. In contrast, high temperatures of the lowland areas provide an excellent environment for the development and transmission of haematozoa. We showed that rising temperatures are likely to lead to increased prevalence of parasites in birds, and may force shifts of bird distribution to higher elevations. We found that upland tropical areas are currently a low-disease habitat and their conservation should be given high priority in management plans under climate change.

Radiosynthesis and characterization of 11C-GSK215083 as a PET radioligand for the 5-HT6 receptor

The development of a PET radioligand for imaging 5-hydroxytryptamine (5-HT) 6 receptors in the brain would, for the first time, enable in vivo imaging of this target along with assessment of its involvement in disease pathophysiology. In addition, such a tool would assist in the development of novel drugs targeting the 5-HT6 receptor.

METHODS

On the basis of in vitro data, GSK215083 was identified as a promising 5-HT6 radioligand candidate and was radiolabeled with (11)C via methylation. The in vivo properties of (11)C-GSK215083 were evaluated first in pigs (to investigate brain penetration and specific binding), second in nonhuman primates (to confirm brain penetration, specific binding, selectivity, and kinetics), and third in human subjects (to confirm brain penetration and biodistribution).

RESULTS

(11)C-GSK215083 readily entered the brain in all 3 species, leading to a heterogeneous distribution (striatum > cortex > cerebellum) consistent with reported 5-HT6 receptor densities and distribution determined by tissue-section autoradiography in preclinical species and humans. In vivo saturation studies using escalating doses of GSK215083 in primates demonstrated saturable, dose-dependent binding to the 5-HT6 receptor in the striatum. Importantly, (11)C-GSK215083 also exhibited affinity for the 5-HT2A receptor; however, given the differential localization of these 2 receptors in the central nervous system, the discrete 5-HT6 binding properties of this radioligand were able to be determined.

CONCLUSION

These data demonstrate the utility of (11)C-GSK215083 as a promising PET radioligand for probing the 5-HT6 receptor in vivo in both preclinical and clinical species.

DNA sequence context conceals α-anomeric lesions

DNA sequence context has long been known to modulate detection and repair of DNA damage. Recent studies using experimental and computational approaches have sought to provide a basis for this observation. We have previously shown that an α-anomeric adenosine (αA) flanked by cytosines (5'CαAC-3') resulted in a kinked DNA duplex with an enlarged minor groove. Comparison of different flanking sequences revealed that a DNA duplex containing a 5'CαAG-3' motif exhibits unique substrate properties. However, this substrate was not distinguished by unusual thermodynamic properties. To understand the structural basis of the altered recognition, we have determined the solution structure of a DNA duplex with a 5'CαAG-3' core, using an extensive set of restraints including dipolar couplings and backbone torsion angles. The NMR structure exhibits an excellent agreement with the data (total R(X) <5.3%). The αA base is intrahelical, in a reverse Watson-Crick orientation, and forms a weak base pair with a thymine of the opposite strand. In comparison to the DNA duplex with a 5'CαAC-3' core, we observe a significant reduction of the local perturbation (backbone, stacking, tilt, roll, and twist), resulting in a straighter DNA with narrower minor groove. Overall, these features result in a less perturbed DNA helix and obscure the presence of the lesion compared to the 5'CαAC-3' sequence. The improved stacking of the 5'CαAG-3' core also affects the energetics of the DNA deformation that is required to form a catalytically competent complex. These traits provide a rationale for the modulation of the recognition by endonuclease IV.

Reconstructing the dynamics of ancient human populations from radiocarbon dates: 10 000 years of population growth in Australia

Measuring trends in the size of prehistoric populations is fundamental to our understanding of the demography of ancient people and their responses to environmental change. Archaeologists commonly use the temporal distribution of radiocarbon dates to reconstruct population trends, but this can give a false picture of population growth because of the loss of evidence from older sites. We demonstrate a method for quantifying this bias, and we use it to test for population growth through the Holocene of Australia. We used model simulations to show how turnover of site occupation across an archaeological landscape, interacting with erasure of evidence at abandoned sites, can create an increase in apparent site occupation towards the present when occupation density is actually constant. By estimating the probabilities of abandonment and erasure from archaeological data, we then used the model to show that this effect does not account for the observed increase in occupation through the Holocene in Australia. This is best explained by population growth, which was low for the first part of the Holocene but accelerated about 5000 years ago. Our results provide new evidence for the dynamism of non-agricultural populations through the Holocene.

Structural basis of the RNase H1 activity on stereo regular borano phosphonate DNA/RNA hybrids

Numerous DNA chemistries for improving oligodeoxynucleotide (ODN)-based RNA targeting have been explored. The majority of the modifications render the ODN/RNA target insensitive to RNase H1. Borano phosphonate ODN's are among the few modifications that are tolerated by RNase H1. To understand the effect of the stereochemistry of the BH(3) modification on the nucleic acid structure and RNase H1 enzyme activity, we have investigated two DNA/RNA hybrids containing either a R(P) or S(P) BH(3) modification by nuclear magnetic resonance (NMR) spectroscopy. T(M) studies show that the stabilities of R(P) and S(P) modified DNA/RNA hybrids are essentially identical (313.8 K) and similar to that of an unmodified control (312.9 K). The similarity is also reflected in the imino proton spectra. To characterize such similar structures, we used a large number of NMR restraints (including dipolar couplings and backbone torsion angles) to determine structural features that were important for RNase H1 activity. The final NMR structures exhibit excellent agreement with the data (total R(x) values of <6%) with helical properties between those of an A and B helix. Subtle backbone variations are observed in the DNA near the modification, while the RNA strands are relatively unperturbed. In the case of the S(P) modification, for which more perturbations are recorded, a slightly narrower minor groove is also obtained. Unique NOE base contacts localize the S(P) BH(3) group in the major groove while the R(P) BH(3) group points away from the DNA. However, this creates a potential clash of the R(P) BH(3) groups with important RNase H1 residues in a complex, while the S(P) BH(3) groups could be tolerated. We therefore predict that on the basis of our NMR structures a fully R(P) BH(3) DNA/RNA hybrid would not be a substrate for RNase H1.

Climate-driven variation in food availability between the core and range edge of the endangered northern bettong (Bettongia tropica)

The endangered northern bettong (Bettongia tropica) occurs in four disjunct populations in far north Queensland, Australia, at a high density only in its range core (RC). A recent study suggested that B. tropica populations are sparse at the northern and southern range edges (SRE) due to more severe droughts and variable climatic conditions causing fluctuations in the availability of their principal food resource, truffle-like fungi. Truffle availability in the Australian tropics is affected by climate, specifically seasonality of precipitation. We aimed to determine whether the differences in weather patterns between the RC and SRE could be translated to actual differences in truffle availability. Truffle density was consistently lower on the SRE although biomass was slightly higher there due to dominance by drought-tolerant truffle taxa that produce few but large truffles. Lower densities of truffles on the SRE could explain why B. tropica is also less abundant there and why they may be less resilient to competition from the more generalist rufous bettong (Aepyprymnus rufescens). Increasing temperatures and, more importantly, harsher droughts predicted for this region as a result of climate change, may have further detrimental impacts on truffle availability and thus population densities of B. tropica and other mycophagous species.

Red in tooth and claw: how top predators shape terrestrial ecosystems

Top predators are increasingly recognized as important regulators of ecosystem structure. Elmhagen et al. in this issue show how a recolonizing population of lynx in Finland is in the process of imposing control of the abundance of a mesopredator, the red fox, and relaxing predation pressure on a prey species. Their study shows how ecological restoration programs could use the power of top predators to limit mesopredator populations and control total predation pressure on prey species.

Species richness and evenness in Australian birds

Species richness and evenness are the two major components of biodiversity, but the way in which they are interrelated is a subject of contention. We found a negative relationship between the two variables for bird communities at 92 woodland sites across Australia and sought an explanation. Actual evapotranspiration (AET) was by far the best predictor of species richness. When AET was controlled for, the relationship between richness and evenness became nonsignificant. Richness is greater at sites with higher AET because such sites support a greater number of individuals. However, such sites have a greater number of rare species, resulting in lower evenness. A complicating factor is that evenness is best predicted by degree of vegetation cover, with sparsely vegetated sites having significantly lower evenness. We conclude that there are two competing ecological processes, related to energy and water availability, that determine richness and evenness. The first drives total abundance (leading to high richness, low evenness), while the second drives productivity and niche availability (leading to high richness, high evenness). The relative strength of these two processes and the observed relationship between richness and evenness are likely to depend on the scale of the analysis and the species and range of habitats studied.

Gap-crossing in fragmented habitats by mahogany gliders (Petaurus gracilis). Do they cross roads and powerline corridors?

The mahogany glider (Petaurus gracilis) is one of the most threatened arboreal mammals in Australia. Although its habitat is affected by fragmentation, gap-crossing behaviour of the species has not been studied. A radio-tracking survey was undertaken on six individuals (three males, three females) in a woodland patch bisected by a 35.8-m-wide highway and a 31.5-m-wide powerline corridor, in north-east Queensland. The mean home ranges of males were 20.1 ± 3.3 ha, 21.3 ± 7.9 ha and 20.9 ± 8.2 ha, as measured by the Minimum Convex Polygon, Kernel and Harmonic Mean methods respectively. The mean home ranges of females were 8.9 ± 0.5 ha, 9.0 ± 4.2 ha and 8.8 ± 2.3 ha, as measured by the Minimum Convex Polygon, Kernel and Harmonic Mean methods respectively. Two males and one female were observed crossing linear gaps. However, there was less crossing than expected, and females were less likely to cross than males. One male used a narrow strip of woodland at the opposite side of the highway as supplemental habitat for foraging. This individual also used scattered trees in a grassland matrix for foraging or denning. Another male used a wooden power pole as a launching site to cross the highway. This study emphasises the importance of protecting large trees along linear barriers in open habitat, and suggests that gliding poles may be used to facilitate gap-crossing by mahogany gliders.

Ecological specialization and population size in a biodiversity hotspot: how rare species avoid extinction

Species with narrow environmental niches typically have small geographic ranges. Small range size is, in turn, often associated with low local abundance. Together, these factors should mean that ecological specialists have very small total populations, putting them at high risk of extinction. But some specialized and geographically restricted species are ancient, and some ecological communities have high proportions of rare and specialized endemics. We studied niche characteristics and patterns of distribution and abundance of terrestrial vertebrates in the rainforests of the Australian Wet Tropics (AWT) to identify mechanisms by which rare species might resist extinction. We show that species with narrow environmental niches and small geographic ranges tend to have high and uniform local abundances. The compensation of geographic rarity by local abundance is exact, such that total population size in the rainforest vertebrates of the AWT is independent of environmental specialization. This effect would tend to help equalize extinction risk for specialists and generalists. Phylogenetic analysis suggests that environmental specialists have been gradually accumulating in this fauna, indicating that small range size/environmental specialization can be a successful trait as long as it is compensated for by demographic commonness. These results provide an explanation of how range-restricted specialists can persist for long periods, so that they now form a major component of high-diversity assemblages such as the AWT.

Abundance and the environmental niche: environmental suitability estimated from niche models predicts the upper limit of local abundance

Ecologists seek to understand patterns of distribution and abundance of species. Studies of distribution often use occurrence data to build models of the environmental niche of a species. Environmental suitability (ES) derived from such models may be used to predict the potential distributions of species. The ability of such models to predict spatial patterns in abundance is unknown; we argue that there should be a positive relationship between ES and local abundance. This will be so if ES reflects how well the species' physiological and ecological requirements are met at a site and if those factors also determine local abundance. However, the presence of other factors may indicate that potential abundance is not attained at all sites. Therefore, ES should predict the upper limit of abundance, and the observed relationship with ES should be wedge shaped. We tested the relationship of ES with local abundance for 69 rain forest vertebrates in the Australian wet tropics. Ordinary least squares and quantile regressions revealed a positive relationship between ES and local abundance for most species (>84%). The relationships for these species were wedge shaped. We conclude that ES modeled from presence-only data provides useful information on spatial patterns of abundance, and we discuss implications of this in addressing important problems in ecology.