Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes

The human mutation rate is an essential parameter for studying the evolution of our species, interpreting present-day genetic variation, and understanding the incidence of genetic disease. Nevertheless, our current estimates of the rate are uncertain. Most notably, recent approaches based on counting de novo mutations in family pedigrees have yielded significantly smaller values than classical methods based on sequence divergence. Here, we propose a new method that uses the fine-scale human recombination map to calibrate the rate of accumulation of mutations. By comparing local heterozygosity levels in diploid genomes to the genetic distance scale over which these levels change, we are able to estimate a long-term mutation rate averaged over hundreds or thousands of generations. We infer a rate of 1.61 ± 0.13 × 10⁻⁸ mutations per base per generation, which falls in between phylogenetic and pedigree-based estimates, and we suggest possible mechanisms to reconcile our estimate with previous studies. Our results support intermediate-age divergences among human populations and between humans and other great apes.     

Free Fatty Acid Effects on the Atrial Myocardium: Membrane Ionic Currents Are Remodeled by the Disruption of T-Tubular Architecture

Background

Epicardial adiposity and plasma levels of free fatty acids (FFAs) are elevated in atrial fibrillation, heart failure and obesity, with potentially detrimental effects on myocardial function. As major components of epicardial fat, FFAs may be abnormally regulated, with a potential to detrimentally modulate electro-mechanical function. The cellular mechanisms underlying such effects of FFAs are unknown.

Objective

To determine the mechanisms underlying electrophysiological effects of palmitic (PA), stearic (SA) and oleic (OA) FFAs on sheep atrial myocytes.

Methods

We used electrophysiological techniques, numerical simulations, biochemistry and optical imaging to examine the effects of acutely (≤ 15 min), short-term (4–6 hour) or 24-hour application of individual FFAs (10 μM) on isolated ovine left atrial myocytes (LAMs).

Results

Acute and short-term incubation in FFAs resulted in no differences in passive or active properties of isolated left atrial myocytes (LAMs). 24-hour application had differential effects depending on the FFA. PA did not affect cellular passive properties but shortened (p<0.05) action potential duration at 30% repolarization (APD₃₀). APD₅₀ and APD₈₀ were unchanged. SA had no effect on resting membrane potential but reduced membrane capacitance by 15% (p<0.05), and abbreviated APD at all values measured (p≤0.001). OA did not significantly affect passive or active properties of LAMs. Measurement of the major voltage-gated ion channels in SA treated LAMs showed a ~60% reduction (p<0.01) of the L-type calcium current (I_Ca-L) and ~30% reduction (p<0.05) in the transient outward potassium current (I_TO). A human atrial cell model recapitulated SA effects on APD. Optical imaging showed that SA incubated for 24 hours altered t-tubular structure in isolated cells (p<0.0001).

Conclusions

SA disrupts t-tubular architecture and remodels properties of membrane ionic currents in sheep atrial myocytes, with potential implications in arrhythmogenesis.     

Chemical Mediation of Prey Recognition by Spider-Hunting Wasps

Predator–prey interactions are important in maintaining the structure and dynamics of ecological communities. Both predators and prey use cues from a range of sensory modalities to detect and assess one another; identification of these cues is necessary to understand how selection operates to shape predator–prey interactions. Mud-dauber wasps (Sphecidae) provision their larval nests with paralyzed spiders, and different genera of wasps specialize on particular spider taxa. Sceliphron caementarium (Drury 1773) wasps preferentially capture spiders that build two-dimensional (2D) webs, rather than those that construct three-dimensional (3D) webs, but the basis of this preference is not clear. Wasps may choose spiders based on an assessment of their web architecture, as 3D webs may provide better defenses against wasp predation than do 2D webs. However, because many hymenopterans use chemical cues to locate and recognize prey, it is also possible that mud-dauber wasps rely on chemical cues associated with the spider and/or the web to assess prey suitability. When we offered foraging S. caementarium wasps 2D and 3D spiders both on and off their webs, we found that in both cases the wasps took 2D spiders and avoided 3D spiders, demonstrating that the web itself is not the impediment. Results of a series of behavioral choice assays involving filter paper discs containing spider cues and chemically manipulated spiders or spider dummies corroborated the importance of spider chemical cues in mediation of prey recognition by mud-dauber wasps. We also discuss the relative importance of visual and chemical cues for prey recognition by wasps, examine the anti-predator behaviors of 2D and 3D spiders, and consider the role of wasp predation in spider diversification.     

Discovery of a novel class of biphenyl pyrazole sodium channel blockers for treatment of neuropathic pain

A series of novel biphenyl pyrazole dicarboxamides were identified as potential sodium channel blockers for treatment of neuropathic pain. Compound 20 had outstanding efficacy in the Chung rat spinal nerve ligation (SNL) model of neuropathic pain.     

Synthesis,in vitro and in vivo studies of Gd-DTPA-XDA-D1-Glc(OH) complex as a new potential MRI contrast agent

A new type of dendritic molecules Gd-DTPA-XDA-D1-Glc(OH), which work as a functionalized ligand coordinating gadolinium(III) ion at the center of their frameworks with two glucose moieties on the molecular surfaces, were readily synthesized with high yield. The structures were established by IR, ¹H, ¹³C NMR, and mass spectral studies. Its bio-distribution patterns were evaluated on rats.     

Relationship between Vehicle Emissions Laws and Incidence of Suicide by Motor Vehicle Exhaust Gas in Australia, 2001–06: An Ecological Analysis

Background

Globally, suicide accounts for 5.2% of deaths among persons aged 15 to 44 years and its incidence is rising. In Australia, suicide rates peaked in 1997 and have been declining since. A substantial part of that decline stems from a plunge in suicides by one particular method: asphyxiation by motor vehicle exhaust gas (MVEG). Although MVEG remains the second most common method of suicide in Australia, its incidence decreased by nearly 70% in the decade to 2006. The extent to which this phenomenon has been driven by national laws in 1986 and 1999 that lowered permissible levels of carbon monoxide (CO) emissions is unknown. The objective of this ecological study was to test the relationship by investigating whether areas of Australia with fewer noxious vehicles per capita experienced lower rates of MVEG suicide.

Methods and Findings

We merged data on MVEG suicides in Australia (2001–06) with data on the number and age of vehicles in the national fleet, as well as socio-demographic data from the national census. Poisson regression was used to analyse the relationship between the incidence of suicide within two levels of geographical area—postcodes and statistical subdivisions (SSDs)—and the population density of pre-1986 and pre-1999 passenger vehicles in those areas. (There was a mean population of 8,302 persons per postcode in the study dataset and 87,413 persons per SSD.) The annual incidence of MVEG suicides nationwide decreased by 57% (from 2.6 per 100,000 in 2001 to 1.1 in 2006) during the study period; the population density of pre-1986 and pre-1999 vehicles decreased by 55% (from 14.2 per 100 persons in 2001 to 6.4 in 2006) and 26% (from 44.5 per 100 persons in 2001 to 32.9 in 2006), respectively. Area-level regression analysis showed that the suicide rates were significantly and positively correlated with the presence of older vehicles. A percentage point decrease in the population density of pre-1986 vehicles was associated with a 6% decrease (rate ratio [RR] = 1.06; 95% confidence interval [CI] 1.05–1.08) in the incidence of MVEG suicide within postcode areas; a percentage point decrease in the population density of pre-1999 vehicles was associated with a 3% decrease (RR = 1.03; 95% CI 1.02–1.04) in the incidence of MVEG suicide.

Conclusions

Areas of Australia with fewer vehicles predating stringent CO emission laws experience lower rates of MVEG suicide. Although those emission laws were introduced primarily for environmental reasons, countries that lack them may miss the benefits of a serendipitous suicide prevention strategy. Please see later in the article for the Editors'' Summary     

Loline alkaloids: Currencies of mutualism

Several species of Lolium and other cool-season grasses (Poaceae subfamily Pooideae) tend to harbor symbiotic, seed-transmitted, fungi that enhance their fitness by various means. These fungal endophytes--species of Neotyphodium or Epichlo? (Clavicipitaceae)--are known for production of antiherbivore metabolites such as the bioprotective loline alkaloids. Lolines are saturated pyrrolizidines with an exo-1-amine and an ether bridge between C-2 and C-7. The ether bridge is an unusual feature for a biogenic compound in that it links two bridgehead carbon atoms. Much of the loline-biosynthetic pathway has been elucidated by administering isotopically labeled precursors to fungal cultures and by comparisons of loline biosynthesis genes to known gene families. The first step appears to be an unusual gamma-substitution reaction involving an enzyme related to O-acetylhomoserine (thiol) lyase, but which uses the secondary amine of L-proline rather than a sulfhydryl group as the nucleophile. The strained ether bridge is added after formation of the pyrrolizidine rings. Lolines with dimethylated or acylated 1-amines have insect antifeedant and insecticidal activities comparable to nicotine, but little or no toxicity to mammals. Considering the surprising abundance of lolines in some grass-endophyte symbiota, possible additional effects on plant stress tolerance and physiology are worth future consideration. In this review, we discuss the history of loline discovery, methods of analysis, biological activities and distribution in nature, as well as progress on the genetics and biochemistry of their biosynthesis, and on the chemical synthesis of these alkaloids.     

Identification of adiponectin as a novel hemopoietic stem cell growth factor

The hemopoietic microenvironment consists of a diverse repertoire of cells capable of providing signals that influence hemopoietic stem cell function. Although the role of osteoblasts and vascular endothelial cells has recently been characterized, the function of the most abundant cell type in the bone marrow, the adipocyte, is less defined. Given the emergence of a growing number of adipokines, it is possible that these factors may also play a role in regulating hematopoiesis. Here, we investigated the role of adiponectin, a secreted molecule derived from adipocytes, in hemopoietic stem cell (HSC) function. We show that adiponectin is expressed by components of the HSC niche and its receptors AdipoR1 and AdipoR2 are expressed by HSCs. At a functional level, adiponectin influences HSCs by increasing their proliferation, while retaining the cells in a functionally immature state as determined by in vitro and in vivo assays. We also demonstrate that adiponectin signaling is required for optimal HSC proliferation both in vitro and in long term hemopoietic reconstitution in vivo. Finally we show that adiponectin stimulation activates p38 MAPK, and that inhibition of this pathway abrogates adiponectin's proliferative effect on HSCs. These studies collectively identify adiponectin as a novel regulator of HSC function and suggest that it acts through a p38 dependent pathway.     

Cryoelectron tomographic analysis of an HIV-neutralizing protein and its complex with native viral gp120

Identifying structural determinants of human immunodeficiency virus (HIV) neutralization is an important component of rational drug and vaccine design. We used cryoelectron tomography and atomic force microscopy to characterize the structure of an extremely potent HIV-neutralizing protein, D1D2-Ig alpha tp (abbreviated as D1D2-IgP), a polyvalent antibody construct that presents dodecameric CD4 in place of the Fab regions. We show that D1D2-IgP has a novel structure, displaying greater flexibility of its antibody arms than the closely related IgM. Using simian immunodeficiency virus in complex with D1D2-IgP, we present unequivocal evidence that D1D2-IgP can cross-link surface spikes on the same virus and on neighboring viruses. The observed binding to the viral envelope spikes is the result of specific CD4-gp120 interaction, because binding was not observed with MICA-IgP, a construct that is identical to D1D2-IgP except that major histocompatibility complex Class I-related Chain A (MICA) replaces the CD4 moiety. CD4-mediated binding was also associated with a significantly elevated proportion of ruptured viruses. The ratio of inactivated to CD4-liganded gp120-gp41 spikes can be much greater than 1:1, because all gp120-gp41 spikes on the closely apposed surfaces of cross-linked viruses should be incapable of accessing the target cell surface and mediating entry, as a result of inter-virus spike cross-linking. These results implicate flexibility rather than steric bulk or polyvalence per se as a structural explanation for the extreme potency of D1D2-IgP and thus suggest polyvalence presented on a flexible scaffold as a key design criterion for small molecule HIV entry inhibitors.