Age of the Jeju pony (Equus caballus) at first reproduction: potential costs for foals and mothers that first reproduce early in life

In a related paper, we showed that mares that reproduced early in life tended to have higher fecundity because of a decrease in the duration of inter-birth intervals relative to mares that reproduced later in life. However, we know that young mares are subordinate to older mares. Hence, costs associated with low dominance rank might offset the benefits of earlier reproduction. We compared harassment of foals of female Jeju ponies that first reproduced at three years of age with that of foals of females that first reproduced at five years of age. As a consequence of their positions in the linear dominance hierarchy, foals born to and guarded by young mares were harassed more frequently than foals whose mothers were older when they first reproduced. A mare that reproduced early in life guarded her offspring more closely and intervened between her foal and neighboring mares more frequently than those mares which first reproduced when older. This need to guard their foals and the harm that might ensue from frequent harassment might counter-balance selection towards earlier reproduction in mares.     

Forest structure of a subtropical mangrove along a river inferred from potential tree height and biomass

The hypothesis was tested that potential tree height and biomass in mangroves decrease downstream with the tidal gradient along the Okukubi River in Okinawa Island, Japan. The mangrove stands consisted of Bruguiera gymnorrhiza (L.) Lamk. and Kandelia obovata (S., L.) Yong (Rhizophoraceae). Four sites were selected considering the distance from the mouth of the river. Soil salinity increased downstream, while soil total nitrogen content decreased. The soil redox potential did not vary along the river. Maximum gross photosynthesis and tree height for each species decreased downstream. The potential tree height (H_max) inferred from the stem diameter (D_0.1)–tree height (H) relationship ( a, h, coefficient) in each species decreased downstream. The tree density (ρ)–mean tree size () relationships ( K, α, coefficient) determined for four sites revealed that the mean tree size at any given tree density decreased downstream, which indicates the decrease of potential biomass. Furthermore, an index for biomass () was homogeneous within a site regardless of tree density, i.e. the value of α at each site did not differ significantly from 1.0 (p > 0.05). The decreases in potential tree height and biomass may be partially ascribed to the stressful environments at the downstream sites characterized by high salinity (>2.6%) and nitrogen-poor soils (<0.25 ppt) in our study area.     

Spatial-explicit assessment of current and future conservation options for the endangered Corsican Red Deer (Cervus elaphus corsicanus) in Sardinia

The Corsican red deer, a sub-species of the European red deer endemic to Sardinia and Corsica, was abundant on both islands at the beginning of 1900. It went extinct in Corsica and reached a minimum of 100 individuals in Sardinia by 1970. Numbers have recovered in Sardinia with more than 1,000 rutting males now present; in the 1980s the deer was reintroduced to Corsica, but the Sardinian population remains fragmented. We developed a potential distribution model in Sardinia using Ecological Niche Factor Analysis. To assess the deer’s protection status we compared the model with the existing and proposed conservation areas and investigated different conservation scenarios in relation to the expansion of its current range and resilience to future changes in land use and predicted trends of desertification. According to our results over 70% of Sardinia is unsuitable to the deer, nevertheless high suitability areas (Mediterranean forests away from main roads) are available throughout the island, particularly in the south and in the central-eastern part. Existing protected areas do not provide for the conservation of the deer but public owned forests, where hunting is prohibited, extend some level of protection, and the protected areas proposed by the Regional administration, if implemented, will be increasing this protection. Three main areas have emerged as conservation priorities to guarantee adequate conservation potential in the future. Our approach provides valuable data to inform conservation policy, and could be easily replicated in other parts of the Mediterranean.     

A simple Cα-SC potential with higher accuracy for protein fold recognition

In this paper, an improved C_α-SC energy potential designed for protein fold recognition was reported. It consists of three extremely simple interaction terms which are supposed to be the dominant interactions in protein folding: residue-residue contact, hydrophobicity and pseudodihedral potentials. The potential function only contains 210 contacts, one hydrophobic and one torsion parameters, which have been optimized using an interior point algorithm of linear programming. Tests of the derived potential function on commonly used decoy sets illustrate that it outperforms most of the existing coarse-grained potentials in terms of its capabilities in recognizing native structures and consistency in achieving high Z-scores across decoy sets, and it has almost equivalent performance to the potentials which considered complex intra-molecular interactions. The results show that our scoring function is a generally prospective potential for protein structure prediction and modeling with regard to its recognition and computation efficacy.     

Ecological risk and contamination history of heavy metals in the Andong tidal flat,Hangzhou Bay,China

In this study, we collected two sediment cores (C1 and C2) from the Andong tidal flat, Hangzhou Bay, and studied the temporal variations of heavy metals in the cores. Vertical distributions of heavy metals were almost unchanged in both the cores before 2000. After 2000, however, the heavy metal concentrations increased dramatically, suggesting that the sediments have been affected by enhanced human pollution in the recent decade. In the core C1, the sediments were severely polluted by Pb, moderately to considerably polluted by Cr and Zn, and low to moderately polluted by other heavy metals. The core C2 was relatively unpolluted before 2000 and low to moderately polluted after 2000. Multi-statistical analyses indicated that the core C1 was additionally contaminated by local human activities such as wastewater discharge and the Hangzhou Bay Bridge. The heavy metals in the core C2, however, were largely contributed by the Yangtze River and controlled by sedimentation process. The calculated sedimentary flux (4–8 g m^?2 a^?1) of heavy metals generally increased with time. It was closely related to the wastewater discharge in adjacent areas. This study reconstructed the local heavy metal pollution history and provides important information for environmental protection and policy making.     

Impairment of survival signaling and efferocytosis in TRPC3-deficient macrophages

We have recently shown that in macrophages proper operation of the survival pathways phosphatidylinositol-3-kinase (PI3K)/AKT and nuclear factor kappa B (NFkB) has an obligatory requirement for constitutive, non-regulated Ca²⁺ influx. In the present work we examined if Transient Receptor Potential Canonical 3 (TRPC3), a member of the TRPC family of Ca²⁺-permeable cation channels, contributes to the constitutive Ca²⁺ influx that supports macrophage survival. We used bone marrow-derived macrophages obtained from TRPC3^−/− mice to determine the activation status of survival signaling pathways, apoptosis and their efferocytic properties. Treatment of TRPC3^+/+ macrophages with the pro-apoptotic cytokine TNFα induced time-dependent phosphorylation of IκBα, AKT and BAD, and this was drastically reduced in TRPC3^−/− macrophages. Compared to TRPC3^+/+ cells TRPC3^−/− macrophages exhibited reduced constitutive cation influx, increased apoptosis and impaired efferocytosis. The present findings suggest that macrophage TRPC3, presumably through its constitutive function, contributes to survival signaling and efferocytic properties.     

Generalized causal mediation analysis

The goal of mediation analysis is to assess direct and indirect effects of a treatment or exposure on an outcome. More generally, we may be interested in the context of a causal model as characterized by a directed acyclic graph (DAG), where mediation via a specific path from exposure to outcome may involve an arbitrary number of links (or "stages"). Methods for estimating mediation (or pathway) effects are available for a continuous outcome and a continuous mediator related via a linear model, while for a categorical outcome or categorical mediator, methods are usually limited to two-stage mediation. We present a method applicable to multiple stages of mediation and mixed variable types using generalized linear models. We define pathway effects using a potential outcomes framework and present a general formula that provides the effect of exposure through any specified pathway. Some pathway effects are nonidentifiable and their estimation requires an assumption regarding the correlation between counterfactuals. We provide a sensitivity analysis to assess the impact of this assumption. Confidence intervals for pathway effect estimates are obtained via a bootstrap method. The method is applied to a cohort study of dental caries in very low birth weight adolescents. A simulation study demonstrates low bias of pathway effect estimators and close-to-nominal coverage rates of confidence intervals. We also find low sensitivity to the counterfactual correlation in most scenarios.     

Gap junctions synchronize action potentials and Ca2+ transients in Caenorhabditis elegans body wall muscle

The sinusoidal locomotion of Caenorhabditis elegans requires synchronous activities of neighboring body wall muscle cells. However, it is unknown whether the synchrony results from muscle electrical coupling or neural inputs. We analyzed the effects of mutating gap junction proteins and blocking neuromuscular transmission on the synchrony of action potentials (APs) and Ca2+ transients among neighboring body wall muscle cells. In wild-type worms, the percentage of synchronous APs between two neighboring cells varied depending on the anatomical relationship and junctional conductance (Gj) between them, and Ca2+ transients were synchronous among neighboring muscle cells. Compared with the wild type, knock-out of the gap junction gene unc-9 resulted in greatly reduced coupling coefficient and asynchronous APs and Ca2+ transients. Inhibition of unc-9 expression specifically in muscle by RNAi also reduced the synchrony of APs and Ca2+ transients, whereas expression of wild-type UNC-9 specifically in muscle rescued the synchrony defect. Loss of the stomatin-like protein UNC-1, which is a regulator of UNC-9-based gap junctions, similarly impaired muscle synchrony as unc-9 mutant did. The blockade of muscle ionotropic acetylcholine receptors by (+)-tubocurarine decreased the frequencies of APs and Ca2+ transients, whereas blockade of muscle GABAA receptors by gabazine had opposite effects. However, both APs and Ca2+ transients remained synchronous after the application of (+)-tubocurarine and/or gabazine. These observations suggest that gap junctions in C. elegans body wall muscle cells are responsible for synchronizing muscle APs and Ca2+ transients.