Mark‐recapture modeling accounting for state uncertainty provides concurrent estimates of survival and fecundity in a protected harbor seal population

Harbor seal breeding behavior and habitats constrain opportunities for individual‐based studies, and no current estimates of both survival and fecundity exist for any of the populations studied worldwide. As a result, the drivers underlying the variable trends in abundance exhibited by harbor seal populations around the world remain uncertain. We developed an individual‐based study of harbor seals in northeast Scotland, whereby data were collected during daily photo‐identification surveys throughout the pupping seasons between 2006 and 2011. However, a consequence of observing seals remotely meant that information on sex, maturity‐stage, or breeding status was not always available. To provide unbiased estimates of survival rates we conditioned initial release of individuals on the first time sex was known to estimate sex‐specific survival rates, while a robust design multistate model accounting for uncertainty in breeding status was used to estimate reproductive rate of multiparous and ≥3‐yr‐old females. Survival rates were estimated at 0.95 (95% CI = 0.91–0.97) for females and 0.92 (0.83–0.96) for males, while reproductive rate was estimated at 0.89 (0.75–0.95) for multiparous and 0.69 (0.64–0.74) for ≥3‐yr‐old females. Stage‐based population modeling indicated that this population should be recovering, even under the current shooting quotas implemented by the recent management plan.     

Standardized,systemic phenotypic analysis of Slc12a1I299F mutant mice

Background

Type I Bartter syndrome is a recessive human nephropathy caused by loss-of-function mutations in the SLC12A1 gene coding for the Na⁺-K⁺-2Cl⁻ cotransporter NKCC2. We recently established the mutant mouse line Slc12a1^I299F exhibiting kidney defects highly similar to the late-onset manifestation of this hereditary human disease. Besides the kidney defects, low blood pressure and osteopenia were revealed in the homozygous mutant mice which were also described in humans. Beside its strong expression in the kidney, NKCC2 has been also shown to be expressed in other tissues in rodents i.e. the gastrointestinal tract, pancreatic beta cells, and specific compartments of the ear, nasal tissue and eye.

Results

To examine if, besides kidney defects, further organ systems and/or metabolic pathways are affected by the Slc12a1^I299F mutation as primary or secondary effects, we describe a standardized, systemic phenotypic analysis of the mutant mouse line Slc12a1^I299F in the German Mouse Clinic. Slc12a1^I299F homozygous mutant mice and Slc12a1^I299F heterozygous mutant littermates as controls were tested at the age of 4–6 months. Beside the already published changes in blood pressure and bone metabolism, a significantly lower body weight and fat content were found as new phenotypes for Slc12a1^I299F homozygous mutant mice. Small additional effects included a mild erythropenic anemia in homozygous mutant males as well as a slight hyperalgesia in homozygous mutant females. For other functions, such as immunology, lung function and neurology, no distinct alterations were observed.

Conclusions

In this systemic analysis no clear primary effects of the Slc12a1^I299F mutation appeared for the organs other than the kidneys where Slc12a1 expression has been described. On the other hand, long-term effects additional and/or secondary to the kidney lesions might also appear in humans harboring SLC12A1 mutations.     

The biology of Placostylus ambagiosus (Pulmonata: Bulimulidae) in New Zealand: Part 2. Population changes,growth, mortality and life expectancy

The large land snail Placostylus ambagiosus (Pulmonata: Bulimulidae) was studied in northernmost New Zealand from 1988 to 2004. At Cape Maria van Diemen (CMvD), more juveniles than adults were found, although estimates showed adults as the most abundant. A cohort, hatched after rodent control commenced in 1990, began maturing in 1995, but 89% died by 1997 (partly through competition with garden snails, Cornu aspersum), before numbers partially recovered by 2003. At Surville Cliffs, adults were estimated to be more abundant than juveniles but few juveniles were observed. Numbers under 12 food plants fluctuated between 425 and 657. Many snails dispersed after horses (Equus caballus) partially defoliated their food plants but returned once these recovered. A translocated population increased after rodent control commenced in 1999, but declined when rodent control ceased in 2002. Another translocated population declined when rodents were present and never recovered even after rodent control commenced in 2002. Snails took 2.8–11.7 years to mature from half-grown juveniles depending on location. Estimated adult life expectancies were 5.2 years at CMvD and 10.0 years at Surville Cliffs. Small juvenile snails experienced the highest mortality, and snails that moved between food plants experienced increased mortality. These results are discussed in relation to conservation management.     

Combining animal movements and behavioural data to detect behavioural states

Animal movement paths show variation in space caused by qualitative shifts in behaviours. I present a method that (1) uses both movement path data and ancillary sensor data to detect natural breakpoints in animal behaviour and (2) groups these segments into different behavioural states. The method can also combine analyses of different path segments or paths from different individuals. It does not assume any underlying movement mechanism. I give an example with simulated data. I also show the effects of random variation, # of states and # of segments on this method. I present a case study of a fisher movement path spanning 8 days, which shows four distinct behavioural states divided into 28 path segments when only turning angles and speed were considered. When accelerometer data were added, the analysis shows seven distinct behavioural states divided into 41 path segments.     

Atrial fibrosis in a chronic murine model of obstructive sleep apnea: mechanisms and prevention by mesenchymal stem cells

Background

OSA increases atrial fibrillation (AF) risk and is associated with poor AF treatment outcomes. However, a causal association is not firmly established and the mechanisms involved are poorly understood. The aims of this work were to determine whether chronic obstructive sleep apnea (OSA) induces an atrial pro-arrhythmogenic substrate and to explore whether mesenchymal stem cells (MSC) are able to prevent it in a rat model of OSA.

Methods

A custom-made setup was used to mimic recurrent OSA-like airway obstructions in rats. OSA-rats (n = 16) were subjected to 15-second obstructions, 60 apneas/hour, 6 hours/day during 21 consecutive days. Sham rats (n = 14) were placed in the setup but no obstructions were applied. In a second series of rats, MSC were administered to OSA-rats and saline to Sham-rats. Myocardial collagen deposit was evaluated in Picrosirius-red stained samples. mRNA expression of genes involved in collagen turnover, inflammation and oxidative stress were quantified by real time PCR. MMP-2 protein levels were quantified by Western Blot.

Results

A 43% greater interstitial collagen fraction was observed in the atria, but not in the ventricles, of OSA-rats compared to Sham-rats (Sham 8.32 ± 0.46% vs OSA 11.90 ± 0.59%, P < 0.01). Angiotensin-I Converting Enzyme (ACE) and Interleukin 6 (IL-6) expression were significantly increased in both atria, while Matrix Metalloproteinase-2 (MMP-2) expression was decreased. MSC administration blunted OSA-induced atrial fibrosis (Sham + Saline 8.39 ± 0.56% vs OSA + MSC 9.57 ± 0.31%, P = 0.11), as well as changes in MMP-2 and IL-6 expression. Interleukin 1-β (IL-1β) plasma concentration correlated to atrial but not ventricular fibrosis. Notably, a 2.5-fold increase in IL-1β plasma levels was observed in the OSA group, which was prevented in rats receiving MSC.

Conclusions

OSA induces selective atrial fibrosis in a chronic murine model, which can be mediated in part by the systemic and local inflammation and by decreased collagen-degradation. MSCs transplantation prevents atrial fibrosis, suggesting that these stem cells could counterbalance inflammation in OSA.     

Cross-species toxicogenomic analyses and phenotypic anchoring in response to groundwater low-level pollution

Background

Comparison of toxicogenomic data facilitates the identification of deregulated gene patterns and maximizes health risk prediction in human.

Results

Here, we performed phenotypic anchoring on the effects of acute exposure to low-grade polluted groundwater using mouse and zebrafish. Also, we evaluated two windows of chronic exposure in mouse, starting in utero and at the end of lactation. Bioinformatic analysis of livers microarray data showed that the number of deregulated biofunctions and pathways is higher after acute exposure, compared to the chronic one. It also revealed specific profiles of altered gene expression in all treatments, pointing to stress response/mitochondrial pathways as major players of environmental toxicity. Of note, dysfunction of steroid hormones was also predicted by bioinformatic analysis and verified in both models by traditional approaches, serum estrogens measurement and vitellogenin mRNA determination in mice and zebrafish, respectively.

Conclusions

In our report, phenotypic anchoring in two vertebrate model organisms highlights the toxicity of low-grade pollution, with varying susceptibility based on exposure window. The overlay of zebrafish and mice deregulated pathways, more than single genes, is useful in risk identification from chemicals implicated in the observed effects.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1067) contains supplementary material, which is available to authorized users.     

Suitable Chemical Properties of Animal Manure Compost to Facilitate Pb Immobilization in Soil

Chemical immobilization using animal manure compost is one of the most useful for low-cost, in-situ soil remediation techniques. The present study aimed to determine suitable chemical properties of animal manure compost to facilitate lead (Pb) immobilization in soil. The level of mobile Pb in soil amended with swine compost was higher than that amended with cattle compost during the early stage of incubation. However, the level of mobile Pb was almost the same in soil amended with both types of compost on day 184 of incubation. The ratio of the residual fraction after sequential extraction was enhanced in soil amended with both types of compost, particularly swine compost. X-ray diffractometer (XRD) results demonstrated the precipitation of Pb phosphate minerals, such as pyromorphite, in Pb-sorbed composts, particularly swine compost. Amendment using swine compost could reduce Pb solubility even when it had a high content of water-soluble organic matter because it significantly lowered Pb phase solubility. The amendment with swine compost improved plant growth and microbial activity. This study suggests that composts with high phosphorus (P) content are suitable for Pb immobilization amendment even if they have a high water-soluble organic matter content.     

正加速度应激致心脑损伤的动物实验研究综述

正加速度（ positive acceleration ,＋Gz）作用下机体的心脑功能防护是航空航天医学领域重点关注的课题。＋Gz作用致机体心脑等重要生命脏器损伤的特点和机制有待深入研究。本文就国内外有关＋Gz作用致实验动物心脑损伤及其机制的研究文献进行综述。     

植物亲缘地理学的研究现状与发展趋势

新生代以来剧烈的地质和气候变化,特别是第四纪冰期和间冰期的反复交错对温带植物类群的地理分布格局、种群结构和物种分化造成了深刻影响。近20年来,随着分子标记技术的发展和分析方法的成熟,植物亲缘地理学利用基因谱系关系和在种群中的时空分布来追溯种群的进化历史,在探讨植物类群对地质气候变迁的响应以及种群分化的历史成因等方面开展了大量工作,取得了一些重要进展。在取得这些成绩的同时,作者也注意到了被研究者所忽略的一些问题。试图对这些问题进行初步的总结,着重于分析方法和几个常用软件的使用,并对今后的发展趋势进行了展望。     

Influence of gene flow on divergence dating – implications for the speciation history of Takydromus grass lizards

Dating the time of divergence and understanding speciation processes are central to the study of the evolutionary history of organisms but are notoriously difficult. The difficulty is largely rooted in variations in the ancestral population size or in the genealogy variation across loci. To depict the speciation processes and divergence histories of three monophyletic Takydromus species endemic to Taiwan, we sequenced 20 nuclear loci and combined with one mitochondrial locus published in GenBank. They were analysed by a multispecies coalescent approach within a Bayesian framework. Divergence dating based on the gene tree approach showed high variation among loci, and the divergence was estimated at an earlier date than when derived by the species‐tree approach. To test whether variations in the ancestral population size accounted for the majority of this variation, we conducted computer inferences using isolation‐with‐migration (IM) and approximate Bayesian computation (ABC) frameworks. The results revealed that gene flow during the early stage of speciation was strongly favoured over the isolation model, and the initiation of the speciation process was far earlier than the dates estimated by gene‐ and species‐based divergence dating. Due to their limited dispersal ability, it is suggested that geographical isolation may have played a major role in the divergence of these Takydromus species. Nevertheless, this study reveals a more complex situation and demonstrates that gene flow during the speciation process cannot be overlooked and may have a great impact on divergence dating. By using multilocus data and incorporating Bayesian coalescence approaches, we provide a more biologically realistic framework for delineating the divergence history of Takydromus.