Unravelling landscape variables with multiple approaches to overcome scarce species knowledge: a landscape genetic study of the slow worm

Landscape genetics was developed to detect landscape elements shaping genetic population structure, including the effects of fragmentation. Multifarious environmental variables can influence gene flow in different ways and expert knowledge is frequently used to construct friction maps. However, the extent of the migration and the movement of single individuals are frequently unknown, especially for non-model species, and friction maps only based on expert knowledge can be misleading. In this study, we used three different methods: isolation by distance (IBD), least-cost modelling and a strip-based approach to disentangle the human implication in the fragmentation process in the slow worm (Anguis fragilis), as well as the specific landscape elements shaping the genetic structure in a highly anthropized 16 km² area in Switzerland. Friction maps were constructed using expert opinion, but also based on the combination of all possible weightings for all landscape elements. The IBD indicated a significant effect of geographic distance on genetic differentiation. Further approaches demonstrated that highways and railways were the most important elements impeding the gene flow in this area. Surprisingly, we also found that agricultural areas and dense forests seemed to be used as dispersal corridors. These results confirmed that the slow worm has relatively unspecific habitat requirements. Finally, we showed that our models based on expert knowledge performed poorly compared to cautious analysis of each variable. This study demonstrated that landscape genetic analyses should take expert knowledge with caution and exhaustive analyses of each landscape element without a priori knowledge and different methods can be recommended.     

Soil‐nutrient availability under a global‐change scenario in a Mediterranean mountain ecosystem

Changes in rainfall availability will alter soil‐nutrient availability under a climate‐change scenario. However, studies have usually analyzed the effect of either drier or wetter soil conditions, despite the fact that both possibilities will coexist in many climatic regions of the world. Furthermore, its effect may vary across the different habitats of the ecosystem. We experimentally investigated the effect of three contrasting climatic scenarios on different carbon (C), nitrogen (N), and phosphorus (P) fractions in soil and microbial compartments among three characteristic habitats in a Mediterranean‐type ecosystem: forest, shrubland, and open areas. The climatic scenarios were dry summers, according to the 30% summer rainfall reduction projected in the Mediterranean; wet summer, simulating summer storms to reach the maximum historical records in the study area; and current climatic conditions (control). Sampling was replicated during two seasons (spring and summer) and 2 years. The climatic scenario did not affect the nutrient content in the litter layer. However, soil and microbial nutrients varied among seasons, habitats, and climatic scenarios. Soil‐nutrient fractions increased with lower soil‐moisture conditions (dry scenario and summer), whereas microbial nutrients increased under the wet summer scenario and spring. This pattern was consistent both studied years, although it was modulated by habitat, differences being lower with denser plant cover. Holm oak seedlings, used as live control of the experiment, tended to increase their N and P content (although not significantly) with water availability. Thus, the results support the idea that higher rainfall boosts microbial and plant‐nutrient uptake, and hence nutrient cycling. By contrast, a rainfall reduction leads to an accumulation of nutrients in the soil, increasing the risk of nutrient loss by leaching or erosion. These results show that the projected climate change will have significant effects on nutrient cycles, and therefore will have important implications on the ecosystem functioning.     

Latent membrane protein 1 is dispensable for Epstein-Barr virus replication in human embryonic kidney 293 cells

Epstein Barr Virus (EBV) replicates in oral epithelial cells and gains entry to B-lymphocytes. In B-lymphocytes, EBV expresses a restricted subset of genes, the Latency III program, which converts B-lymphocytes to proliferating lymphoblasts. Latent Membrane Protein 1 (LMP1) and the other Latency III associated proteins are also expressed during virus replication. LMP1 is essential for virus replication and egress from Akata Burkitt Lymphoma cells, but a role in epithelial cell replication has not been established. Therefore, we have investigated whether LMP1 enhances EBV replication and egress from HEK293 cells, a model epithelial cell line used for EBV recombinant molecular genetics. We compared wild type (wt) and LMP1-deleted (LMP1Δ) EBV bacterial artificial chromosome (BAC) based virus replication and egress from HEK293. Following EBV immediate early Zta protein induction of EBV replication in HEK293 cells, similar levels of EBV proteins were expressed in wt- and LMP1Δ-infected HEK293 cells. LMP1 deletion did not impair EBV replication associated DNA replication, DNA encapsidation, or mature virus release. Indeed, virus from LMP1Δ-infected HEK293 cells was as infectious as EBV from wt EBV infected HEK cells. Trans-complementation with LMP1 reduced Rta expression and subsequent virus production. These data indicate that LMP1 is not required for EBV replication and egress from HEK293 cells.     

Clioquinol Synergistically Augments Rescue by Zinc Supplementation in a Mouse Model of Acrodermatitis Enteropathica

Background

Zinc deficiency due to poor nutrition or genetic mutations in zinc transporters is a global health problem and approaches to providing effective dietary zinc supplementation while avoiding potential toxic side effects are needed.

Methods/Principal Findings

Conditional knockout of the intestinal zinc transporter Zip4 (Slc39a4) in mice creates a model of the lethal human genetic disease acrodermatitis enteropathica (AE). This knockout leads to acute zinc deficiency resulting in rapid weight loss, disrupted intestine integrity and eventually lethality, and therefore provides a model system in which to examine novel approaches to zinc supplementation. We examined the efficacy of dietary clioquinol (CQ), a well characterized zinc chelator/ionophore, in rescuing the Zip4 ^{intest KO} phenotype. By 8 days after initiation of the knockout neither dietary CQ nor zinc supplementation in the drinking water was found to be effective at improving this phenotype. In contrast, dietary CQ in conjunction with zinc supplementation was highly effective. Dietary CQ with zinc supplementation rapidly restored intestine stem cell division and differentiation of secretory and the absorptive cells. These changes were accompanied by rapid growth and dramatically increased longevity in the majority of mice, as well as the apparent restoration of the homeostasis of several essential metals in the liver.

Conclusions

These studies suggest that oral CQ (or other 8-hydroxyquinolines) coupled with zinc supplementation could provide a facile approach toward treating zinc deficiency in humans by stimulating stem cell proliferation and differentiation of intestinal epithelial cells.     

Effects of age,territoriality and breeding on survival of Bonelli’s Eagle Aquila fasciata

Survival typically contributes most to population trends in long‐lived birds and its accurate estimation is therefore vital for population management and conservation. We evaluated the effects of age, territoriality and reproduction on survival in Bonelli’s Eagle Aquila fasciata through multistate capture‐mark‐recapture analyses on a long‐term dataset. Monitoring was carried out in southeast France (1990–2008) and involved the surveying of territorial Eagles, the marking of fledged chicks, and the recording of resightings and recoveries of marked non‐territorial and territorial birds. Survival improved with age, but territoriality was not retained in the best model; yearly survival was estimated at 0.479 for fledglings (to 1 year of age), 0.570 for 1‐ and 2‐year‐olds, and 0.870 for 3‐year‐old and older individuals. The second best model supported a further increase in survival from 3‐year‐olds (0.821) to older individuals (0.880). In the third best supported model, territoriality enhanced survival, but only in 2‐year‐olds (0.632 vs. 0.562 for non‐territorial). We found no correlation between the previous breeding stage and future survival, consistent with the long lifespan of the study species. Nevertheless, 4‐year‐old and older successful breeders were more likely to breed the following year than failed adult breeders (0.869 vs. 0.582), suggesting that the cost of reproduction is small in comparison with the variation in quality among individuals or their territories.     

A new Late Jurassic turtle from Spain: phylogenetic implications,taphonomy and palaeoecology

Abstract: The Jurassic was an important period in the evolution of Testudinata and encompasses the origin of many clades, and this is especially true of Jurassic turtles from Western Europe. A new genus and species of Late Jurassic turtle, Hispaniachelys prebetica gen. et sp. nov. from the upper Oxfordian of the Prebetic (Southern Spain), is described on the basis of postcranial material. The specimen is the only known tetrapod from the Mesozoic of the Prebetic and the oldest turtle from southern Europe. A mosaic of characters indicates this is a new genus: it displays basal features including dorsal epiplastral processes/reduced cleithra, no medial contact of the extragulars and a long first thoracic rib, alongside derived characters including an absence of mesoplastra and the vertebral 3/4 sulcus crossing neural 5. The phylogenetic position of the new taxon is hard to resolve, and it might be either a paracryptodire or a basal testudine, but it is distinct from Plesiochelys. A complex taphonomic history is shown by a range of overlying grazing traces and bioerosion on the carapace. The carapace was subsequently overturned and buried ventrally up, terminating grazing activity, and was then bored by sponges before final burial. Scanning electron microscopy reveals phosphatic microspheroids associated with bacterial decay in the vascular cavities of the cancellous bone, suggesting the carapace may have acted as a closed microenvironment in which decay‐derived authigenic minerals formed.     

Crystal structure of human estrogen-related receptor alpha in complex with a synthetic inverse agonist reveals its novel molecular mechanism

Inverse agonists of the constitutively active human estrogen-related receptor alpha (ERRalpha, NR3B1) are of potential interest for several disease indications (e.g. breast cancer, metabolic diseases, or osteoporosis). ERRalpha is constitutively active, because its ligand binding pocket (LBP) is practically filled with side chains (in particular with Phe(328), which is replaced by Ala in ERRbeta and ERRgamma). We present here the crystal structure of the ligand binding domain of ERRalpha (containing the mutation C325S) in complex with the inverse agonist cyclohexylmethyl-(1-p-tolyl-1H-indol-3-ylmethyl)-amine (compound 1a), to a resolution of 2.3A(.) The structure reveals the dramatic multiple conformational changes in the LBP, which create the necessary space for the ligand. As a consequence of the new side chain conformation of Phe(328) (on helix H3), Phe(510)(H12) has to move away, and thus the activation helix H12 is displaced from its agonist position. This is a novel mechanism of H12 inactivation, different from ERRgamma, estrogen receptor (ER) alpha, and ERbeta. H12 binds (with a surprising binding mode) in the coactivator groove of its ligand binding domain, at a similar place as a coactivator peptide. This is in contrast to ERRgamma but resembles the situation for ERalpha (raloxifene or 4-hydroxytamoxifen complexes). Our results explain the novel molecular mechanism of an inverse agonist for ERRalpha and provide the basis for rational drug design to obtain isotype-specific inverse agonists of this potential new drug target. Despite a practically filled LBP, the finding that a suitable ligand can induce an opening of the cavity also has broad implications for other orphan nuclear hormone receptors (e.g. the NGFI-B subfamily).