The effects of species properties and community context on establishment success

Understanding whether factors important for species establishment in a local community are predictable or context‐ dependent is key for determining the features that affect community stability and species coexistence. A major challenge for scientists addressing this question is that natural systems are complex. This makes it difficult to test multiple properties of species and features of the resident community simultaneously to determine what factors are most important for establishment success of a species into a novel community. We used the model aquatic system inside the leaves of the pitcher plant Sarracenia purpurea to test whether properties predicted to be important for establishment success of a species (initial density, competitive ability, body size) are generalizable across communities varying in resource availability and the presence of a top predator. For intermediate trophic‐level species, we found that both competitive dominance and initial density were important for establishment success. Although a less competitive species was also able to successfully establish in the communities, high resource availability and high initial density were important for its establishment success. Body size of the introduced species, although correlated with competitive ability, was not an important characteristic for establishment success. The presence of a top predator significantly decreased the densities of the introduced species when resources were low, but did not completely inhibit establishment success. The relative importance of each of these factors, and interactions among them, could not have been discerned through single hypothesis testing. The results from this work show the need for detailed experiments that focus on combinations of factors to understand if mechanisms determining community assembly and species establishment can be generalized across systems.     

Maternal genealogical patterns of chicken breeds sampled in Europe

The aim of this study was to investigate the maternal genealogical pattern of chicken breeds sampled in Europe. Sequence polymorphisms of 1256 chickens of the hypervariable region (D‐loop) of mitochondrial DNA (mtDNA) were used. Median‐joining networks were constructed to establish evolutionary relationships among mtDNA haplotypes of chickens, which included a wide range of breeds with different origin and history. Chicken breeds which have had their roots in Europe for more than 3000 years were categorized by their founding regions, encompassing Mediterranean type, East European type and Northwest European type. Breeds which were introduced to Europe from Asia since the mid‐19th century were classified as Asian type, and breeds based on crossbreeding between Asian breeds and European breeds were classified as Intermediate type. The last group, Game birds, included fighting birds from Asia. The classification of mtDNA haplotypes was based on Liu et al.'s (2006) nomenclature. Haplogroup E was the predominant clade among the European chicken breeds. The results showed, on average, the highest number of haplotypes, highest haplotype diversity, and highest nucleotide diversity for Asian type breeds, followed by Intermediate type chickens. East European and Northwest European breeds had lower haplotype and nucleotide diversity compared to Mediterranean, Intermediate, Game and Asian type breeds. Results of our study support earlier findings that chicken breeds sampled in Europe have their roots in the Indian subcontinent and East Asia. This is consistent with historical and archaeological evidence of chicken migration routes to Europe.     

Organic anions facilitate the mobilization of soil organic phosphorus and its subsequent lability to phosphatases

Plant and Soil - Organic anions commonly released from plant roots and microorganisms are widely reported to mobilize soil phosphorus (P). We characterized soil organic P that was mobilized by...     

Hyaluronidase 1 and β-hexosaminidase have redundant functions in hyaluronan and chondroitin sulfate degradation

Hyaluronan (HA), a member of the glycosaminoglycan (GAG) family, is a critical component of the extracellular matrix. A model for HA degradation that invokes the activity of both hyaluronidases and exoglycosidases has been advanced. However, no in vivo studies have been done to determine the extent to which these enzymes contribute to HA breakdown. Herein, we used mouse models to investigate the contributions of the endoglycosidase HYAL1 and the exoglycosidase β-hexosaminidase to the lysosomal degradation of HA. We employed histochemistry and fluorophore-assisted carbohydrate electrophoresis to determine the degree of HA accumulation in mice deficient in one or both enzyme activities. Global HA accumulation was present in mice deficient in both enzymes, with the highest levels found in the lymph node and liver. Chondroitin, a GAG similar in structure to HA, also broadly accumulated in mice deficient in both enzymes. Accumulation of chondroitin sulfate derivatives was detected in mice deficient in both enzymes, as well as in β-hexosaminidase-deficient mice, indicating that both enzymes play a significant role in chondroitin sulfate breakdown. Extensive accumulation of HA and chondroitin when both enzymes are lacking was not observed in mice deficient in only one of these enzymes, suggesting that HYAL1 and β-hexosaminidase are functionally redundant in HA and chondroitin breakdown. Furthermore, accumulation of sulfated chondroitin in tissues provides in vivo evidence that both HYAL1 and β-hexosaminidase cleave chondroitin sulfate, but it is a preferred substrate for β-hexosaminidase. These studies provide in vivo evidence to support and extend existing knowledge of GAG breakdown.     

IAPs regulate the plasticity of cell migration by directly targeting Rac1 for degradation

Inhibitors of apoptosis proteins (IAPs) are a highly conserved class of multifunctional proteins. Rac1 is a well-studied Rho GTPase that controls numerous basic cellular processes. While the regulation of nucleotide binding to Rac1 is well understood, the molecular mechanisms controlling Rac1 degradation are not known. Here, we demonstrate X-linked IAP (XIAP) and cellular IAP1 (c-IAP1) directly bind to Rac1 in a nucleotide-independent manner to promote its polyubiquitination at Lys147 and proteasomal degradation. These IAPs are also required for degradation of Rac1 upon CNF1 toxin treatment or RhoGDI depletion. Consistently, downregulation of XIAP or c-IAP1 by various strategies led to an increase in Rac1 protein levels in primary and tumour cells, leading to an elongated morphology and enhanced cell migration. Further, XIAP counteracts Rac1-dependent cellular polarization in the developing zebrafish hindbrain and promotes the delamination of neurons from the normal tissue architecture. These observations unveil an evolutionarily conserved role of IAPs in controlling Rac1 stability thereby regulating the plasticity of cell migration and morphogenesis.     

Rare copy number variants disrupt genes regulating vascular smooth muscle cell adhesion and contractility in sporadic thoracic aortic aneurysms and dissections

Thoracic aortic aneurysms and dissections (TAAD) cause significant morbidity and mortality, but the genetic origins of TAAD remain largely unknown. In a genome-wide analysis of 418 sporadic TAAD cases, we identified 47 copy number variant (CNV) regions that were enriched in or unique to TAAD patients compared to population controls. Gene ontology, expression profiling, and network analysis showed that genes within TAAD CNVs regulate smooth muscle cell adhesion or contractility and interact with the smooth muscle-specific isoforms of α-actin and β-myosin, which are known to cause familial TAAD when altered. Enrichment of these gene functions in rare CNVs was replicated in independent cohorts with sporadic TAAD (STAAD, n = 387) and inherited TAAD (FTAAD, n = 88). The overall prevalence of rare CNVs (23%) was significantly increased in FTAAD compared with STAAD patients (Fisher's exact test, p = 0.03). Our findings suggest that rare CNVs disrupting smooth muscle adhesion or contraction contribute to both sporadic and familial disease.     

A Bayesian Outlier Criterion to Detect SNPs under Selection in Large Data Sets

Background

The recent advent of high-throughput SNP genotyping technologies has opened new avenues of research for population genetics. In particular, a growing interest in the identification of footprints of selection, based on genome scans for adaptive differentiation, has emerged.

Methodology/Principal Findings

The purpose of this study is to develop an efficient model-based approach to perform Bayesian exploratory analyses for adaptive differentiation in very large SNP data sets. The basic idea is to start with a very simple model for neutral loci that is easy to implement under a Bayesian framework and to identify selected loci as outliers via Posterior Predictive P-values (PPP-values). Applications of this strategy are considered using two different statistical models. The first one was initially interpreted in the context of populations evolving respectively under pure genetic drift from a common ancestral population while the second one relies on populations under migration-drift equilibrium. Robustness and power of the two resulting Bayesian model-based approaches to detect SNP under selection are further evaluated through extensive simulations. An application to a cattle data set is also provided.

Conclusions/Significance

The procedure described turns out to be much faster than former Bayesian approaches and also reasonably efficient especially to detect loci under positive selection.     

The D153del mutation in GNB3 gene causes tissue specific signalling patterns and an abnormal renal morphology in Rge chickens

Background

The GNB3 gene is expressed in cone but not rod photoreceptors of vertebrates, where it acts as the β transducin subunit in the colour visual transduction process. A naturally occurring mutation ‘D153del’ in the GNB3 gene causes the recessively inherited blinding phenotype retinopathy globe enlarged (rge) disease in chickens. GNB3 is however also expressed in most other vertebrate tissues suggesting that the D153del mutation may exert pathological effects that outlie from eye.

Principal Findings

Recombinant studies in COS-7 cells that were transfected with normal and mutant recombinant GNB3 constructs and subjected to cycloheximide chase showed that the mutant GNB3d protein had a much shorter half life compared to normal GNB3. GNB3 codes for the Gβ3 protein subunit that, together with different Gγ and Gα subunits, activates and regulates phosphorylation cascades in different tissues. As expected, the relative levels of cGMP and cAMP secondary messengers and their activated kinases such as MAPK, AKT and GRK2 were also found to be altered significantly in a tissue specific manner in rge chickens. Histochemical analysis on kidney tissue sections, from rge homozygous affected chickens, showed the chickens had enlargement of the glomerular capsule, causing glomerulomegaly and tubulointerstitial inflammation whereas other tissues (brain, heart, liver, pancreas) were unaffected.

Significance

These findings confirm that the D153del mutation in GNB3 gene targets GNB3 protein to early degradation. Lack of GNB3 signalling causes reduced phosphorylation activity of ERK2 and AKT leading to severe pathological phenotypes such as blindness and renal abnormalities in rge chickens.     

Effects of cold on activity and exploration by wild house mice in a residential maze

Summary Wild house mice,Mus musculus, were bred in environments kept at 23 °C (warm-reared) or 3 °C (cold-reared). Males of the fourth generation in each condition were observed for 4 days in a residential maze with a central nest box and four arms radiating from it. One maze arm contained food, one contained water, and two were empty until Day 4, when one had soft (balsa) wood. Mice of each type were run in a maze at each temperature.Mice of all classes responded to the novel environment of the maze with a high rate of visiting the arms on Day 1. The novel presence of balsa wood also provoked extra visits to the arm that contained it, and a longer stay in that arm on Day 4 than on Day 3. Visits to the arms were fewer in the cold than in the warm, and time spent in the arms was less.Cold-reared mice in the cold environment spent more time outside the nest on Day 1, that is, were more responsive to novelty than were the warmreared. Hence for the cold-reared mice the competitive balance between exploring and energy conservation was altered. This difference, we suggest, is an aspect of cold-adaptation.These experiments were done in part while JLW held an award from the National Science Foundation under the US/Australia Agreement for Scientific Cooperation. We are also grateful to Rhondda G. Dickson for help with the statistical analysis.