Invasion by mobile aquatic consumers enhances secondary production and increases top-down control of lower trophic levels

Increased biological diversity due to invasion by non-indigenous species (NIS) is a global phenomenon with potential effects on trophic interactions and ecosystem processes in the invaded habitat. We assessed the effects of resource availability and invasion of three non-indigenous invertebrate grazers (two crustaceans and a snail) on secondary production, relative dominance of NIS grazers and resource depletion in experimental freshwater mesocosms. The relative dominance of NIS grazers increased with increasing initial resource availability, although the effect was largest for one of the three species. The effect was due to the fact that all the included non-indigenous grazers were able to expand their populations quickly in response to resource addition. For the most dominating species, the increased grazer diversity due to invasion in turn resulted in higher production of grazer biomass and a more efficient depletion of the periphyton resource. The effect was largest at high initial resource availability, where NIS dominance was most pronounced. Our results show that an invasion-induced increase in species diversity can increase resource depletion and consequently production, but that the effect depends on identity of the introduced species. The results also suggest that properties of the recipient system, such as resource availability, can modulate ecosystem effects of NIS by affecting invader success and dominance.     

Cloning and characterization of the trout perforin

The pore-forming protein, perforin is one of the effectors of cell-mediated killing. A perforin cDNA clone was isolated from rainbow trout (Oncorhynchus mykiss) after screening of a spleen cDNA library. The full-length cDNA is 2070 bp in size, encoding for a polypeptide of 589 amino acids. The predicted amino acid sequence of the trout perforin is 64, 58 and 40% identical to those of Japanese flounder, zebrafish and human perforins, respectively. Although its membrane attack complex/perforin (MACPF) domain is conserved, trout perforin shows low homology to human and trout terminal complement components (C6, C7, C8 and C9), ranging from 19 to 26% identity. Expression analysis reveals that the trout perforin gene is expressed in the blood, brain, heart, kidney, intestine and spleen. Phylogenetic analysis of proteins which belong to the MACPF superfamily clusters the trout perforin in the same group with other known perforins.     

A Genome Wide Meta-Analysis Study for Identification of Common Variation Associated with Breast Cancer Prognosis

Objective

Genome wide association studies (GWAs) of breast cancer mortality have identified few potential associations. The concordance between these studies is unclear. In this study, we used a meta-analysis of two prognostic GWAs and a replication cohort to identify the strongest associations and to evaluate the loci suggested in previous studies. We attempt to identify those SNPs which could impact overall survival irrespective of the age of onset.

Methods

To facilitate the meta-analysis and to refine the association signals, SNPs were imputed using data from the 1000 genomes project. Cox-proportional hazard models were used to estimate hazard ratios (HR) in 536 patients from the POSH cohort (Prospective study of Outcomes in Sporadic versus Hereditary breast cancer) and 805 patients from the HEBCS cohort (Helsinki Breast Cancer Study). These hazard ratios were combined using a Mantel-Haenszel fixed effects meta-analysis and a p-value threshold of 5×10⁻⁸ was used to determine significance. Replication was performed in 1523 additional patients from the POSH study.

Results

Although no SNPs achieved genome wide significance, three SNPs have significant association in the replication cohort and combined p-values less than 5.6×10⁻⁶. These SNPs are; rs421379 which is 556 kb upstream of ARRDC3 (HR = 1.49, 95% confidence interval (CI) = 1.27–1.75, P = 1.1×10⁻⁶), rs12358475 which is between ECHDC3 and PROSER2 (HR = 0.75, CI = 0.67–0.85, P = 1.8×10⁻⁶), and rs1728400 which is between LINC00917 and FOXF1.

Conclusions

In a genome wide meta-analysis of two independent cohorts from UK and Finland, we identified potential associations at three distinct loci. Phenotypic heterogeneity and relatively small sample sizes may explain the lack of genome wide significant findings. However, the replication at three SNPs in the validation cohort shows promise for future studies in larger cohorts. We did not find strong evidence for concordance between the few associations highlighted by previous GWAs of breast cancer survival and this study.     

Parietal lobe variation in cercopithecid endocasts

In extant primates, the posterior parietal cortex is involved in visuospatial integration, attention, and eye‐hand coordination, which are crucial functions for foraging and feeding behaviors. Paleoneurology studies brain evolution through the analysis of endocasts, that is molds of the inner surface of the braincase. These may preserve imprints of cortical structures, such as sulci, which might be of interest for locating the boundaries of major cortical regions. Old World monkeys (Cercopithecidae) represent an interesting zoological group for evolutionary studies, because of their diverse ecologies and locomotor behaviors. In this study, we quantify parietal lobe variation within the cercopithecid family, in a sample of 30 endocasts including 11 genera and 17 species, by combining landmark‐based and landmark‐free geometric morphometric analyses. More specifically, we quantitatively assess variation of the parietal proportions based on landmarks placed on reliable anatomical references and of parietal lobe surface morphology through deformation‐based methods. The main feature associated with the cercopithecid endocranial variation regards the inverse proportions of parietal and occipital lobes, with colobines, Theropithecus, and Papio displaying relatively larger parietal lobes and smaller occipital lobes compared with cercopithecins. The parietal surface is anteroposteriorly longer and mediolaterally flatter in colobines, while longitudinally shorter but laterally bulging in baboons. Large parietal lobes in colobines and baboons are likely to be independent evolutionary traits, and not necessarily associated with analogous functions or morphogenetic mechanisms.     

Fungal‐host diversity among mycoheterotrophic plants increases proportionally to their fungal‐host overlap

The vast majority of plants obtain an important proportion of vital resources from soil through mycorrhizal fungi. Generally, this happens in exchange of photosynthetically fixed carbon, but occasionally the interaction is mycoheterotrophic, and plants obtain carbon from mycorrhizal fungi. This process results in an antagonistic interaction between mycoheterotrophic plants and their fungal hosts. Importantly, the fungal‐host diversity available for plants is restricted as mycoheterotrophic interactions often involve narrow lineages of fungal hosts. Unfortunately, little is known whether fungal‐host diversity may be additionally modulated by plant–plant interactions through shared hosts. Yet, this may have important implications for plant competition and coexistence. Here, we use DNA sequencing data to investigate the interaction patterns between mycoheterotrophic plants and arbuscular mycorrhizal fungi. We find no phylogenetic signal on the number of fungal hosts nor on the fungal hosts shared among mycoheterotrophic plants. However, we observe a potential trend toward increased phylogenetic diversity of fungal hosts among mycoheterotrophic plants with increasing overlap in their fungal hosts. While these patterns remain for groups of plants regardless of location, we do find higher levels of overlap and diversity among plants from the same location. These findings suggest that species coexistence cannot be fully understood without attention to the two sides of ecological interactions.     

Effects of predator exposure on baseline and stress-induced glucocorticoid hormone concentrations in pumpkinseed Lepomis gibbosus

We compared baseline and maximal cortisol concentrations between predator exposure and prey blood samples in pumpkinseed Lepomis gibbosus, captured using a standardised fishing event underneath osprey Pandion haliaetus nests and away from osprey nests. We did not detect differences in cortisol or glucose between sites. These findings suggest that predictable sources of predation risk may not confer stress-related costs in teleosts.     

Escherichia coli DnaE Polymerase Couples Pyrophosphatase Activity to DNA Replication

DNA Polymerases generate pyrophosphate every time they catalyze a step of DNA elongation. This elongation reaction is generally believed as thermodynamically favoured by the hydrolysis of pyrophosphate, catalyzed by inorganic pyrophosphatases. However, the specific action of inorganic pyrophosphatases coupled to DNA replication in vivo was never demonstrated. Here we show that the Polymerase-Histidinol-Phosphatase (PHP) domain of Escherichia coli DNA Polymerase III α subunit features pyrophosphatase activity. We also show that this activity is inhibited by fluoride, as commonly observed for inorganic pyrophosphatases, and we identified 3 amino acids of the PHP active site. Remarkably, E. coli cells expressing variants of these catalytic residues of α subunit feature aberrant phenotypes, poor viability, and are subject to high mutation frequencies. Our findings indicate that DNA Polymerases can couple DNA elongation and pyrophosphate hydrolysis, providing a mechanism for the control of DNA extension rate, and suggest a promising target for novel antibiotics.     

Enrichment experiments and primary production at Sagres (SW Portugal)

Water was collected from the Sagres station (SW Portugal) in September 2002, at a site adjacent to the upwelling centre of Cabo São Vicente, during relaxation of upwelling conditions. Surface and depth samples were enriched with inorganic nutrients in order to evaluate their relative influence on the microalgal assemblage. Small-scale, short-term bioassays involved separate in vitro additions of nitrogen and phosphorus. Enrichments with nitrogen led to a general increase of primary production, suggesting nitrogen as the primary potential nutrient limiting microalgal growth during this period, as well as altering the relative microplanktonic composition in favour of diatoms.