Phylogeny of the genus Merluccius based on mitochondrial and nuclear genes

Genus Merluccius is considered one of the most important groups within the Teleostei, and comprises 12 extant species distributed along the coasts of America, Europe and Africa, being its fisheries very important in these continents. Despite their noticeable economical importance for humans, to date the phylogeny of hakes has not been clearly established. In this study we used mitochondrial sequences (the ribosomal genes 12S rDNA and 16S rDNA, the coding gene cytochrome b and the control region) and the nuclear 5S rDNA conserved region in order to determine the phylogenetic and biogeographical relationships within the genus Merluccius. This is the first time that all the species of this genus recognized by the FAO are included in a phylogeny. Maximum Parsimony, Maximum Likelihood and Bayesian analyses of the mitochondrial sequences suggest that the geographical origin of the genus was the North Atlantic Ocean, and indicate that two main clades, early separated in the evolution, exist within the genus: one American (7 species) and one Euro-African (5 species). Among the American species, M. bilinearis seems to be the most ancient one, and the rise of the Panama Isthmus could act as a physical barrier leading to further processes of speciation. Within the Euro-African clade, successive events of geographical differentiation could explain the observed pattern of species distribution. Therefore, we propose both vicariant speciation and geographical dispersion as main mechanisms to explain the evolutionary history of the genus Merluccius.     

Sucrose regulated expression of a Ca2+-dependent protein kinase (TaCDPK1) gene in excised leaves of wheat.

Sucrose (Suc) can influence the expression of a large number of genes and thereby regulates many metabolic and developmental processes. However, the Suc sensing and the components of the ensuing signaling transduction pathway leading to the regulation of gene expression are not fully understood. We have shown that protein kinases and phosphatases are involved in the Suc induced expression of fructosyltransferase (FT) genes and fructan accumulation by an hexokinase independent pathway in wheat (Triticum aestivum). In the present study, using an RT-PCR based strategy, we have cloned a calcium-dependent protein kinase (TaCDPK1) cDNA that is upregulated during Suc treatment of excised wheat leaves. The deduced amino-acid sequence of CDPK1 has high sequence similarity (>70%) to known CDPKs from both monocots and dicots. Based on sequence homology, TaCDPK1 sequence shows a variable domain preceding a catalytic domain, an autoinhibitory function domain, and a C-terminal calmodulin-domain containing 4 EF-hand calcium-binding motifs, along with a N-myristoylation motif in the N-terminal variable domain. The recombinant Escherichia coli expressed TaCDPK1 was able to phosphorylate histone III-S in a calcium dependent manner in in vitro assays. The TaCDPK1 gene expression, as determined by quantitative RT-PCR, is induced by Suc and this effect is repressed by the inhibitors of the putative components of the Suc signal transduction pathway (calcium, Ser/Thr protein kinases and protein phosphatases). We propose that TaCDPK1 is involved in the Suc induced signaling pathway in wheat leaves.     

A comparison of methods for selecting non-target species for risk assessment of the biological control agent <Emphasis Type="Italic">Cotesia urabae</Emphasis>

A computer-based tool called PRONTI (priority ranking of non-target invertebrates) has been developed to aid the selection of non-target species (NTS) for pre-release testing with entomophagous biological control agents. To test whether PRONTI can improve NTS selection, we used it to produce a prioritised list of NTS for the agent Cotesia urabae Austin & Allen (Hymenoptera: Braconidae), and compared it with the original list that was produced before this species was released in New Zealand in 2011. While the two lists were similar, with five NTS occurring in the top nine of both lists, the remaining four NTS in the top nine of each list were different, primarily because the selection criteria used by the two methods were weighted differently (e.g., PRONTI put more weight on the likelihood of a NTS being exposed to the agent). Post-release testing has demonstrated that C. urabae is able to oviposit in two NTS that were ranked highly on both lists, suggesting both methods are useful for species selection. The main advantages of PRONTI were considered to be its ability to rank hundreds of NTS simultaneously, and to provide a body of information that can be used to both understand each NTS’ ranking and to justify more objectively the selection of NTS for pre-release testing.     

Automated identification of reference genes based on RNA-seq data

Background

Gene expression analyses demand appropriate reference genes (RGs) for normalization, in order to obtain reliable assessments. Ideally, RG expression levels should remain constant in all cells, tissues or experimental conditions under study. Housekeeping genes traditionally fulfilled this requirement, but they have been reported to be less invariant than expected; therefore, RGs should be tested and validated for every particular situation. Microarray data have been used to propose new RGs, but only a limited set of model species and conditions are available; on the contrary, RNA-seq experiments are more and more frequent and constitute a new source of candidate RGs.

Results

An automated workflow based on mapped NGS reads has been constructed to obtain highly and invariantly expressed RGs based on a normalized expression in reads per mapped million and the coefficient of variation. This workflow has been tested with Roche/454 reads from reproductive tissues of olive tree (Olea europaea L.), as well as with Illumina paired-end reads from two different accessions of Arabidopsis thaliana and three different human cancers (prostate, small-cell cancer lung and lung adenocarcinoma). Candidate RGs have been proposed for each species and many of them have been previously reported as RGs in literature. Experimental validation of significant RGs in olive tree is provided to support the algorithm.

Conclusion

Regardless sequencing technology, number of replicates, and library sizes, when RNA-seq experiments are designed and performed, the same datasets can be analyzed with our workflow to extract suitable RGs for subsequent PCR validation. Moreover, different subset of experimental conditions can provide different suitable RGs.

     

External Ca2+ regulates polycystin-2 (TRPP2) cation currents in LLC-PK1 renal epithelial cells

Polycystin-2 (PC2, TRPP2) is a nonselective cation channel whose dysfunction is associated with the onset of autosomal dominant polycystic kidney disease (ADPKD). PC2 contributes to Ca²⁺ transport and cell signaling in renal epithelia and other tissues. Little is known however, as to the external Ca²⁺ regulation of PC2 channel function. In this study, we explored the effect of external Ca²⁺ on endogenous PC2 in wild type LLC-PK1 renal epithelial cells. We obtained whole cell currents at different external Ca²⁺ concentrations, and observed that the basal whole cell conductance in normal Ca²⁺(1.2 mM), decreased by 30.2% in zero (nominal) Ca²⁺ and conversely, increased by 38% in high external Ca²⁺(6.2 mM). The high Ca²⁺-increased whole cell currents were completely inhibited by either PC2 gene silencing, or intracellular dialysis with active, but not denatured by boiling, PC2 antibody. Exposure of cells to high Ca²⁺ was also associated with relocation of PC2 to the plasma membrane. To explore whether a Ca²⁺ sensing receptor (CaSR) was implicated in the external Ca²⁺ modulation of PC2 currents, we tested the effect of the CaSR agonists, spermine and the calcimimetic R-568, which largely mimicked the effect of high Ca²⁺ under Ca²⁺-free conditions. The CaSR agonist gentamicin also increased the PC2 currents in the presence of normal Ca²⁺. The presence of CaSR was confirmed by immunocytochemistry, which partially colocalized with the intracellular PC2 protein, in an external Ca²⁺-dependent manner. The data support a novel Ca²⁺ sensing mechanism for PC2 expression and functional regulation in renal epithelial cells.     

Prey preferences and recent changes in diet of a breeding population of the Northern Goshawk Accipiter gentilis in Southwestern Europe

Capsule: Northern Goshawk Accipiter gentilis diet has changed significantly since the 1980s, probably due to changes in populations of preferred prey species.

Aims and methods: To assess changes to the breeding season diet of the Northern Goshawk in southwest Europe over three decades. We examined prey remains at and around nests and assessed avian prey availability using point count and line transect surveys.

Results: During 2008–11, Goshawks mainly ate birds, with Feral Pigeons Columba livia f. domestica being the most important prey species. Goshawks preferred prey of 100?400?g and forest prey species to non-forest species. Goshawk diet has changed significantly over recent decades: 22% of current prey items belong to species that were not part of the diet in the 1980s. We suggest that these dietary changes reflect changes in the abundance of prey species of the preferred size caused by changes in land use leading to an increase in forest cover, new prey species colonization and changes in the abundance and management of domestic prey.

Conclusion: This study emphasizes that major transformations occurring in agroforestry systems are affecting the main preferred prey of important forest predators, which may have consequences for conservation of both the predators and their prey.