Environmental drivers of sardine (Sardina pilchardus) in the Catalan Sea (NW Mediterranean Sea)

In the area surrounding the Ebro Delta, similar to the rest of the north-western Mediterranean Sea, the sardine (Sardina pilchardus), one of the most exploited small pelagic fishes, has suffered a decreasing trend in abundance and biomass in the last decade, with low values in evidence since 2007. The dependence of this species on environmental factors makes it vulnerable to environmental changes; consequently, the abundance of the species is highly variable. Using segmented regression, we evaluated the presence of discontinuities in the temporal pattern of the seasonally adjusted landings per unit effort (LPUE), which was used as a proxy for abundance, between 2000 and 2013. The results suggested a sudden increase in mid-2005, followed by a sharp decrease starting in 2006. A generalized additive mixed model (GAMM), incorporating the linear correlation structure, was used to identify relationships between the seasonally adjusted LPUE and trends of the Western Mediterranean Oscillation index (WeMOI), sea surface temperature (SST), salinity (SAL) and the Zonal and Meridional Currents (ZC and MC, respectively). The variance inflation factors (VIFs) were calculated between all environmental variables to avoid high-dimensional collinearities. The final GAMM, selected using the Akaike information criterion, indicated that positive WeMOI values, which favour the productivity of the area, along with SAL (at ca. 38) and a northward-flowing MC, favoured LPUE. Our results, obtained by applying a method in which variation due to season, non-linearity, autocorrelation and collinearity of the covariates was taken into account, provided further evidence of the dependence of the sardine population upon specific hydrographic variables.     

Development of thioquinazolinones,allosteric Chk1 kinase inhibitors

A high throughput screening campaign was designed to identify allosteric inhibitors of Chk1 kinase by testing compounds at high concentration. Activity was then observed at K_m for ATP and at near-physiological concentrations of ATP. This strategy led to the discovery of a non-ATP competitive thioquinazolinone series which was optimized for potency and stability. An X-ray crystal structure for the complex of our best inhibitor bound to Chk1 was solved, indicating that it binds to an allosteric site ～13 Å from the ATP binding site. Preliminary data is presented for several of these compounds.     

Comparing tree shapes: beyond symmetry

This paper describes two types of problems related to tree shapes, as well as algorithms that can be used to solve these problems. The first problem is that of comparing the similarity of the unlabelled shapes instead of merely their degree of balance, in a manner analogous to that routinely used to compare topologies for labelled trees. There are possible practical applications for this comparison, such as determining, based on tree shape similarity alone, whether the taxa in two phylogenies are likely to have a correspondence (e.g. hosts and parasites with high specificity). It is shown that tree balance is insufficient for this task and that standard measures of topological difference (Robinson–Foulds distances, SPR distances or retention indices of the matrices representing the trees, MRPs) can be easily adapted to the problem. The second type of problem is to determine whether taxa of uncertain matching unique to two different phylogenies could correspond to each other (e.g. the same species in larvae and adults of metamorphic animals, fossils known from different body parts). This second problem can be solved by either relabelling taxa in such a way that the number of consensus nodes is maximized, or relabelling taxa in such a way that the sum of the number of steps in the MRP of each tree mapped onto the other is minimum.     

The Spt-Ada-Gcn5 Acetyltransferase (SAGA) Complex in Aspergillus nidulans

A mutation screen in Aspergillus nidulans uncovered mutations in the acdX gene that led to altered repression by acetate, but not by glucose. AcdX of A. nidulans is highly conserved with Spt8p of Saccharomyces cerevisiae, and since Spt8p is a component of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) complex, the SAGA complex may have a role in acetate repression in A. nidulans. We used a bioinformatic approach to identify genes encoding most members of the SAGA complex in A. nidulans, and a proteomic analysis to confirm that most protein components identified indeed exist as a complex in A. nidulans. No apparent compositional differences were detected in mycelia cultured in acetate compared to glucose medium. The methods used revealed apparent differences between Yeast and A. nidulans in the deubiquitination (DUB) module of the complex, which in S. cerevisiae consists of Sgf11p, Sus1p, and Ubp8p. Although a convincing homologue of S. cerevisiae Ubp8p was identified in the A. nidulans genome, there were no apparent homologues for Sus1p and Sgf11p. In addition, when the SAGA complex was purified from A. nidulans, members of the DUB module were not co-purified with the complex, indicating that functional homologues of Sus1p and Sgf11p were not part of the complex. Thus, deubiquitination of H2B-Ub in stress conditions is likely to be regulated differently in A. nidulans compared to S. cerevisiae.     

Floral bagging differentially affects handling behaviours and single-visit pollen deposition by honey bees and native bees

1. Measurements of pollinator performance are crucial to pollination studies, enabling researchers to quantify the relative value of different pollinator species to plant reproduction. One of the most widely employed measures of pollinator performance is single-visit pollen deposition, the number of conspecific pollen grains deposited to a stigma after one pollinator visit. To ensure a pollen-free stigma, experimenters must first bag flowers before exposing them to a pollinator. 2. Bagging flowers, however, may unintentionally manipulate floral characteristics to which pollinators respond. In this study, we quantified the effect of bagging on nectar volume in watermelon (Citrullus lanatus) flowers, and how this affects pollinator performance and behaviour. 3. Experimental bagging resulted in roughly 30-fold increases in nectar volume relative to unmanipulated, open-pollinated field flowers after only a few hours. Honey bees, but not native bees, consistently displayed elevated handling times and single-visit pollen deposition on unmanipulated bagged flowers relative to those from which we removed nectar to mimic volumes in open-pollinated flowers. 4. Furthermore, we identify specific bee foraging behaviours during a floral visit that account for differences in pollen deposition, and how these differ between honey bees and native bees. 5. Our findings suggest that experimental bagging of flowers, without accounting for artificially accumulated nectar, can lead to biased estimates of pollinator performance in pollinator taxa that respond strongly to nectar volume. We advise that pollination studies be attentive to nectar secretion dynamics in their focal plant species to ensure unbiased estimates of pollinator performance across multiple pollinator species.