Body size and group size of Cuban tree frog (<Emphasis Type="Italic">Osteopilus septentrionalis</Emphasis>) tadpoles influence their escape behaviour

Tadpoles risk attack from both aquatic and aerial predators. We investigated how body size and group size influenced the behaviour of tadpoles before and during a predatory attack from above to test the predictions of the theoretical economic escape model. We examined escape (swimming) response of small and large Cuban tree frog (Osteopilus septentrionalis) tadpoles kept under three density treatments and predicted that increased group size, body size and depth in the water column would all reduce perceived risk and, therefore, escape responses to simulated predation. Compared with the lower density groups, tadpoles in higher density groups moved shorter distances, and many individuals did not even move away in response to being touched. Contrary to our predictions based on the economic escape model, smaller tadpoles (which should be more vulnerable to a greater suite of predators) were less reactive than larger tadpoles, and this result may reflect different costs of escape. Finally, although tadpoles might be exposed to a wider range of predator species (aerial as well as aquatic predators), we found no effect of initial depth on escape responses. In conclusion, it appears that the main benefit of increased group density in O. septentrionalis tadpoles is likely to be predator dilution, and that variation in densities of tadpoles influences the escape behaviour of individual tadpoles, regardless of tadpole size.     

Key challenges for the creation and maintenance of specialist protein resources

As the volume of data relating to proteins increases, researchers rely more and more on the analysis of published data, thus increasing the importance of good access to these data that vary from the supplemental material of individual articles, all the way to major reference databases with professional staff and long‐term funding. Specialist protein resources fill an important middle ground, providing interactive web interfaces to their databases for a focused topic or family of proteins, using specialized approaches that are not feasible in the major reference databases. Many are labors of love, run by a single lab with little or no dedicated funding and there are many challenges to building and maintaining them. This perspective arose from a meeting of several specialist protein resources and major reference databases held at the Wellcome Trust Genome Campus (Cambridge, UK) on August 11 and 12, 2014. During this meeting some common key challenges involved in creating and maintaining such resources were discussed, along with various approaches to address them. In laying out these challenges, we aim to inform users about how these issues impact our resources and illustrate ways in which our working together could enhance their accuracy, currency, and overall value. Proteins 2015; 83:1005–1013. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.     

Two new species of Ginkgoales from the Middle Jurassic of Mexico

This paper reports two new species of Ginkgoales collected from the Cañada Alejandro and Río Ñumi (Zorrillo and Zorrillo–Taberna Undifferentiated Formations, Middle Jurassic). Thirty-one fossils were selected and compared with 14 species from different localities. A numerical taxonomy analysis was performed through a data matrix formed by 15 characters. Results indicate an important speciation process of the Ginkgoales during the Jurassic in the southeast of Mexico. New evidence suggests the existence of eight species from the Ginkgoidium Yokoyama, 1889 and Sphenobaiera (Florin) Harris and Millington, 1974 genera and two new species Ginkgoidiumnundichii Velasco-de León, Lozano-Carmona, Flores, Martínez and Silva and Sphenobaieramixteca Velasco-de León, Lozano-Carmona, Flores, Martínez and Silva     

THO2, a core member of the THO/TREX complex,is required for microRNA production in Arabidopsis

The THO/TREX complex mediates transport of nascent mRNAs from the nucleus towards the cytoplasm in animals, and has a role in small interfering RNA‐dependent processes in plants. Here we describe five mutant alleles of Arabidopsis thaliana THO2, which encodes a core subunit of the plant THO/TREX complex. tho2 mutants present strong developmental defects resembling those in plants compromised in microRNA (miRNA) activity. In agreement, not only were the levels of siRNAs reduced in tho2 mutants, but also those of mature miRNAs. As a consequence, a feedback mechanism is triggered, increasing the amount of miRNA precursors, and finally causing accumulation of miRNA‐targeted mRNAs. Yeast two‐hybrid experiments and confocal microscopy showed that THO2 does not appear to interact with any of the known miRNA biogenesis components, but rather with the splicing machinery, implying an indirect role of THO2 in small RNA biogenesis. Using an RNA immunoprecipitation approach, we found that THO2 interacts with miRNA precursors, and that tho2 mutants fail to recruit such precursors into the miRNA‐processing complex, explaining the reduction in miRNA production in this mutant background. We also detected alterations in the splicing pattern of genes encoding serine/arginine‐rich proteins in tho2 mutants, supporting a previously unappreciated role of the THO/TREX complex in alternative splicing.     

Comparison of broad-scope assays of nucleotide sugar-dependent glycosyltransferases

Glycosyltransferases (GTs) are abundant in nature and diverse in their range of substrates. Application of GTs is, however, often complicated by their narrow substrate specificity. GTs with tailored specificities are highly demanded for targeted glycosylation reactions. Engineering of such GTs is, however, restricted by lack of practical and broad-scope assays currently available. Here we present an improvement of an inexpensive and simple assay that relies on the enzymatic detection of inorganic phosphate cleaved from nucleoside phosphate products released in GT reactions. This phosphatase-coupled assay (PCA) is compared with other GT assays: a pH shift assay and a commercially available immunoassay in Escherichia coli cell-free extract (CE). Furthermore, we probe PCA with three GTs with different specificities. Our results demonstrate that PCA is a versatile and apparently general GT assay with a detection limit as low as 1 mU. The detection limit of the pH shift assay is roughly 4 times higher. The immunoassay, by contrast, detected only nucleoside diphosphates (NDPs) but had the lowest detection limit. Compared with these assays, PCA showed superior robustness and, therefore, appears to be a suitable general screening assay for nucleotide sugar-dependent GTs.     

Guanine Nucleotide Exchange Factor αPIX Leads to Activation of the Rac 1 GTPase/Glycogen Phosphorylase Pathway in Interleukin (IL)-2-stimulated T Cells

Recently, we have reported that the active form of Rac 1 GTPase binds to the glycogen phosphorylase muscle isoform (PYGM) and modulates its enzymatic activity leading to T cell proliferation. In the lymphoid system, Rac 1 and in general other small GTPases of the Rho family participate in the signaling cascades that are activated after engagement of the T cell antigen receptor. However, little is known about the IL-2-dependent Rac 1 activator molecules. For the first time, a signaling pathway leading to the activation of Rac 1/PYGM in response to IL-2-stimulated T cell proliferation is described. More specifically, αPIX, a known guanine nucleotide exchange factor for the small GTPases of the Rho family, preferentially Rac 1, mediates PYGM activation in Kit 225 T cells stimulated with IL-2. Using directed mutagenesis, phosphorylation of αPIX Rho-GEF serines 225 and 488 is required for activation of the Rac 1/PYGM pathway. IL-2-stimulated serine phosphorylation was corroborated in Kit 225 T cells cultures. A parallel pharmacological and genetic approach identified PKCθ as the serine/threonine kinase responsible for αPIX serine phosphorylation. The phosphorylated state of αPIX was required to activate first Rac 1 and subsequently PYGM. These results demonstrate that the IL-2 receptor activation, among other early events, leads to activation of PKCθ. To activate Rac 1 and consequently PYGM, PKCθ phosphorylates αPIX in T cells. The biological significance of this PKCθ/αPIX/Rac 1 GTPase/PYGM signaling pathway seems to be the control of different cellular responses such as migration and proliferation.