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 topological clustering within protein networks using edge metrics that evaluate full sequence,full structure,and active site microenvironment similarity

The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods.     

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.     

Effect of phorid fly density on the foraging of Atta vollenweideri leafcutter ants in the field

Leafcutter ants in the genus Atta (Hymenoptera: Formicidae: Attini) are considered major pests of agriculture and forestry in the Neotropics. Phorid flies (Diptera: Phoridae) have been proposed as viable candidates for biological control of ants because of the importance of their trait‐mediated effects on their hosts. However, the impact of different densities of phorid flies has never been assessed in the field. Experiments were conducted by isolating 3‐m sections of Atta vollenweideri Forel foraging trails with tunnels, and sampling ants in trails with 0, 1, or 4 Eibesfeldtphora trilobata Disney female parasitoid flies. Samples were collected every 30 min from these trails. We also collected a sample before introducing the parasitoids and another one 30 min after removing them from the trail. We measured traffic of ants on the trails, weight and type of plant material transported, and the proportion and size of the workers collected. The presence of phorids on the trails reduced the ant traffic and amount of plant material transported into the nests and decreased the proportion of workers on the trails in the size range preferred as hosts by the flies. The effect on worker size, as well as the lag effect recorded after phorids were removed from the tunnels, was more pronounced with four phorids. The presence of phorids also affected the weight of monocotyledon and dicotyledon material transported. Even at the minimum density possible, phorids significantly influenced a key aspect of the colony life, the food intake through foraging. From an applied point of view, our results show that releases of these phorids into the field should not necessarily involve many individuals to reduce foraging by A. vollenweideri, making them potentially useful candidates for biological control of these ants.     

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.