Ultra‐Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera,Chalcidoidea)

Recent technical advances combined with novel computational approaches have promised the acceleration of our understanding of the tree of life. However, when it comes to hyperdiverse and poorly known groups of invertebrates, studies are still scarce. As published phylogenies will be rarely challenged by future taxonomists, careful attention must be paid to potential analytical bias. We present the first molecular phylogenetic hypothesis for the family Chalcididae, a group of parasitoid wasps, with a representative sampling (144 ingroups and seven outgroups) that covers all described subfamilies and tribes, and 82% of the known genera. Analyses of 538 Ultra‐Conserved Elements (UCEs) with supermatrix (RAx ML and IQTREE) and gene tree reconciliation approaches (ASTRAL, ASTRID) resulted in highly supported topologies in overall agreement with morphology but reveal conflicting topologies for some of the deepest nodes. To resolve these conflicts, we explored the phylogenetic tree space with clustering and gene genealogy interrogation methods, analyzed marker and taxon properties that could bias inferences and performed a thorough morphological analysis (130 characters encoded for 40 taxa representative of the diversity). This joint analysis reveals that UCEs enable attainment of resolution between ancestry and convergent/divergent evolution when morphology is not informative enough, but also shows that a systematic exploration of bias with different analytical methods and a careful analysis of morphological features is required to prevent publication of artifactual results. We highlight a GC content bias for maximum‐likelihood approaches, an artifactual mid‐point rooting of the ASTRAL tree and a deleterious effect of high percentage of missing data (>85% missing UCEs) on gene tree reconciliation methods. Based on the results we propose a new classification of the family into eight subfamilies and ten tribes that lay the foundation for future studies on the evolutionary history of Chalcididae.     

A general synthetic method toward uridylylated picornavirus VPg proteins

Small proteins called viral protein genome‐linked (VPg), attached to the 5′‐end of the viral RNA genome are found as common structure in the large family of picornaviruses. The replication of these viruses is primed by this VPg protein linked to a single uridylyl residue. We report a general procedure to obtain such nucleoproteins employing a pre‐uridylylated tyrosine building block in an on‐line solid phase‐based approach. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.     

Saving a tropical ecosystem from a destructive ant-scale (Pheidole megacephala, Pulvinaria urbicola) mutualism with support from a diverse natural enemy assemblage

Ants can disrupt the natural biological control of serious hemipteran pests by interfering with natural enemies, resulting in a change in ecosystem functioning. We focus here on interference by a highly invasive ant Pheidole megacephala on the regulation of a tree destroying hemipteran scale insect Pulvinaria urbicola on Cousine Island in the Seychelles archipelago, a tropical island ecosystem. We show how a diverse natural enemy assemblage contributes substantially to the collapse of the ant-scale mutualism following managed ant suppression. Natural enemy abundance and species richness increased significantly after ant suppression, with varying responses among the different functional guilds. Primary parasitoids coexisted with tending ants before ant suppression, but could not regulate the enormously high scale densities alone. After ant suppression, a significant increase in predators caused a collapse of the scale population. Guilds external to the mutualism were also affected, with primary parasitoids of various non-hemipteran taxa also increasing, which contributed significantly to the recovery of the community to its pre-invasion composition. Our results highlight the far-reaching and pervasive effects of the hemipteran-tending invasive ant within the natural enemy assemblage. In turn, we also illustrate the potential to restore the tropical ecosystem by encouraging an array of natural enemies through precision management of the ant.     

A thin‐walled polydimethylsiloxane bioreactor for high‐density hepatocyte sandwich culture

In vitro drug testing requires long‐term maintenance of hepatocyte liver specific functions. Hepatocytes cultured at a higher seeding density in a sandwich configuration exhibit an increased level of liver specific functions when compared to low density cultures due to the better cell to cell contacts that promote long term maintenance of polarity and liver specific functions. However, culturing hepatocytes at high seeding densities in a standard 24‐well plate poses problems in terms of the mass transport of nutrients and oxygen to the cells. In view of this drawback, we have developed a polydimethylsiloxane (PDMS) bioreactor that was able to maintain the long‐term liver specific functions of a hepatocyte sandwich culture at a high seeding density. The bioreactor was fabricated with PDMS, an oxygen permeable material, which allowed direct oxygenation and perfusion to take place simultaneously. The mass transport of oxygen and the level of shear stress acting on the cells were analyzed by computational fluid dynamics (CFD). The combination of both direct oxygenation and perfusion has a synergistic effect on the liver specific function of a high density hepatocyte sandwich culture over a period of 9 days. Biotechnol. Bioeng. 2013; 110: 1663–1673. © 2012 Wiley Periodicals, Inc.     

Measuring 3D Hand and Finger Kinematics—A Comparison between Inertial Sensing and an Opto-Electronic Marker System

Objective analysis of hand and finger kinematics is important to increase understanding of hand function and to quantify motor symptoms for clinical diagnosis. The aim of this paper is to compare a new 3D measurement system containing multiple miniature inertial sensors (PowerGlove) with an opto-electronic marker system during specific finger tasks in three healthy subjects. Various finger movements tasks were performed: flexion, fast flexion, tapping, hand open/closing, ab/adduction and circular pointing. 3D joint angles of the index finger joints and position of the thumb and index were compared between systems. Median root mean square differences of the main joint angles of interest ranged between 3.3 and 8.4deg. Largest differences were found in fast and circular pointing tasks, mainly in range of motion. Smallest differences for all 3D joint angles were observed in the flexion tasks. For fast finger tapping, the thumb/index amplitude showed a median difference of 15.8mm. Differences could be explained by skin movement artifacts caused by relative marker movements of the marker system, particularly during fast tasks; large movement accelerations and angular velocities which exceeded the range of the inertial sensors; and by differences in segment calibrations between systems. The PowerGlove is a system that can be of value to measure 3D hand and finger kinematics and positions in an ambulatory setting. The reported differences need to be taken into account when applying the system in studies understanding the hand function and quantifying hand motor symptoms in clinical practice.     

Comparative genomics for reliable protein-function prediction from genomic data

Genomic data provide invaluable, yet unreliable information about protein function. However, if the overlap in information among various genomic datasets is taken into account, one observes an increase in the reliability of the protein-function predictions that can be made. Recently published approaches achieved this either by comparing the same type of data from multiple species (horizontal comparative genomics) or by using subtle, Bayesian methods to compare different types of genomic data from a single species (vertical comparative genomics). In this article, we discuss these methods, illustrating horizontal comparative genomics by comparing yeast two-hybrid (Y2H) data from Saccharomyces cerevisiae with Y2H data from Drosophila melanogaster, and illustrating vertical comparative genomics by comparing RNA expression data with proteomic data from Plasmodium falciparum.     

Bioinformatic analysis of functional differences between the immunoproteasome and the constitutive proteasome

Intracellular proteins are degraded largely by proteasomes. In cells stimulated with gamma interferon , the active proteasome subunits are replaced by "immuno" subunits that form immunoproteasomes. Phylogenetic analysis of the immunosubunits has revealed that they evolve faster than their constitutive counterparts. This suggests that the immunoproteasome has evolved a function that differs from that of the constitutive proteasome. Accumulating experimental degradation data demonstrate, indeed, that the specificity of the immunoproteasome and the constitutive proteasome differs. However, it has not yet been quantified how different the specificity of two forms of the proteasome are. The main question, which still lacks direct evidence, is whether the immunoproteasome generates more MHC ligands. Here we use bioinformatics tools to quantify these differences and show that the immunoproteasome is a more specific enzyme than the constitutive proteasome. Additionally, we predict the degradation of pathogen proteomes and find that the immunoproteasome generates peptides that are better ligands for MHC binding than peptides generated by the constitutive proteasome. Thus, our analysis provides evidence that the immunoproteasome has co-evolved with the major histocompatibility complex to optimize antigen presentation in vertebrate cells.     

Dispersal and fighting in male pollinating fig wasps

For more than two decades, it has been the dogma that the males of pollinating fig wasps do not fight and that they only mate in their native fig. Their extreme degree of local mating leads to highly female biased sex ratios that should eliminate the benefits of fighting and dispersal by males. Furthermore, males sharing a fig are often brothers, and fighting may be barred by kin selection. Therefore, theory supported the presumed absence of fighting and dispersal in pollinating fig wasp males. However, we report here that in pollinating fig wasps, fighting between brothers evolved at least four and possibly six time, and dispersal by males at least twice. This finding supports the idea that competition between relatives can cancel the ameliorating effects of relatedness. The explanation to this evolutionary puzzle, as well as the consequences of male dispersal and fighting, opens the doors to exciting new research.