Going nuclear: gene family evolution and vertebrate phylogeny reconciled

Gene duplications have been common throughout vertebrate evolution, introducing paralogy and so complicating phylogenctic inference from nuclear genes. Reconciled trees are one method capable of dealing with paralogy, using the relationship between a gene phylogeny and the phylogeny of the organisms containing those genes to identify gene duplication events. This allows us to infer phylogenies from gene families containing both orthologous and paralogous copies. Vertebrate phylogeny is well understood from morphological and palaeontological data, but studies using mitochondrial sequence data have failed to reproduce this classical view. Reconciled tree analysis of a database of 118 vertebrate gene families supports a largely classical vertebrate phylogeny

Arbeidsvoorwaardenvorming in het onderwijs: een vergelijking tussen Nederland en Vlaanderen

Hervorming Sociale Regelgevin

The dermal skeleton of the jawless vertebrate Tremataspis mammilata (Osteostraci, stem-Gnathostomata)

Osteostracans are the closest jawless relatives of jawed vertebrates, informing the gradual assembly of the vertebrate mineralised skeleton. Conflicting interpretations of their dermal skeletal histology arise from failure to account for topological variation, obscuring their significance in elucidating vertebrate skeletal evolution. To resolve this, we characterize the cranial and trunk dermal skeleton of a single individual of Tremataspis mammilata (Osteostraci, Thyestiida) at submicron resolution using synchrotron tomography. Our results show that the architecture of the Tremataspis dermal skeleton is, for the most part, conserved over the skeleton and is broadly consistent with previous histological hypotheses based on 2-dimensional thin section study. We resolve debate over the homology of the basal layer, identifying it as osteogenic acellular isopedin rather than odontogenic elasmodine or metaplastic ossification of the stratum compactum of the dermis. We find topological variation between all dermal skeletal elements studied, and particularly between the cranial and postcranial dermal skeleton. This variation can be largely explained by reduction in differentiation due to geometric constraints imposed within smaller skeletal elements, such as scales. Our description of the dermal skeleton of Tremataspis mammilata provides a foundation for interpreting data from cursory topological samples of dermal skeletal diversity obtained in other osteostracans. This reveals general aspects of histological structure that must be primitive for osteostracans and, likely, ancestral jawed vertebrates. Finally, we draw the distinction between hypotheses and descriptions in palaeohistology

Representing addition and subtraction : learning the formal conventions

The study was designed to test the effects of a structured intervention in teaching children to represent addition and subtraction. In a post-test only control group design, 90 five-year-olds experienced the intervention entitled Bi-directional Translation whilst 90 control subjects experienced typical teaching. Post-intervention testing showed some significant differences between the two groups both in terms of being able to effect the addition and subtraction operations and in being able to determine which operation was appropriate. The results suggest that, contrary to historical practices, children's exploration of real world situations should precede practice in arithmetical symbol manipulation

Recognition of dileucine-based sorting signals from HIV-1 Nef and LIMP-II by the AP-1 γ–σ1 and AP-3 δ–σ3 hemicomplexes

The sorting of transmembrane proteins to endosomes and lysosomes is mediated by signals present in the cytosolic tails of the proteins. A subset of these signals conform to the [DE]XXXL[LI] consensus motif and mediate sorting via interactions with heterotetrameric adaptor protein (AP) complexes. However, the identity of the AP subunits that recognize these signals remains controversial. We have used a yeast three-hybrid assay to demonstrate that [DE]XXXL[LI]-type signals from the human immunodeficiency virus negative factor protein and the lysosomal integral membrane protein II interact with combinations of the γ and σ1 subunits of AP-1 and the δ and σ3 subunits of AP-3, but not the analogous combinations of AP-2 and AP-4 subunits. The sequence requirements for these interactions are similar to those for binding to the whole AP complexes in vitro and for function of the signals in vivo. These observations reveal a novel mode of recognition of sorting signals involving the γ/δ and σ subunits of AP-1 and AP-3

On the Spatial Coherence of Magnetic Ejecta: Measurements of Coronal Mass Ejections by Multiple Spacecraft Longitudinally Separated by 0.01 AU

Measurements of coronal mass ejections (CMEs) by multiple spacecraft at small radial separations but larger longitudinal separations is one of the ways to learn about the three-dimensional structure of CMEs. Here, we take advantage of the orbit of the Wind spacecraft that ventured to distances of up to 0.012 astronomical units (au) from the Sun-Earth line during the years 2000 to 2002. Combined with measurements from ACE, which is in a tight halo orbit around L1, the multipoint measurements allow us to investigate how the magnetic field inside magnetic ejecta (MEs) changes on scales of 0.005 - 0.012 au. We identify 21 CMEs measured by these two spacecraft for longitudinal separations of 0.007 au or more. We find that the time-shifted correlation between 30-minute averages of the non-radial magnetic field components measured at the two spacecraft is systematically above 0.97 when the separation is 0.008 au or less, but is on average 0.89 for greater separations. Overall, these newly analyzed measurements, combined with 14 additional ones when the spacecraft separation is smaller, point towards a scale length of longitudinal magnetic coherence inside MEs of 0.25 - 0.35 au for the magnitude of the magnetic field but 0.06 - 0.12 au for the magnetic field components. This finding raises questions about the very nature of MEs. It also highlights the need for additional "mesoscale" multi-point measurements of CMEs with longitudinal separations of 0.01 - 0.2 au.Comment: Published in ApJL, 6 page

The Epstein-Barr Virus G-Protein-Coupled Receptor Contributes to Immune Evasion by Targeting MHC Class I Molecules for Degradation

Epstein-Barr virus (EBV) is a human herpesvirus that persists as a largely subclinical infection in the vast majority of adults worldwide. Recent evidence indicates that an important component of the persistence strategy involves active interference with the MHC class I antigen processing pathway during the lytic replication cycle. We have now identified a novel role for the lytic cycle gene, BILF1, which encodes a glycoprotein with the properties of a constitutive signaling G-protein-coupled receptor (GPCR). BILF1 reduced the levels of MHC class I at the cell surface and inhibited CD8+ T cell recognition of endogenous target antigens. The underlying mechanism involves physical association of BILF1 with MHC class I molecules, an increased turnover from the cell surface, and enhanced degradation via lysosomal proteases. The BILF1 protein of the closely related CeHV15 c1-herpesvirus of the Rhesus Old World primate (80% amino acid sequence identity) downregulated surface MHC class I similarly to EBV BILF1. Amongst the human herpesviruses, the GPCR encoded by the ORF74 of the KSHV c2-herpesvirus is most closely related to EBV BILF1 (15% amino acid sequence identity) but did not affect levels of surface MHC class I. An engineered mutant of BILF1 that was unable to activate G protein signaling pathways retained the ability to downregulate MHC class I, indicating that the immune-modulating and GPCR-signaling properties are two distinct functions of BILF1. These findings extend our understanding of the normal biology of an important human pathogen. The discovery of a third EBV lytic cycle gene that cooperates to interfere with MHC class I antigen processing underscores the importance of the need for EBV to be able to evade CD8+ T cell responses during the lytic replication cycle, at a time when such a large number of potential viral targets are expressed

A critical appraisal of appendage disparity and homology in fishes

Fishes are both extremely diverse and morphologically disparate. Part of this disparity can be observed in the numerous possible fin configurations that may differ in terms of the number of fins as well as fin shapes, sizes and relative positions on the body. Here, we thoroughly review the major patterns of disparity in fin configurations for each major group of fishes and discuss how median and paired fin homologies have been interpreted over time. When taking into account the entire span of fish diversity, including both extant and fossil taxa, the disparity in fin morphologies greatly complicates inferring homologies for individual fins. Given the phylogenetic scope of this review, structural and topological criteria appear to be the most useful indicators of fin identity. We further suggest that it may be advantageous to consider some of these fin homologies as nested within the larger framework of homologous fin‐forming morphogenetic fields. We also discuss scenarios of appendage evolution and suggest that modularity may have played a key role in appendage disparification. Fin modules re‐expressed within the boundaries of fin‐forming fields could explain how some fins may have evolved numerous times independently in separate lineages (e.g., adipose fin), or how new fins may have evolved over time (e.g., anterior and posterior dorsal fins, pectoral and pelvic fins). We favour an evolutionary scenario whereby median appendages appeared from a unique field of competence first positioned throughout the dorsal and ventral midlines, which was then redeployed laterally leading to paired appendages.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151971/1/faf12402_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151971/2/faf12402.pd