On the consistency of seismically imaged lower mantle slabs.

The geoscience community is increasingly utilizing seismic tomography to interpret mantle heterogeneity and its links to past tectonic and geodynamic processes. To assess the robustness and distribution of positive seismic anomalies, inferred as subducted slabs, we create a set of vote maps for the lower mantle with 14 global P-wave or S-wave tomography models. Based on a depth-dependent threshold metric, an average of 20% of any given tomography model depth is identified as a potential slab. However, upon combining the 14 models, the most consistent positive wavespeed features are identified by an increasing vote count. An overall peak in the most robust anomalies is found between 1000-1400 km depth, followed by a decline to a minimum around 2000 km. While this trend could reflect reduced tomographic resolution in the middle mantle, we show that it may alternatively relate to real changes in the time-dependent subduction flux and/or a mid-lower mantle viscosity increase. An apparent secondary peak in agreement below 2500 km depth may reflect the degree-two lower mantle slow seismic structures. Vote maps illustrate the potential shortcomings of using a limited number or type of tomography models and slab threshold criteria.

A link between RNA interference and nonsense-mediated decay in Caenorhabditis elegans.

Double-stranded RNA (dsRNA) inhibits expression of homologous genes by a process involving messenger RNA degradation. To gain insight into the mechanism of degradation, we examined how RNA interference is affected by mutations in the smg genes, which are required for nonsense-mediated decay. For three of six smg genes tested, mutations resulted in animals that were initially silenced by dsRNA but then recovered; wild-type animals remained silenced. The levels of target messenger RNAs were restored during recovery, and RNA editing and degradation of the dsRNA were identical to those of the wild type. We suggest that persistence of RNA interference relies on a subset of smg genes.

pha-4, an HNF-3 homolog, specifies pharyngeal organ identity in Caenorhabditis elegans.

To build complex organs, embryos have evolved mechanisms that integrate the development of cells unrelated to one another by cell type or ancestry. Here we show that the pha-4 locus establishes organ identity for the Caenorhabditis elegans pharynx. In pha-4 mutants, pharyngeal cells are transformed into ectoderm. Conversely, ectopic pha-4 expression produces excess pharyngeal cells. pha-4 encodes an HNF-3 homolog selectively expressed in the nascent digestive tract, including all pharynx precursors at the time they are restricted to a pharyngeal fate. We suggest that pha-4 is a key component of a transcription-based mechanism to endow cells with pharyngeal organ identity.

Recognition of contiguous allele-specific peptide elements in the rubella virus E1 envelope protein.

Peptides which bind to human HLA-DRB1 class II molecules in an allele-specific fashion were derived from the immunodominant E1 envelope protein of rubella virus. Two nonoverlapping E1 peptide epitopes were recognized by rubella virus-specific T cells in the context of independent HLA alleles when presented either separately or as a contiguous polypeptide containing both epitopes. Direct binding analysis of potential peptide epitopes to distinct HLA molecules provides a direct approach for selecting antigenic peptides useful for epitope-based vaccine targeted to multiple HLA types.

Characterization of the HLA-restrictive elements of a rubella virus-specific cytotoxic T cell clone: influence of HLA-DR4 beta chain residue 74 polymorphism on antigenic peptide-T cell interaction.

The influence of glutamic acid (E)-alanine (A) dimorphism at position 74 of the DR4 beta chain on cytotoxic T cell recognition of an antigenic rubella virus peptide, E1(273-284), was studied using a panel of B cell lines and B cell transfectants expressing different HLA-DRB1 alleles as antigen-presenting cells and targets in 51Cr-release assays. Only B cell lines expressing the DRB1*0403, DRB1*0406 or DRB1*0407 subtypes which shared a residue, E, at position 74 in the DR4 beta chain when sensitized with E1(273-284) elicited strong cytotoxic T lymphocyte responses. However, in direct binding and antibody inhibition assays, it was shown that biotinylated E1(272-285) could bind to DR molecules with residues other than E at position 74, including DRB1*0401, DRB1*0404 and DRB1*1101 expressed on transfectants. E1(272-285) bound with similar affinity to the transfectant with DRB1*0403, which has E at position 74, as well as the transfectant with DRB1*0404, which does not. When T-B cell engagement rates were compared in cell conjugate assays, the percentage of T-B conjugates was higher when peptide-pulsed transfectants with DRB1*0403 were used than with transfectants expressing DRB1*0404. Hence, the HLA DR beta 1 polymorphism at position 74, while not critical for the binding affinity of E1(272-285) to the HLA molecule, appears to be a primary determinant of restricted recognition and subsequent activation of the peptide-specific T cells.

Recognition of altered self major histocompatibility complex molecules modulated by specific peptide interactions.

Antigen-specific and major histocompatibility complex (MHC)-restricted recognition by the T cell receptor involves multiple structural contacts over a large molecular surface area. Using a human T cell clone specific for a rubella viral peptide restricted by subsets of HLA DR4 molecules, we identified structurally diverse combinations of peptide-MHC complexes which were functionally equivalent to T cell recognition. Presentation of the rubella-derived peptide on DR4 molecules with an E-74 polymorphism triggered T cell recognition, as did presentation of a single amino acid-substituted peptide in the context of DR4 molecule which lacked the E-74 site. Peptide binding and molecular modeling analysis indicates the structural and functional complementarity of T cell recognition for a specific amino acid side chain, whether contributed by the peptide or by the MHC molecule.

HLA-DQB1 codon 57 is critical for peptide binding and recognition.

The association of specific HLA-DQ alleles with autoimmunity is correlated with discrete polymorphisms in the HLA-DQ sequence that are localized within sites suitable for peptide recognition. The polymorphism at residue 57 of the DQB1 polypeptide is of particular interest since it may play a major structural role in the formation of a salt bridge structure at one end of the peptide-binding cleft of the DQ molecules. This polymorphism at residue 57 is a recurrent feature of HLA-DQ evolution, occurring in multiple distinct allelic families, which implies a functional selection for maintaining variation at this position in the class II molecule. We directly tested the amino acid polymorphism at this site as a determinant for peptide binding and for antigen-specific T cell stimulation. We found that a single Ala-->Asp amino acid 57 substitution in an HLA-DQ3.2 molecule regulated binding of an HSV-2 VP-16-derived peptide. A complementary single-residue substitution in the peptide abolished its binding to DQ3.2 and converted it to a peptide that can bind to DQ3.1 and DQ3.3 Asp-57-positive MHC molecules. These binding studies were paralleled by specific T cell recognition of the class II-peptide complex, in which the substituted peptide abolished T cell reactivity, which was directed to the DQ3.2-peptide complex, whereas the same T cell clone recognized the substituted peptide presented by DQ3.3, a class II restriction element differing from DQ3.2 only at residue 57. This structural and functional complementarity for residue 57 and a specific peptide residue identifies this interaction as a key controlling determinant of restricted recognition in HLA-DQ-specific immune response.

Allele-specific motifs characterize HLA-DQ interactions with a diabetes-associated peptide derived from glutamic acid decarboxylase.

Polymorphic residues of HLA class II molecules influence immune activation in part by determining specific structural constraints for binding antigenic peptides. We identified a peptide from glutamic acid decarboxylase, a diabetes-associated autoantigen that preferentially bound to HLA-DQ3.2 molecules, one of the HLA determinants highly associated with insulin-dependent diabetes. We analyzed interactions of specific HLA-DQ residues with modified peptide analogues and found a pattern of permissive site-specific amino acids that accommodated allele-specific binding. Four anchor residues constrain binding to different DQ alleles; limited variation at two of these sites, residues 4 and 9, accounts for the unique pattern of peptide binding to HLA-DQ3.1 or HLA-DQ3.2.