transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences

Background  

Alignments of homologous DNA sequences are crucial for comparative genomics and phylogenetic analysis. However, multiple alignment represents a computationally difficult problem. For protein-coding DNA sequences, it is more advantageous in terms of both speed and accuracy to align the amino-acid sequences specified by the DNA sequences rather than the DNA sequences themselves. Many implementations making use of this concept of "translated alignments" are incomplete in the sense that they require the user to manually translate the DNA sequences and to perform the amino-acid alignment. As such, they are not well suited to large-scale automated alignments of large and/or numerous DNA data sets.     

Secretion of a lipolytic protein aggregate by barley aleurone and its dissociation by starchy endosperm

Acidic and basic lysophospholipase activities (LPL) have been separated by ion-exchange chromatography of barley extracts. The basic activity predominates in the starchy endosperm of germinating barley and in the medium of hormone-stimulated half-seeds; the acidic activity is the predominant form in the medium of hormone-stimulated aleurone layers. Addition of either starchy endosperm or EDTA to the acidic activity produces the basic activity. The two activities display the same pH optimum and have similar Km values. Inactivation profiles of LPLs with immunoglobulin G (IgG) prepared against the purified basic LPL are the same. The acidic LPL obtained from the incubation medium from stimulated aleurone layers appears in the void volume on gel filtration with Bio-Gel P100. Acid phosphatase and alpha-amylase in the same incubation medium appear at their expected elution volumes on this column. Gel filtration in the presence of EDTA results in the acidic activity eluting in a volume characteristic of the basic LPL (Mr, 40,000). On Bio-Gel P300 the acidic activity peak is centered at Mr, 160,000. SDS-gel electrophoresis of fractions across this peak shows a simple distribution of proteins eluting with Mr greater than or equal to 160,000. The potential role of an aggregate in the secretion of lipolytic proteins is discussed.     

Neuregulin 3 promotes excitatory synapse formation on hippocampal interneurons

Hippocampal GABAergic interneurons are crucial for cortical network function and have been implicated in psychiatric disorders. We show here that Neuregulin 3 (Nrg3), a relatively little investigated low‐affinity ligand, is a functionally dominant interaction partner of ErbB4 in parvalbumin‐positive (PV) interneurons. Nrg3 and ErbB4 are located pre‐ and postsynaptically, respectively, in excitatory synapses on PV interneurons in vivo. Additionally, we show that ablation of Nrg3 results in a similar phenotype as the one described for ErbB4 ablation, including reduced excitatory synapse numbers on PV interneurons, altered short‐term plasticity, and disinhibition of the hippocampal network. In culture, presynaptic Nrg3 increases excitatory synapse numbers on ErbB4⁺ interneurons and affects short‐term plasticity. Nrg3 mutant neurons are poor donors of presynaptic terminals in the presence of competing neurons that produce recombinant Nrg3, and this bias requires postsynaptic ErbB4 but not ErbB4 kinase activity. Furthermore, when presented by non‐neuronal cells, Nrg3 induces postsynaptic membrane specialization. Our data indicate that Nrg3 provides adhesive cues that facilitate excitatory neurons to synapse onto ErbB4⁺ interneurons.     

Correlates of substitution rate variation in mammalian protein-coding sequences

Background  

Rates of molecular evolution in different lineages can vary widely, and some of this variation might be predictable from aspects of species' biology. Investigating such predictable rate variation can help us to understand the causes of molecular evolution, and could also help to improve molecular dating methods. Here we present a comprehensive study of the life history correlates of substitution rate variation across the mammals, comparing results for mitochondrial and nuclear loci, and for synonymous and non-synonymous sites. We use phylogenetic comparative methods, refined to take into account the special nature of substitution rate data. Particular attention is paid to the widespread correlations between the components of mammalian life history, which can complicate the interpretation of results.