Loss of Hoxa5 function affects Hox gene expression in different biological contexts.

Hoxa5 plays numerous roles in development, but its downstream molecular effects are mostly unknown. We applied bulk RNA-seq assays to characterize the transcriptional impact of the loss of Hoxa5 gene function in seven different biological contexts, including developing respiratory and musculoskeletal tissues that present phenotypes in Hoxa5 mouse mutants. This global analysis revealed few common transcriptional changes, suggesting that HOXA5 acts mainly via the regulation of context-specific effectors.

Context and Mutation in Gymnosperm Chloroplast DNA.

Mutations and subsequent repair processes are known to be strongly context-dependent in the flowering-plant chloroplast genome. At least six flanking bases, three on each side, can have an influence on the relative rates of different types of mutation at any given site. In this analysis, examine context and substitution at noncoding and fourfold degenerate coding sites in gymnosperm DNA.

Evidence for Strand Asymmetry in Different Plastid Genomes.

A common genome composition pattern in eubacteria is an asymmetry between the leading and lagging strands resulting in opposite skew patterns in the two replichores that lie between the origin and terminus of replication. Although this pattern has been reported for a couple of isolated plastid genomes, it is not clear how widespread it is overall in this chromosome. Using a random walk approach, we examine plastid genomes outside of the land plants, which are excluded since they are known not to initiate replication at a single site, for such a pattern of asymmetry.

Do Noncoding and Coding Sites in Angiosperm Chloroplast DNA Have Different Mutation Processes?

Fourfold degenerate sites within coding regions and intergenic sites have both been used as estimates of neutral evolution. In chloroplast DNA, the pattern of substitution at intergenic sites is strongly dependent on the composition of the surrounding hexanucleotide composed of the three base pairs on each side, which suggests that the mutation process is highly context-dependent in this genome. This study examines the context-dependency of substitutions at fourfold degenerate sites in protein-coding regions and compares the pattern to what has been observed at intergenic sites.

Substitution rate heterogeneity across hexanucleotide contexts in noncoding chloroplast DNA.

Substitutions between closely related noncoding chloroplast DNA sequences are studied with respect to the composition of the 3 bases on each side of the substitution, that is the hexanucleotide context. There is about 100-fold variation in rate, among the contexts, particularly on substitutions of A and T. Rate heterogeneity of transitions differs from that of transversions, resulting in a more than 200-fold variation in the transitions: transversion bias.

Context-Dependent Substitution Dynamics in Plastid DNA Across a Wide Range of Taxonomic Groups.

The influence of neighboring base composition, or context, on substitution bias at fourfold degenerate coding sites and in intergenic regions in plastid DNA is compared across the angiosperms, gymnosperms, ferns, liverworts, chlorophytes, stramenopiles and rhodophytes. An influence of flanking base G + C content on the relative rates of transitions and transversions is observed in all lineages and extends up to four nucleotides from the site of substitution in some. Despite finding context effects in all lineages, significant differences were observed between lineages.

Context-Dependent Mutation Dynamics, Not Selection, Explains the Codon Usage Bias of Most Angiosperm Chloroplast Genes.

Two competing proposals about the degree to which selection affects codon usage of angiosperm chloroplast genes are examined. The first, based on observations that codon usage does not match expectations under the naïve assumption that base composition will be identical at all neutral sites, is that selection plays a significant role. The second is that codon usage is determined almost solely by mutation bias and drift, with selection influencing only one or two highly expressed genes, in particular psbA.

Evidence from simulation studies for selective constraints on the codon usage of the Angiosperm psbA gene.

The codon usage of the Angiosperm psbA gene is atypical for flowering plant chloroplast genes but similar to the codon usage observed in highly expressed plastid genes from some other Plantae, particularly Chlorobionta, lineages. The pattern of codon bias in these genes is suggestive of selection for a set of translationally optimal codons but the degree of bias towards these optimal codons is much weaker in the flowering plant psbA gene than in high expression plastid genes from lineages such as certain green algal groups. Two scenarios have been proposed to explain these observations.

The origins, relationships, evolution and conservation of the weirdest marine bivalves: The watering pot shells. A review.

The fossil record shows that the two clavagelloid or watering pot families evolved at different times, the Clavagellidae first in the late Mesozoic (100-66mya), the Penicillidae later in the Cenozoic (33-23mya)-the former originally with, thus, a near-global Tethyan distribution, the latter restricted to the Indo-West Pacific. Representatives of the two clavagelloid families, moreover, have wholly different adventitious tube/crypt structures and, thus, methods of formation suggesting that evolutionary experiments have been undertaken to achieve such radical architectural novelties. This has resulted in one of the most surprising examples of convergent evolution in the Bivalvia.

Predatory marine bivalves: A review.

Most bivalves are suspension feeders. On the deep sea floor, however, some are predators, typically of meiobenthic crustaceans: copepods, cumaceans and ostracods. Propeamusiid scallops are one such group of predators.

Cannabinoid CB2R receptors are upregulated with corneal injury and regulate the course of corneal wound healing.

CB2R receptors have demonstrated beneficial effects in wound healing in several models. We therefore investigated a potential role of CB2R receptors in corneal wound healing. We examined the functional contribution of CB2R receptors to the course of wound closure in an in vivo murine model.

Mass spawning by the date mussel Lithophaga lithophaga.

Lithophaga lithophaga is one of the commonest bivalves in the Mediterranean Sea and is present in almost every subtidal calcareous rock. Its reproductive cycle is known only from laboratory studies. Herein, we present data on the species reproductive activities based on localised but mass synchronized spawning events.

The role of microRNA-155/liver X receptor pathway in experimental and idiopathic pulmonary fibrosis.

Background: Idiopathic pulmonary fibrosis (IPF) is progressive and rapidly fatal. Improved understanding of pathogenesis is required to prosper novel therapeutics. Epigenetic changes contribute to IPF; therefore, microRNAs may reveal novel pathogenic pathways.

Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta.

Manduca sexta, known as the tobacco hornworm or Carolina sphinx moth, is a lepidopteran insect that is used extensively as a model system for research in insect biochemistry, physiology, neurobiology, development, and immunity. One important benefit of this species as an experimental model is its extremely large size, reaching more than 10 g in the larval stage. M.