Complete mitochondrial genome sequence of Urechis caupo, a representative of the phylum Echiura

BACKGROUND: Mitochondria contain small genomes that are physically separate from those of nuclei. Their comparison serves as a model system for understanding the processes of genome evolution. Although hundreds of these genome sequences have been reported, the taxonomic sampling is highly biased toward vertebrates and arthropods, with many whole phyla remaining unstudied. This is the first description of a complete mitochondrial genome sequence of a representative of the phylum Echiura, that of the fat innkeeper worm, Urechis caupo. RESULTS: This mtDNA is 15,113 nts in length and 62% A+T. It contains the 37 genes that are typical for animal mtDNAs in an arrangement somewhat similar to that of annelid worms. All genes are encoded by the same DNA strand which is rich in A and C relative to the opposite strand. Codons ending with the dinucleotide GG are more frequent than would be expected from apparent mutational biases. The largest non-coding region is only 282 nts long, is 71% A+T, and has potential for secondary structures. CONCLUSIONS: Urechis caupo mtDNA shares many features with those of the few studied annelids, including the common usage of ATG start codons, unusual among animal mtDNAs, as well as gene arrangements, tRNA structures, and codon usage biases

The complete sequence of the mitochondrial genome of Nautilus macromphalus (Mollusca: Cephalopoda)

BACKGROUND: Mitochondria contain small genomes that are physically separate from those of nuclei. Their comparison serves as a model system for understanding the processes of genome evolution. Although complete mitochondrial genome sequences have been reported for more than 600 animals, the taxonomic sampling is highly biased toward vertebrates and arthropods, leaving much of the diversity yet uncharacterized. RESULTS: The mitochondrial genome of the bellybutton nautilus, Nautilus macromphalus, a cephalopod mollusk, is 16,258 nts in length and 59.5% A+T, both values that are typical of animal mitochondrial genomes. It contains the 37 genes that are almost universally found in animal mtDNAs, with 15 on one DNA strand and 22 on the other. The arrangement of these genes can be derived from that of the distantly related Katharina tunicata (Mollusca: Polyplacophora) by a switch in position of two large blocks of genes and transpositions of four tRNA genes. There is strong skew in the distribution of nucleotides between the two strands, and analysis of this yields insight into modes of transcription and replication. There is an unusual number of non-coding regions and their function, if any, is not known; however, several of these demark abrupt shifts in nucleotide skew, and there are several identical sequence elements at these junctions, suggesting that they may play roles in transcription and/or replication. One of the non-coding regions contains multiple repeats of a tRNA-like sequence. Some of the tRNA genes appear to overlap on the same strand, but this could be resolved if the polycistron were cleaved at the beginning of the downstream gene, followed by polyadenylation of the product of the upstream gene to form a fully paired structure. CONCLUSION: Nautilus macromphalus mtDNA contains an expected gene content that has experienced few rearrangements since the evolutionary split between cephalopods and polyplacophorans. It contains an unusual number of non-coding regions, especially considering that these otherwise often are generated by the same processes that produce gene rearrangements. The skew in nucleotide composition between the two strands is strong and associated with the direction of transcription in various parts of the genomes, but a comparison with K. tunicata implies that mutational bias during replication also plays a role. This appears to be yet another case where polyadenylation of mitochondrial tRNAs restores what would otherwise be an incomplete structure

Epibiont Guilds as Paleoecological Tools in Environmental Analysis: An Example From Modern and Ordovician Shell Substrates

Paleocommunities of encrusting organisms exhibit characteristics that allow comparisons of modern and fossil systems and subsequent environmental analyses. Encrusting organisms attach to a substrate that is generally limited in area. Interactions between bionts and the host organism, and bionts and the environment, are preserved on epibiont encrusted fossils. Modern biont communities from known environments can be compared to fossil biont communities in order to determine the ancient environment experienced by that fossil. Using epibionts as a tool in paleo-environmental analyses employs the somewhat problematic idea that the present can be used as a key to the past. I suggest that by using guilds (as opposed to species) of bionts, defined by parameters of lifestyle and habitat, the present can be a key to the past with regard to encrusting communities. A modern data set from off the coast of Lee Stocking Island, Bahamas, was used in this study. Mytilus edulis shells were experimentally deployed at seven depths from 15m to 275m for a period of two years. After retrieval by the SSETI team, I collected, epibiont data from a total of 52 disarticulated bivalve shells. To test the method of guild use in paleoenvironmental analysis, I used a fossil data set from the Richmond Group in Indiana, Ordovician in age. I obtained Rafinesquina alternata shells from three shell beds in one rock outcrop and collected epibiont data from a total of 208 of these articulated shells. I compared epibiont data from the modern and Ordovician data sets using a number of different variables, including: presence of guilds, percent area of shell covered by guilds, relative abundance of guilds, and guild richness. I analyzed results for significant differences in order to determine if the Ordovician data were similar to data from any of the modem environments. In addition to an analysis of the environment experienced by the Ordovician R. alternata and its encrusting organisms, I will explore several larger concepts. One major question is what parameters will be most useful in the comparison of guilds of encrusting organisms that are separated by a gap of 400 million years. I will also address the viability of using guilds as a tool in making comparisons of once living assemblages across such a large time span. Finally, the underpinning assumption of this research, that the modern can be used as a model for the past, will be discussed

Attractors of directed graph IFSs that are not standard IFS attractors and their Hausdorff measure

For directed graph iterated function systems (IFSs) defined on R, we prove that a class of 2-vertex directed graph IFSs have attractors that cannot be the attractors of standard (1-vertex directed graph) IFSs, with or without separation conditions. We also calculate their exact Hausdorff measure. Thus we are able to identify a new class of attractors for which the exact Hausdorff measure is known

Wavelet-based response spectrum compatible synthesis of accelerograms-Eurocode application (EC8)

An integrated approach for addressing the problem of synthesizing artificial seismic accelerograms compatible with a given displacement design/target spectrum is presented in conjunction with aseismic design applications. Initially, a stochastic dynamics solution is used to obtain a family of simulated non-stationary earthquake records whose response spectrum is on the average in good agreement with the target spectrum. The degree of the agreement depends significantly on the adoption of an appropriate parametric evolutionary power spectral form, which is related to the target spectrum in an approximate manner. The performance of two commonly used spectral forms along with a newly proposed one is assessed with respect to the elastic displacement design spectrum defined by the European code regulations (EC8). Subsequently, the computational versatility of the family of harmonic wavelets is employed to modify iteratively the simulated records to satisfy the compatibility criteria for artificial accelerograms prescribed by EC8. In the process, baseline correction steps, ordinarily taken to ensure that the obtained accelerograms are characterized by physically meaningful velocity and displacement traces, are elucidated. Obviously, the presented approach can be used not only in the case of the EC8, for which extensive numerical results/examples are included, but also for any code provisions mandated by regulatory agencies. In any case, the presented numerical results can be quite useful in any aseismic design process dominated by the EC8 specifications

Peak ground accelerations from large (M≥7.2) shallow crustal earthquakes : a comparison with predictions from eight recent ground-motion models

Strong-motion data from large (M≥7.2) shallow crustal earthquakes invariably make up a small proportion of the records used to develop empirical ground motion prediction equations (GMPEs). Consequently GMPEs are more poorly constrained for large earthquakes than for small events. In this article peak ground accelerations (PGAs) observed in 38 earthquakes worldwide with M≥7.2 are compared with those predicted by eight recent GMPEs. Well over half of the 38 earthquakes were not considered when deriving these GMPEs but the data were identified by a thorough literature review of strong-motion reports from the past sixty years. These data are provided in an electronic supplement for future investigations on ground motions from large earthquakes. The addition of these data provides better constraint of the between-event ground-motion variability in large earthquakes. It is found that the eight models generally provide good predictions for PGAs from these earthquakes, although there is evidence for slight under- or over-prediction of motions by some models (particularly for M>7.5). The between-event variabilities predicted by most models match the observed variability, if data from two events (2001 Bhuj and 2005 Crescent City) that are likely atypical of earthquakes in active regions are excluded. For some GMPEs there is evidence that they are over-predicting PGAs in the near-source region of large earthquakes as well as over-predicting motions on hard rock. Overall, however, all the considered models, despite having been derived using limited data, provide reliable predictions of PGAs in the largest crustal earthquakes

Gene translocation links insects and crustaceans

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62560/1/392667a0.pd