Complete mitochondrial genome of the Asian paddle crab Charybdis japonica (Crustacea: Decapoda: Portunidae): gene rearrangement of the marine brachyurans and phylogenetic considerations of the decapods

Given the commercial and ecological importance of the Asian paddle crab, Charybdis japonica, there is a clearly need for genetic and molecular research on this species. Here, we present the complete mitochondrial genome sequence of C. japonica, determined by the long-polymerase chain reaction and primer walking sequencing method. The entire genome is 15,738 bp in length, encoding a standard set of 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes, plus the putative control region, which is typical for metazoans. The total A+T content of the genome is 69.2%, lower than the other brachyuran crabs except for Callinectes sapidus. The gene order is identical to the published marine brachyurans and differs from the ancestral pancrustacean order by only the position of the tRNA (His) gene. Phylogenetic analyses using the concatenated nucleotide and amino acid sequences of 13 protein-coding genes strongly support the monophyly of Dendrobranchiata and Pleocyemata, which is consistent with the previous taxonomic classification. However, the systematic status of Charybdis within subfamily Thalamitinae of family Portunidae is not supported. C. japonica, as the first species of Charybdis with complete mitochondrial genome available, will provide important information on both genomics and molecular ecology of the group.

The complete mitochondrial genome of the mantid shrimp Oratosquilla oratoria (Crustacea: Malacostraca: Stomatopoda): Novel non-coding regions features and phylogenetic implications of the Stomatopoda

The complete mitochondrial (mt) genome sequence of Oratosquilla oratoria (Crustacea: Malacostraca: Stomatopoda) was determined; a circular molecule of 15,783 bp in length. The gene content and arrangement are consistent with the pancrustacean ground pattern. The mt control region of O. oratoria is characterized by no GA-block near the 3' end and different position of [TA(A)]n-blocks compared with other reported Stomatopoda species. The sequence of the second hairpin structure is relative conserved which suggests this region may be a synapomorphic character for the Stomatopoda. In addition, a relative large intergenic spacer (101 bp) with higher A + T content than that in control region was identified between the tRNA(Glu) and tRNA(Phe) genes. Phylogenetic analyses based on the current dataset of complete mt genomes strongly support the Stomatopoda is closely related to Euphausiacea. They in turn cluster with Penaeoidea and Caridea clades while other decapods form a separate group, which rejects the monophyly of Decapoda. This challenges the suitability of Stomatopoda as an outgroup of Decapoda in phylogenetic analyses. The basal position of Stomatopoda within Eumalacostraca according to the morphological characters is also questioned. (C) 2010 Elsevier Inc. All rights reserved.

The complete mitochondrial genomes of the whistling duck (Dendrocygna javanica) and black swan (Cygnus atratus): dating evolutionary divergence in Galloanserae

Galloanserae is an ancient and diverse avian group, for which comprehensive molecular evidence relevant to phylogenetic analysis in the context of molecular chronology is lacking. In this study, we present two additional mitochondrial genome sequences of Galloanserae (the whistling duck, Dendrocygna javanica, and the black swan, Cygnus atratus) to broaden the scope of molecular phylogenetic reconstruction. The lengths of the whistling duck's and black swan's mitochondrial genomes are 16,753 and 16,748 bases, respectively. Phylogenetic analyses suggest that Dendrocygna is more likely to be in a basal position of the branch consisting of Anatinae and Anserinae, an affiliation that does not conform to its traditional classification. Bayesian approaches were employed to provide a rough timescale for Galloanserae evolution. In general, a narrow range of 95% confidence intervals gave younger estimates than those based on limited genes and estimated that at least two lineages originated before the Coniacian epoch around 90 MYA, well before the Cretaceous-Tertiary boundary. In addition, these results, which were compatible with estimates from fossil evidence, also imply that the origin of numerous genera in Anseriformes took place in the late Oligocene to early Miocene. Taken together, the results presented here provide a working framework for future research on Galloanserae evolution, and they underline the utility of whole mitochondrial genome sequences for the resolution of deep divergence.

A close phylogenetic relationship between Sipuncula and Annelida evidenced from the complete mitochondrial genome sequence of Phascolosoma esculenta

Background: There are many advantages to the application of complete mitochondrial (mt) genomes in the accurate reconstruction of phylogenetic relationships in Metazoa. Although over one thousand metazoan genomes have been sequenced, the taxonomic sampling is highly biased, left with many phyla without a single representative of complete mitochondrial genome. Sipuncula (peanut worms or star worms) is a small taxon of worm-like marine organisms with an uncertain phylogenetic position. In this report, we present the mitochondrial genome sequence of Phascolosoma esculenta, the first complete mitochondrial genome of the phylum. Results: The mitochondrial genome of P. esculenta is 15,494 bp in length. The coding strand consists of 32.1% A, 21.5% C, 13.0% G, and 33.4% T bases (AT = 65.5%; AT skew = -0.019; GC skew = -0.248). It contains thirteen protein-coding genes (PCGs) with 3,709 codons in total, twenty-two transfer RNA genes, two ribosomal RNA genes and a non-coding AT-rich region (AT = 74.2%). All of the 37 identified genes are transcribed from the same DNA strand. Compared with the typical set of metazoan mt genomes, sipunculid lacks trnR but has an additional trnM. Maximum Likelihood and Bayesian analyses of the protein sequences show that Myzostomida, Sipuncula and Annelida (including echiurans and pogonophorans) form a monophyletic group, which supports a closer relationship between Sipuncula and Annelida than with Mollusca, Brachiopoda, and some other lophotrochozoan groups. Conclusion: This is the first report of a complete mitochondrial genome as a representative within the phylum Sipuncula. It shares many more similar features with the four known annelid and one echiuran mtDNAs. Firstly, sipunculans and annelids share quite similar gene order in the mitochondrial genome, with all 37 genes located on the same strand; secondly, phylogenetic analyses based on the concatenated protein sequences also strongly support the sipunculan + annelid clade (including echiurans and pogonophorans). Hence annelid "key-characters" including segmentation may be more labile than previously assumed.

The complete mitochondrial genome of the ridgetail white prawn Exopalaemon carinicauda Holthuis, 1950 (Crustacean: Decapoda: Palaemonidae) revealed a novel rearrangement of tRNA genes

The complete mitochondrial (mt) DNA sequence was determined for a ridgetail white prawn, Exopalaemon carinicauda Holthuis, 1950 (Crustacea: Decopoda: Palaemonidae). The mt genome is 15,730 bp in length, encoding a standard set of 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, which is typical for metazoans. The majority-strand consists of 33.6% A, 23.0% C, 13.4% G, and 30.0% T bases (AT skew = 0.057: GC skew = -0.264). A total of 1045 bp of non-coding nucleotides were observed in 16 intergenic regions,,including a major A+ T rich (79.7%) noncoding region (886 bp). A novel translocation of tRNA(Pro) and tRNA(Thr) was found when comparing this genome with the pancrustacean ground pattern indicating that gene order is not conserved among caridean mitochondria. Furthermore, the rate of Ka/Ks in 13 protein-coding genes between three caridean species is Much less than 1, which indicates a strong Purifying selection within this group. To investigate the phylogenetic relationship within Malacostraca, phylogenetic trees based oil Currently available malacostracan complete mitochondrial sequences were built with the maximum likelihood and Bayesian models. All analyses based oil nucleotide and amino acid data strongly support the monophyly of Decapoda. The Penaeidae, Reptantia, Caridea, and Meiura clades were also recovered as monophyletic groups with Strong Statistical Support. However, the phylogenetic relationships within Pleocyemata are unstable, as represented by the inclusion or exclusion of Caridea. (C) 2009 Elsevier B.V. All rights reserved.

地震数据波动方程反演方法研究

Geophysical inversion is a theory that transforms the observation data into corresponding geophysical models. The goal of seismic inversion is not only wave velocity models, but also the fine structures and dynamic process of interior of the earth, expanding to more parameters such as density, aeolotropism, viscosity and so on. As is known to all, Inversion theory is divided to linear and non-linear inversion theories. In rencent 40 years linear inversion theory has formed into a complete and systematic theory and found extensive applications in practice. While there are still many urgent problems to be solved in non-linear inversion theory and practice. Based on wave equation, this dissertation has been mainly involved in the theoretical research of several non-linear inversion methods: waveform inversion, traveltime inversion and the joint inversion about two methods. The objective of gradient waveform inversion is to find a geologic model, thus synthetic seismograms generated by this geologic model are best fitted to observed seismograms. Contrasting with other inverse methods, waveform inversion uses all characteristics of waveform and has high resolution capacity. But waveform inversion is an interface by interface method. An artificial parameter limit should be provided in each inversion iteration. In addition, waveform information will tend to get stuck in local minima if the starting model is too far from the actual model. Based on velocity scanning in traditional seismic data processing, a layer-by-layer waveform inversion method is developed in this dissertation to deal with weaknesses of waveform inversion. Wave equation is used to calculate the traveltime and derivative (perturbation of traveltime with respect to velocity) in wave-equation traveltime inversion (WT). Unlike traditional ray-based travetime inversion, WT has many advantages. No ray tracing or traveltime picking and no high frequency assumption is necessary and good result can be got while starting model is far from real model. But, comparing with waveform inversion, WT has low resolution. Waveform inversion and WT have complementary advantages and similar algorithm, which proves that the joint inversion is a better inversion method. And another key point which this dissertation emphasizes is how to give fullest play to their complementary advantages on the premise of no increase of storage spaces and amount of calculation. Numerical tests are implemented to prove the feasibility of inversion methods mentioned above in this dissertation. Especially for gradient waveform inversion, field data are inversed. This field data are acquired by our group in Wali park and Shunyi district. Real data processing shows there are many problems for waveform inversion to deal with real data. The matching of synthetic seismograms with observed seismograms and noise cancellation are two primary problems. In conclusion, on the foundation of the former experiences, this dissertation has implemented waveform inversions on the basis of acoustic wave equation and elastic wave equation, traveltime inversion on the basis of acoustic wave equation and traditional combined waveform traveltime inversion. Besides the traditional analysis of inversion theory, there are two innovations: layer by layer inversion of seimic reflection data inversion and rapid method for acoustic wave-equation joint inversion.

Formalizing Triggers: A Learning Model for Finite Spaces

In a recent seminal paper, Gibson and Wexler (1993) take important steps to formalizing the notion of language learning in a (finite) space whose grammars are characterized by a finite number of parameters. They introduce the Triggering Learning Algorithm (TLA) and show that even in finite space convergence may be a problem due to local maxima. In this paper we explicitly formalize learning in finite parameter space as a Markov structure whose states are parameter settings. We show that this captures the dynamics of TLA completely and allows us to explicitly compute the rates of convergence for TLA and other variants of TLA e.g. random walk. Also included in the paper are a corrected version of GW's central convergence proof, a list of "problem states" in addition to local maxima, and batch and PAC-style learning bounds for the model.

Stable Mixing of Complete and Incomplete Information

An increasing number of parameter estimation tasks involve the use of at least two information sources, one complete but limited, the other abundant but incomplete. Standard algorithms such as EM (or em) used in this context are unfortunately not stable in the sense that they can lead to a dramatic loss of accuracy with the inclusion of incomplete observations. We provide a more controlled solution to this problem through differential equations that govern the evolution of locally optimal solutions (fixed points) as a function of the source weighting. This approach permits us to explicitly identify any critical (bifurcation) points leading to choices unsupported by the available complete data. The approach readily applies to any graphical model in O(n^3) time where n is the number of parameters. We use the naive Bayes model to illustrate these ideas and demonstrate the effectiveness of our approach in the context of text classification problems.

The role of Sn in Pt-Sn/CeO2 catalysts for the complete oxidation of ethanol

The structural features and catalytic properties of Pt-Sn/CeO2 catalysts prepared by modified polyol method were extensively investigated for the complete oxidation of ethanol. CO chemisorption, TPR, DTA and XPS measurements identically indicated that the electronic configuration of Pt by Sn as well as the formation of PtSn alloy were the key factors in determining the nature of the active sites, A strong Pt/Sn atomic ratio dependence of catalytic perfortmances was observed. which was explained in terms of the change., in the Surface structure of metal phases and the electronic Pt-Sn interaction. (c) 2005 Elsevier B.V. All rights reserved.

Complete hydrodechlorination of chlorobenzene and its derivatives over supported nickel catalysts under liquid phase conditions

Liquid phase hydrodechlorination of chlorobenzene was studied over Ni/active carbon (Ni/AC), Ni/gamma-Al2O3, Ni/SiO2 and Raney Ni. The complete hydrodechlorination of chlorobenzene was realized at 333-343 K on Ni/AC under hydrogen atmosphere of 1.0 MPa in the presence of alkaline hydroxide. Aryl halides, three chlorotoluenes (o-, m- and p-), three chloroanilines, three chlorobenzotrifluorides, three dichlorobenzenes and two trichlorobenzenes (1,2,3- and 1,2,4-) were also completely hydrodechlorinated under the similar conditions. Chlorobenzene derivatives having either an electron-donating group or an electron-withdrawing group decreased their reactivities with respect to the unsubstituted chlorobenzene.

From Limen to Lumen: computing students in liminal spaces.From Limen to Lumen: computing students in liminal spaces

Eckerdal, A., McCartney, R., Mostr?m, J. E., Sanders, K., Thomas, L., and Zander, C. 2007. From Limen to Lumen: computing students in liminal spaces. In Proceedings of the Third international Workshop on Computing Education Research (Atlanta, Georgia, USA, September 15 - 16, 2007). ICER '07. ACM, New York, NY, 123-132.

Przydatność taksonomiczna cech morfologicznych stadiów młodocianych mechowców z podrodziny Crotoniinae Thorell, 1876 (Acari, Oribatida, Camisiidae)

Wydział Biologii: Instytut Biologii Środowiska