A multi-locus phylogeny of Nectogalini shrews and influences of the paleoclimate on speciation and evolution

Nectogaline shrews are a major component of the small mammalian fauna of Europe and Asia, and are notable for their diverse ecology, including utilization of aquatic habitats. So far, molecular phylogenetic analyses including nectogaline species have been unable to infer a well-resolved, well-supported phylogeny, thus limiting the power of comparative evolutionary and ecological analyses of the group. Here, we employ Bayesian phylogenetic analyses of eight mitochondrial and three nuclear genes to infer the phylogenetic relationships of nectogaline shrews. We subsequently use this phylogeny to assess the genetic diversity within the genus Episoriculus, and determine whether adaptation to aquatic habitats evolved independently multiple times. Moreover, we both analyze the fossil record and employ Bayesian relaxed clock divergence dating analyses of DNA to assess the impact of historical global climate change on the biogeography of Nectogalini. We infer strong support for the polyphyly of the genus Episoriculus. We also find strong evidence that the ability to heavily utilize aquatic habitats evolved independently in both Neomys and Chimarrogale + Nectogale lineages. Our Bayesian molecular divergence analysis suggests that the early history of Nectogalini is characterized by a rapid radiation at the Miocene/Pliocene boundary, thus potentially explaining the lack of resolution at the base of the tree. Finally, we find evidence that nectogalines once inhabited northern latitudes, but the global cooling and desiccating events at the Miocene/Pliocene and Pliocene/Pleistocene boundaries and Pleistocene glaciation resulted in the migration of most Nectogalini lineages to their present day southern distribution. (C) 2010 Elsevier Inc. All rights reserved.

A new species, Gerres septemfasciatus (Perciformes: Gerreidae) from the Chinese coastal waters of the South China Sea

We describe a new species of gerreid fish, Gerres septemfasciatus, based on four specimens collected from the northern South China Sea. G septemfasciatus most closely resembles G limbatus in general appearance. However, G. septemfasciatus is distinguished from the latter and other congeners by having 3 to 3.5 scales between the base of. the fifth dorsal spine and lateral line. This species has a distinctive color pattern, including 7-8 regular, vertical, blue-grayish bands on its side. The distribution of this species is currently known to include the Chinese coastal waters of the South China Sea, but may be also include the coastal waters of southeastern Asia.

Radiation and diversification within the Ligularia-Cremanthodium-Parasenecio complex (Asteraceae) triggered by uplift of the Qinghai-Tibetan Plateau

The Ligularia-Cremanthodium-Parasenecio (L-C-P) complex of the Tussilagininae (Asteraceae: Senecioneae) contains more than 200 species that are endemic to the Qinghai-Tibetan Plateau in eastern Asia. These species are morphologically distinct; however, their relationships appear complex. A phylogenetic analysis of members of the complex and selected taxa, of the tribe Senecioneae was conducted using chloroplast (ndhF and trnL-F) and nuclear (ITS) sequences. Phylogenetic trees were constructed from individual and combined datasets of the three different sequences. All analyses suggested that Doronicum, a genus that has been included in the Tussilagininae, should be excluded from this subtribe and placed at the base of the tribe Senecioneae. In addition, the Tussilagininae should be broadly circumscribed to include the Tephroseridinae. Within the expanded Tussilagininae containing all 13 genera occurring in eastern Asia, Tussilago and NSPetasites diverged early as a separate lineage, while the remaining I I genera comprise an expanded L-C-P complex clade. We suggest that the L-C-P clade, which is largely unresolved, most likely originated as a consequence of an explosive radiation. The few monophyletic subclades identified in the L-C-P clade with robust support further suggest that some genera of Tussilagininae from eastern Asia require generic re-circumscriptions given the occurrence of subclades containing species of the same genus in different parts of the phylogentic tree due to homoplasy of important morphological characters used to delimit them. Molecular-clock analyses suggest that the explosive radiation of the L-C-P complex occurred mostly within the last 20 million years, which falls well within the period of recent major uplifts of the Qinghai-Tibetan Plateau between the early Miocene to the Pleistocene. It is proposed that significant increases in geological and ecological diversity that accompanied such uplifting, most likely promoted rapid and continuous allopatric speciation in small and isolated populations, and allowed fixation or acquisition of similar morphological characters within unrelated lineages. This phenomenon, possibly combined with interspecific diploid hybridization because of secondary sympatry during relatively stable stages between different uplifts, could be a major cause of high species diversity in the Qinghai-Tibetan Plateau and adjacent areas of eastern Asia. (c) 2005 Elsevier Inc. All rights reserved.

Single base-resolution methylome of the silkworm reveals a sparse epigenomic map

Epigenetic regulation in insects may have effects on diverse biological processes. Here we survey the methylome of a model insect, the silkworm Bombyx mori, at single-base resolution using Illumina high-throughput bisulfite sequencing (MethylC-Seq). We conservatively estimate that 0.11% of genomic cytosines are methylcytosines, all of which probably occur in CG dinucleotides. CG methylation is substantially enriched in gene bodies and is positively correlated with gene expression levels, suggesting it has a positive role in gene transcription. We find that transposable elements, promoters and ribosomal DNAs are hypomethylated, but in contrast, genomic loci matching small RNAs in gene bodies are densely methylated. This work contributes to our understanding of epigenetics in insects, and in contrast to previous studies of the highly methylated genomes of Arabidopsis(1) and human(2), demonstrates a strategy for sequencing the epigenomes of organisms such as insects that have low levels of methylation.

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

Understanding the dynamics of eukaryotic transcriptome is essential for studying the complexity of transcriptional regulation and its impact on phenotype. However, comprehensive studies of transcriptomes at single base resolution are rare, even for modern organisms, and lacking for rice. Here, we present the first transcriptome atlas for eight organs of cultivated rice. Using high-throughput paired-end RNA-seq, we unambiguously detected transcripts expressing at an extremely low level, as well as a substantial number of novel transcripts, exons, and untranslated regions. An analysis of alternative splicing in the rice transcriptome revealed that alternative cis-splicing occurred in similar to 33% of all rice genes. This is far more than previously reported. In addition, we also identified 234 putative chimeric transcripts that seem to be produced by trans-splicing, indicating that transcript fusion events are more common than expected. In-depth analysis revealed a multitude of fusion transcripts that might be by-products of alternative splicing. Validation and chimeric transcript structural analysis provided evidence that some of these transcripts are likely to be functional in the cell. Taken together, our data provide extensive evidence that transcriptional regulation in rice is vastly more complex than previously believed.

Analysis of the energies of the triple base triplets

Sixty-four sets of three-dimensional models of DNA triplex base triplets (TBT) were built up based on codons by homologous modeling method and their energies were minimized. According to sequence of TBT and orientation of the third ODN strand third, the energies of monomers and water-K+-TBT ternary complexes of TBT were analyzed. The results showed: (i) The energies of the symmetric parallel monomers are generally lower than those of the symmetric anti-parallel monomers of TBT, but the energies of the symmetric parallel ternary complexes are higher than those of the symmetric anti-parallel ternary complexes of TBT. (ii) No matter TBTs are monomers or ternary complexes, the energies of asymmetric parallel TBTs are generally lower than those of the asymmetric anti-parallel ones. (iii) Although the energies of the parallel TBTs are correlated with those of the anti-parallel ones, the energy differences are significant between them. The results here suggest the sequences of TBTs and the orientations of the third ODN strands are two of the key factors that can influence the formation and stability of TBT. (C) 2002 Elsevier Science B.V. All rights reserved.

The comparative analysis of the energies of conjugated triple base triplets and their applications

We built 64 sets of 3D models of DNA triplex base triplets (TBT) and minimized their energies. The TBTs were divided into 32 pairs of conjugated ones on the basis of their sequence characteristic, and the energies of each pair of them were compared and analyzed, the results showed: (i) The duplex DNA of which any strand contains at least a couple of A or T, has a preference for selecting the oligodeoxyribonucleic acid (ODN) strand containing abundant T to form TBT. (ii) The duplex DNA of which any strand contains at least a couple of G or C has a preference for selecting ODN containing abundant G to form symmetric antiparallel TBT, but selecting ODN containing abundant C to form asymmetric parallel TBT. (iii) The duplex DNA of which any strand contains only one of A, T, G or C has a preference for selecting ODN containing abundant pyrimidines (T or C) to form antiparallel TBT. Additionally, two examples of TBTs applications, in designing ODN to form triplex with duplex were presented. The energy calculation result revealed that 15-TCG is the best ligand of the HIV PPT duplex. The comparative analysis of energies of the conjugated TBTs provides directive significance for designing ODN strand that is easy to form triplex in theory. (C) 2002 Elsevier Science B.V. All rights reserved.

Tentative study of the coding sequences without 3-base periodicity

Fourier spectra of 120 short coding sequences (<1 200 bp) show that not all coding sequences are characterized by 3-base periodicity. Statistical analysis suggests that whether a coding sequence has 3-base periodicity may be related to the composition and distribution of bases, the usage and the order of the amino acids of the encoded protein as well as the synonymous codon usage. Generally, the content of A+U is higher than that of G+C in non-period-3 sequences, inversely in period-3 sequences. In the three codon positions, the base distribution in the non-periodic-3 sequences is more uniform than in the periodic-3 sequences. The usage biases of the amino acids and the codons in non-period-3 sequences are weaker than that in period-3 sequences. All of these phenomena should be considered sufficiently in predicting the genes and exons of DNA sequences by Fourier analysis method.

Rashba spin splitting of the minibands of coupled InAs/GaAs pyramid quantum dots

The Rashba spin splitting of the minibands of coupled InAs/GaAs pyramid quantum dots is investigated using the k center dot p method and valence force field model. The Rashba splitting of the two dimensional miniband in the lateral directions is found due to the structure inversion asymmetry in the vertical direction while the miniband in the vertical direction has no Rashba spin splitting. As the space between dots increases, the Rashba coefficients decrease and the conduction-band effective mass increases. This Rashba spin splitting of the minibands will significantly affect the spin transport properties between quantum dots. (C) 2008 American Institute of Physics.

Synthesis, molecular structures, and norbornene addition polymerization activity of the neutral nickel catalysts supported by beta-diketiminato [N, N], ketiminato [N, O], and Schiff-Base [N, O] ligands

A series of neutral nickel complexes [Ni(Ph)(PPh3)(N, O)] with Schiff-base ligands (N, O) [N, O = 5-Me-3-tert-Bu-(Ar-N=CH)C6H2O (1, Ar = 2,6-Me2C6H3; 2, Ar = 2,6-i-Pr2C6H3)], [Ni(Ph)(PPh3)(N,O)1, with beta-ketiminato ligands (N, O) [N, O = CH3COCHC=(CH3)N-Ar (3, Ar = 2,6-Me2C6H3; 4, Ar = 2,6-i-Pr2C6H3)] and [Ni(N, N)(PPh3)], and with beta-diketiminato ligands (N, N) [5, N, N = [2,6-i-Pr-2(C6H3)N=C(CH3)](2)CH] have been synthesized and characterized. The molecular structures of complexes 1, 4, and 5 have been confirmed by X-ray single-crystal analyses. Although their ligands have similar structures, complex 4 possesses a structure similar to that of four-coordination nickel with complex 1, while complex 5 reveals a rare three-coordination nickel geometry. These compounds show high catalytic activities of up to 3.16 x 10(7) g PNB mol(-1) Ni h(-1) for the addition polymerization of norbornene in the presence of modified methylaluminoxane (MMAO) as cocatalyst. Catalytic activities, polymer yield, molecular weights, and molecular weight distributions of polyborbornene have been investigated under various reaction conditions.

Synthesis, structure characterization of the complexes of beta-alkoxycarbonylethyltin trichlorides with Schiff base ligands

Thirty - two title complexes (ROCOCHRCH2SnCl3)-C-1 . (2 - HOC6H4CH = NC6H4 - X) (R = Me, Et, n - Bu; R-1 = H, Me; X = H,4' - Cl, 3' - Pr, 3' - OH, 3', 4' - Cl-2, 4' - OMe) were synthesized and characterized by elemental analysis,UV - vis, IR, H-1 NMR. The crystal structure of n - BuOCOCH2CH2SnCl3 . (2 - HOC6H4CH - NC6H4OMe - 4') were determined by the X - ray diffraction analysis, The crystal belongs to monoclinic system, with a = 1.4661 (3)nm, b = 0.9307 (2)nm, c = 1.7888 (4)nm, beta = 94.04 (3)degrees, V = 2.4348nm(3), D-c = 1.581mg/m(3), Z = 4, F(000) = 1160, mu = 1.405mm(-1), R = 0.0354, R-w = 0,0486, space group: P2(1)/c. The complexes exist as a discrete monomer. The tin atom has a distorted octahedral geometry due to intramolecular coordination of the carbonyl oxygen and the phenolic oxygen of the Schiff base ligands, The coordination number of tin atom is 6.

Synthesis of the first mono(cyclopentadienyl)lanthanide Schiff base complex bearing C-2-symmetric tetradentate ligand: crystal structure of [(eta(5)-C5H5)Yb(mu-OC20H20N2O)](2)(mu-THF)(THF)

Reaction of YbCl3 with 3 equimolar CpNa (Cp = cyclopentadienide) in THF, followed by treatment with trans-(+/-)-N,N'-bis(salicylidene)-1,2-cyclohexanediamine led to the isolation of first mono(cyclopentadienyl) lanthanide Schiff base complex, [(eta(5)-C5H5)Yb(mu-OC20H20N2O)](2) (mu-THF)(THF) (1). The molecular structure of 1 shows that it is a dimer in which the two [(eta(5)-C5H5)Yb(mu-OC20H20N2O)] units connecting via a bridging THF oxygen and two bridging oxygen atoms from Schiff base ligands. (C) 1998 Elsevier Science S.A.