Phycobilisomes linker family in cyanobacterial genomes: divergence and evolution

Cyanobacteria are the oldest life form making important contributions to global CO2 fixation on the Earth. Phycobilisomes (PBSs) are the major light harvesting systems of most cyanobacteria species. Recent availability of the whole genome database of cyanobacteria provides us a global and further view on the complex structural PBSs. A PBSs linker family is crucial in structure and function of major light-harvesting PBSs complexes. Linker polypeptides are considered to have the same ancestor with other phycobiliproteins (PBPs), and might have been diverged and evolved under particularly selective forces together. In this paper, a total of 192 putative linkers including 167 putative PBSs-associated linker genes and 25 Ferredoxin-NADP oxidoreductase (FNR) genes were detected through whole genome analysis of all 25 cyanobacterial genomes (20 finished and 5 in draft state). We compared the PBSs linker family of cyanobacteria in terms of gene structure, chromosome location, conservation domain, and polymorphic variants, and discussed the features and functions of the PBSs linker family. Most of PBSs-associated linkers in PBSs linker family are assembled into gene clusters with PBPs. A phylogenetic analysis based on protein data demonstrates a possibility of six classes of the linker family in cyanobacteria. Emergence, divergence, and disappearance of PBSs linkers among cyanobacterial species were due to speciation, gene duplication, gene transfer, or gene loss, and acclimation to various environmental selective pressures especially light.

Lineage-specific domain fusion in the evolution of purine nucleotide cyclases in cyanobacteria

Cyclic nucleotides (both cAMP and cGMP) play extremely important roles in cyanobacteria, such as regulating heterocyst formation, respiration, or gliding. Catalyzing the formation of cAMP and cGMP from ATP and GTP is a group of functionally important enzymes named adenylate cyclases and guanylate cyclases, respectively. To understand their evolutionary patterns, in this study, we presented a systematic analysis of all the cyclases in cyanobacterial genomes. We found that different cyanobacteria had various numbers of cyclases in view of their remarkable diversities in genome size and physiology. Most of these cyclases exhibited distinct domain architectures, which implies the versatile functions of cyanobacterial cyclases. Mapping the whole set of cyclase domain architectures from diverse prokaryotic organisms to their phylogenetic tree and detailed phylogenetic analysis of cyclase catalytic domains revealed that lineage-specific domain recruitment appeared to be the most prevailing pattern contributing to the great variability of cyanobacterial cyclase domain architectures. However, other scenarios, such as gene duplication, also occurred during the evolution of cyanobacterial cyclases. Sequence divergence seemed to contribute to the origin of putative guanylate cyclases which were found only in cyanobacteria. In conclusion, the comprehensive survey of cyclases in cyanobacteria provides novel insight into their potential evolutionary mechanisms and further functional implications.

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.

H5N1 avian influenza re-emergence of Lake Communication Qinghai: phylogenetic and antigenic analyses of the newly isolated viruses and roles of migratory birds in virus circulation

Highly pathogenic avian influenza H5N1 virus has swept west across the globe and caused serious debates on the roles of migratory birds in virus circulation since the first large-scale outbreak in migratory birds of Lake Qinghai, 2005. In May 2006, another outbreak struck Lake Qinghai and six novel strains were isolated. To elucidate these QH06 viruses, the six isolates were subjected to whole-genome sequencing. Phylogenetic analyses show that QH06 viruses are derived from the lineages of Lake Qinghai, 2005. Five of the six novel isolates are adjacent to the strain A/Cygnus olor/Croatia/1/05, and the last one is related to the strain A/duck/Novosibirsk/ 02/05, an isolate of the flyway. Antigenic analyses suggest that QH06 and QH05 viruses are similar to each other. These findings implicate that QH06 viruses of Lake Qinghai may travel back via migratory birds, though not ruling out the possibility of local circulation of viruses of Lake Qinghai.

Molecular phylogeny, recent radiation and evolution of gross morphology of the rhubarb genus Rheum (Polygonaceae) inferred from chloroplast DNA trnL-F sequences

Background and Aims Rheum, a highly diversified genus with about 60 species, is mainly confined to the mountainous and desert regions of the Qinghai-Tibetan plateau and adjacent areas. This genus represents a good example of the extensive diversification of the temperate genera in the Qinghai-Tibetan plateau, in which the forces to drive diversification remain unknown. To date, the infrageneric classification of Rheum has been mainly based on morphological characters. However, it may have been subject to convergent evolution under habitat pressure, and the systematic position of some sections are unclear, especially Sect. Globulosa, which has globular inflorescences, and Sect. Nobilia, which has semi-translucent bracts. Recent palynological research has found substantial contradictions between exine patterns and the current classification of Rheum. Two specific objectives of this research were (1) to evaluate possible relationships of some ambiguous sections with a unique morphology, and (2) to examine possible occurrence of the radiative speciation with low genetic divergence across the total genus and the correlation between the extensive diversification time of Rheum and past geographical events, especially the recent large-scale uplifts of the Qinghai-Tibetan Plateau.Methods The chloroplast DNA trnL-F region of 29 individuals representing 26 species of Rheum, belonging to seven out of eight sections, was sequenced and compared. The phylogenetic relationships were further constructed based on the sequences obtained.Key Results Despite the highly diversified morphology, the genetic variation in this DNA fragment is relatively low. The molecular phylogeny is highly inconsistent with gross morphology, pollen exine patterns and traditional classifications, except for identifying all samples of Sect. Palmata, three species of Sect. Spiciformia and a few species of Sect. Rheum as corresponding monophyletic groups. The monotypic Sect. Globulosa showed a tentative position within the clade comprising five species of Sect. Rheum. All of the analyses revealed the paraphyly of R. nobile and R. alexandrae, the only two species of Sect. Nobilia circumscribed by the possession of large bracts. The crude calibration of lineages based on trnL-F sequence differentiation implied an extensive diversification of Rheum within approx. 7 million years.Conclusions Based on these results, it is suggested that the rich geological and ecological diversity caused by the recent large-scale uplifts of the Qinghai-Tibetan Plateau since the late Tertiary, coupled with the oscillating climate of the Quaternary stage, might have promoted rapid speciation in small and isolated populations, as well as allowing the fixation of unique or rare morphological characters in Rheum. Such a rapid radiation, combined with introgressive hybridization and reticulate evolution, may have caused the transfer of cpDNA haplotypes between morphologically dissimilar species, and might account for the inconsistency between morphological classification and molecular phylogeny reported here.

Phylogenetic analyses of Saussurea sect. Pseudoeriocoryne (Asteraceae : Cardueae) based on chloroplast DNA trnL-F sequences

The genus Saussurea is distributed mainly in the temperate and subarctic regions of Eurasia and consists of about 300 species classified into six subgenera and 20 sections. Sect. Pseudoeriocoryne in the subgenus Eriocoryne comprises four species, and is delimited mainly by acaulescence and an inflorescence with congested capitula surrounded by a rosette of leaves. All of these species are endemic to the and Qinghai-Tibet Plateau. Sequences from the chloroplast DNA trnL-F region were obtained for the four species in this section and 26 other species from four subgenera of Saussurea to resolve phylogenetic relationships among these species and to determine whether the shared characters that define sect. Pseudoeriocoryne are synapomorphic or were acquired by convergent evolution. The resulting phylogenies indicated that Saussurea sect. Pseudoeriocoryne as traditionally defined does not constitute a monophyletic group and that each of its species belongs to separate clades. Furthermore, none of these species showed a close relationship with the other species of subgenus Eriocoryne. Our results further indicated that none of the investigated subgenera are monophyletic, and that species from different subgenera clustered together. All these conclusions are provisional and their confirmation would require stronger phylogenetic support. Two possible explanations are suggested for low sequence divergence, poor resolution of internal clades and clustering of species with the rather distinct morphology of Saussurea detected in the present study. The first is rapid radiation and diversification triggered by fast habitat fragmentation due to the recent lifting of the Qinghai-Tibet Plateau and the Quaternary climate oscillations. This could have led to rapid morphological divergence while sequences diverged very little, and also caused the convergent acquisition of similar characteristics in unrelated lineages due to similar selection pressures. The second possible explanation is that both introgressive hybridization and reticulate evolution might have caused the transferring of cpDNA sequences between morphologically dissimilar species, thus leading to homogenization of sequences between lineages. (C) 2004 Elsevier Ltd. All rights reserved.

Structural Evolution and Property Changes in Nd_{60}Al_{10}Fe_{20}Co_{10} Bulk Metallic Glass During Crystallization

The structural evolution and property changes in Nd60Al10Fe20Co10 bulk metallic glass (BMG) upon crystallization are investigated by the ultrasonic method, x-ray diffraction, density measurement, and differential scanning calorimetry. The elastic constants and Debye temperature of the BMG are obtained as a function of annealing temperature. Anomalous changes in ultrasonic velocities, elastic constants, and density are observed between 600–750 K, corresponding to the formation of metastable phases as an intermediate product in the crystallization process. The changes in acoustic velocities, elastic constants, density, and Debye temperature of the BMG relative to its fully crystallized state are much smaller, compared with those of other known BMGs, the differences being attributed to the microstructural feature of the BMG.

Spallation analysis with a closed trans-scale formulation damage evolution

A closed, trans-scale formulation of damage evolution based on the statistical microdamage mechanics is summarized in this paper. The dynamic function of damage bridges the mesoscopic and macroscopic evolution of damage. The spallation in an aluminium plate is studied with this formulation. It is found that the damage evolution is governed by several dimensionless parameters, i.e., imposed Deborah numbers De* and De, Mach number M and damage number S. In particular, the most critical mode of the macroscopic damage evolution, i.e., the damage localization, is deter-mined by Deborah number De+. Deborah number De* reflects the coupling and competition between the macroscopic loading and the microdamage growth. Therefore, our results reveal the multi-scale nature of spallation. In fact, the damage localization results from the nonlinearity of the microdamage growth. In addition, the dependence of the damage rate on imposed Deborah numbers De* and De, Mach number M and damage number S is discussed.

Nonequilibrium microstructures and their evolution in a Fe-Cr-W-Ni-C laser clad coating

The laser-solidified microstructural and compositional characterization and phase evolution during tempering at 963 K were investigated using an analytical transmission electron microscope with energy dispersive X-ray analysis. The cladded alloy, a powder mixture of Fe, Cr, W, Ni, and C with a weight ratio of 10:5:1:1:1, was processed with a 3 kW continuous wave CO2 laser. The processing parameters were 16 mm/s beam scanning speed, 3 mm beam diameter. 2 kW laser power, and 0.3 g/s feed rate. The coating was metallurgically bonded to the substrate, with a maximum thickness of 730 mu m, a microhardness of about 860 Hv and a volumetric dilution ratio of about 6%. Microanalyses revealed that the cladded coating possessed the hypoeutectic microstructure comprising the primary dendritic gamma-austenite and interdendritic eutectic consisted of gamma-austenite and M7C3 carbide. The gamma-austenite was a non-equilibrium phase with extended solid solution of alloying elements and a great deal of defect structures, i.e. a high density of dislocations, twins, and stacking faults existed in gamma phase. During high temperature aging, in situ carbide transformation occurred of M7C3 to M23C6 and M6C. The precipitation of M23C6, MC and M2C carbides from austenite was also observed.

Microstructure and Evolution of Mechanically-Induced Ultrafine Grain in Surface Layer of Al-Alloy Subjected to USSP

Experiments were conducted to investigate the ultrafine-grained (UFG) microstructures in the surface layer of an aluminum alloy 7075 heavily worked by ultrasonic shot peening. Conventional and high-resolution electron microscopy was performed at various depths of the deformed layer. Results showed that UFG structures were introdued into the surface layer of 62 μm thick. With increasing strain, the various microstructural features, e.g., the dislocation emission source, elongated microbands, dislocation cells, dislocation cell blocks, equiaxed submicro-, and nano-crystal grains etc., were successively produced. The grain subdivision into the subgrains was found to be the main mechanism responsible for grain refinement. The simultaneous evolution of high boundary misorientations was ascribed to the subgrain boundary rotation for accommodating further strains. Formed microstructures were highly nonequilibratory.  2002 Acta Materialia Inc. Published by Elsevier Science Ltd. All rights reserved.

Damage evolution, localization and failure of solids subjected to impact loading

In order to reveal the underlying mesoscopic mechanism governing the experimentally observed failure in solids subjected to impact loading, this paper presents a model of statistical microdamage evolution to macroscopic failure, in particular to spallation. Based on statistical microdamage mechanics and experimental measurement of nucleation and growth of microcracks in an Al alloy subjected to plate impact loading, the evolution law of damage and the dynamical function of damage are obtained. Then, a lower bound to damage localization can be derived. It is found that the damage evolution beyond the threshold of damage localization is extremely fast. So, damage localization can serve as a precursor to failure. This is supported by experimental observations. On the other hand, the prediction of failure becomes more accurate, when the dynamic function of damage is fitted with longer experimental observations. We also looked at the failure in creep with the same idea. Still, damage localization is a nice precursor to failure in creep rupture.

The Structure and Evolution of a Two-Dimensional H2/O2/Ar Cellular Detonation

This paper reports on two-dimensional numerical simulation of cellular detonation wave in a / / mixture with low initial pressure using a detailed chemical reaction model and high order WENO scheme. Before the final equilibrium structure is produced, a fairly regular but still non-equilibrium mode is observed during the early stage of structure formation process. The numerically tracked detonation cells show that the cell size always adapts to the channel height such that the cell ratio is fairly independent of the grid sizes and initial and boundary conditions. During the structural evolution in a detonation cell, even as the simulated detonation wave characteristics suggest the presence of an ordinary detonation, the evolving instantaneous detonation state indicates a mainly underdriven state. As a considerable region of the gas mixture in a cell is observed to be ignited by the incident wave and transverse wave, it is further suggested that these two said waves play an essential role in the detonation propagation.

The evolution of shear bands of saturated soil

The development of the shear bands of saturated soil in coupling-rate- and pore-pressure-dependent simple shear has been discussed, using a simple model and a matching technique at the moving boundary of a shear band. Tt is shown that the development of shear bands are dominated by the coupling-rate and pore-pressure effect of the material. The strength of the soil acts as a destabilizer, whilst pore pressure diffusion makes the band expand. The theory is discussed and some computational solutions have been presented.

Morphological Evolution During Synthesis of New AlPO4 Center dot H2O Crystal

A new crystal of aluminophosphate, AIPO(4)(.)H(2)O, is synthesized from two-batch aqueous solution under hydrothermal conditions. Three types of the crystal habits, i.e. the tetragonal double pyramid, the tetragonal prism and the plate-type tetragonal prism, are found from batch-A solution. Two types of the crystal habits, i.e. the hexagonal pyramid and the strip-type tetragonal prism, are found from batch-B solution. The change of crystal morphology is originated from the fluctuation of the synthesis conditions, such as the supersaturation, the temperature and the impurity content. It causes change of the step energies, the defect density and the step roughness, and further, change of the growth rates. Since the crystal morphology is sensitive to the mass transport mechanism, the crystal habits could be changed under the microgravity.

Contingent sensitivity to configuration in a nonlinear evolution system

A trans-scopic sensitivity of macroscopic failure to slight differentiation in the meso-scopic structure of a system with nonlinear evolution is reported. A periodical chain following a non-local load-sharing evolution was applied as a propotype in failure study. The results demonstrate that there is a transition region composed of globally stable (GS) and evolution induced catastrophic (EIC) modes. That is different from a critical threshold as predicted by percolation and renormalization group theories. Moreover, the EIC mode shows a distinctive sample specific behaviour. For instance, some neighbouring initial states may evolve into completely different final states, though different initial states can evolve into the same final states. As an example, a marginal configuration of EIC mode, a quasi-Fibonacci skeleton, is constructed.