The dazzling array of basal branches in the mtDNA macrohaplogroup M from India as inferred from complete genomes

Many efforts based on complete mitochondrial DNA (mtDNA) genomes have been made to depict the global mtDNA landscape, but the phylogeny of Indian macrohaplogroup M has not yet been resolved in detail. To fill this lacuna, we took the same strategy as in o

Influence of short chain branches on crystallization and melting behavior of low molecular weight polyethylenes

The crystallization and melting behavior of mellocene-catalized branched and linear polyethylenes of low molecular weight was studied. It was found that the crystalline lattice of branched polyethylene is larger than that of linear polyethylene because of the existence of branched chains. The melting behavior of branched polyethylene is similar to that of linear polyethylene since the branched chains can not enter the lattice. However, the crystalline behavior of low molecular weight branched polyethylene is the same as that of high molecular weight linear polyethylene, but different with that of low molecular weigh linear polyethylene. Kinetics theory analysis evidenced that the transition temperature of growth regime of the branched polyethylene is about 20 degreesC lower than that of linear polyethylene with the same molecular weight. It may be attributed to the existence of short branched chains.

An acidic polysaccharide with xylose branches from Porphyra yezoensis

An acidic polysaccharide (PY3) was isolated from the hot water extract of the red algae Porphyra yezoensis by successive column chromatographies over DEAE-cellulose and Sephadex G-200. PY3 with an average molecular weight of 1.8x10(5) was demonstrated to be composed of galactose (Gal), 3,6-anhydrogalactose (3,6-AnGal), 6-OSO3-galactose (6-OSO3-Gal) and xylose (Xyl) in an approximate molar ratio of 25 : 15, 10, 1. In view of Smith degradation and methylation and on the basis of spectral evidence including those of IR, GC, GC-MS, and H-1 and C-13 NMR, the most probable repeating unit of PY3 could be proposed as [(1-->3)beta -D-Gal(1 --> 4)alpha -L-3,6-AnGal](3)-[(1 --> 3)beta -D-Gal(1 --> 4)alpha -L-6-OSO3-Gal](2) with a xylose moiety at the C-6 of one of every twenty-five beta -D-Gal residues. To our knowledge, PY3 was shown to be the first porphyran possessing occasional xylose branches.

Optimization of conditions for tetraspore release and assessment of photosynthetic activities for different generation branches of Gracilaria lemaneiformis Bory

Gracilaria lemaneiformis Bory is an economically important alga that is primarily used for agar production. Although tetraspores are ideal seeds for the cultivation of G. lemaneiformis, the most popular culture method is currently based on vegetative fragments, which is labor-intensive and time-consuming. In this study, we optimized the conditions for tetraspore release and evaluated the photosynthetic activities of different colonies formed from the branches of G. lemaneiformis using a PAM (pulse-amplitude-modulated) measuring system. The results showed that variations in temperature and salinityhad significant effects on tetraspore yield. However, variations in the photon flux density (from 15 mu mol m(-2) s(-1) to 480 mu mol m(-2) s(-1)) had no apparent effect on tetraspore yield. Moreover, the PAM-parameters Y(I), Y(II), ETR(I), ETR(II) and F (v)/F (m) of colonies formed from different branches showed the same trend: parameter values of first generation branches > second generation branches > third generation branches. These results suggest that the photosynthetic activities of different colonies of branches changed with the same trend. Furthermore, photosynthesis in G. lemaneiformis was found to be involved in vegetative reproduction and tetraspore formation. Finally, the first generation branches grew slowly, but accumulated organic compounds to form large numbers of tetraspores. Taken together, these results showed that the first generation branches are ideal materials for the release of tetraspores.

Two critical crack propagating velocities for PMMA fracture surface

Ultrasonic fractography and scanning electronic microscopy (SEM) are used to determine the direct relationship between the fracture surface morphology and the main crack velocity during the rapid rupture of polymethylmethacrylate (PMMA). Two critical crack velocities are found for the fracture. Quasi-parabolic markings will appear when the crack speed exceeds the first critical speed. Crack propagating at speed above the second critical speed leaves a thicket of small branches penetrating the surface behind them. Both critical speeds are functions of the thickness of the specimens.

Flood Routing Models in Confluent and Dividing Channels

By introducing a water depth connecting formula, the hydraulic equations in the dividing channel system were coupled and the relation of discharge distribution between the branches of the dividing channels can be yielded. In this manner, a numerical model for the confluent channels was established to study the variation of backwater effects with the parameters in the channel junction. The meeting of flood peaks in the mainstream and tributary can be analyzed with this model. The flood peak meeting is found to be a major factor for the extremely high water level in the mainstream during the 1998 Yangtze River flood. Subsequently the variations of discharge distribution and water level with channel parameters between each branch in this system were studied as well. As a result, flood evolution caused by Jingjiang River shortcut and sediment deposition in the entrance of dividing channels of the Yangtze River may be qualitatively elucidated. It is suggested to be an effective measure for flood mitigation to enhance regulation capability of reservoirs available upstream of the tributaries and harness branch entrance channels.

Influence of liquid bridge volume on the onset of oscillation in floating-zone convection III. Three-dimensional model

An unsteady and three-dimensional model of the floating-half-zone convection on the ground is studied by the direct numerical simulation for the medium of 10 cSt silicon oil, and the influence of the liquid bridge volume on the critical applied temperature difference is especially discussed. The marginal curves for the onset of oscillation are separated into two branches related, respectively, to the slender liquid bridge and the fat liquid bridge. The oscillatory features of the floating-half-zone convection are also discussed.

Studies on two-phase co-current air/non-Newtonian shear-thinning fluid flows in inclined smooth pipes

In this work. co-current flow characteristics of air/non-Newtonian liquid systems in inclined smooth pipes are studied experimentally and theoretically using transparent tubes of 20, 40 and 60 turn in diameter. Each tube includes two 10 m lone pipe branches connected by a U-bend that is capable of being inclined to any angle, from a completely horizontal to a fully vertical position. The flow rate of each phase is varied over a wide range. The studied flow phenomena are bubbly, plug flow, slug flow, churn flow and annular flow. These are observed and recorded by a high flow. stratified flow. -speed camera over a wide range of operating conditions. The effects of the liquid phase properties, the inclination angle and the pipe diameter on two-phase flow characteristics are systematically studied. The Heywood-Charles model for horizontal flow was modified to accommodate stratified flow in inclined pipes, taking into account the average void fraction and pressure drop of the mixture flow of a gas/non-Newtonian liquid. The pressure drop gradient model of Taitel and Barnea for a gas/Newtonian liquid slug flow was extended to include liquids possessing shear-thinning flow behaviour in inclined pipes. The comparison of the predicted values with the experimental data shows that the models presented here provide a reasonable estimate of the average void fraction and the corresponding pressure drop for the mixture flow of a gas/ non-Newtonian liquid. (C) 2007 Elsevier Ltd. All rights reserved.

Internal resonance of an L-shaped beam with a limit stop .2. Forced vibration

A limit stop is placed at the elbow of an L-shaped beam whose linear natural frequencies are nearly commensurable. As a result of this hardening device the non-linear system exhibits multiple internal resonances, which involve various degree of coupling between the first five modes of the beam in free vibration. A point load is so placed as to excite several modes and the resulting forced vibration is examined. In the undamped case, three in-phase and two out-of-phase solution branches have been found. The resonance curve is extremely complicated, with multiple branches and interactions between the first four modes. The amplitudes of the higher harmonics are highly influenced by damping, the presence of which can effectively attenuate internal resonances. Consequently parts of the resonance curve may be eliminated, with the resulting response comprising different distinctive branches. (C) 1996 Academic Press Limited

Optimization of multi-cycle two-color laser fields for the generation of an isolated attosecond pulse

The effect of the mixing of pulsed two color fields on the generation of an isolated attosecond pulse has been systematically investigated. One main color is 800 nm and the other color (or secondary color) is varied from 1.2 to 2.4 mu m. This work shows that the continuum length behaves in a similar way to the behavior of the difference in the square of the amplitude of the strongest and next strongest cycle. As the mixing ratio is increased, the optimal wavelength for the extended continuum shifts toward shorter wavelength side. There is a certain mixing ratio of intensities at which the continuum length bifurcates, i.e., the existence of two optimal wavelengths. As the mixing ratio is further increased, each branch bifurcates again into two sub-branches. This 2D map analysis of the mixing ratio and the wavelength of the secondary field easily allows one to select a proper wavelength and the mixing ratio for a given pulse duration of the primary field. The study shows that an isolated sub-100 attosecond pulse can be generated mixing an 11 fs full-width-half-maximum (FWHM), 800 laser pulse with an 1840 nm FWHM pulse. Furthermore the result reveals that a 33 fs FWHM, 800 nm pulse can produce an isolated pulse below 200 as, when properly mixed. (c) 2008 Optical Society of America.

Episodic evolution of prolactin receptor gene in mammals: coevolution with its ligand

Divergence of proteins in signaling pathways requires ligand and receptor coevolution to maintain or improve binding affinity and/or specificity. In this paper we show a clear case of coevolution between the prolactin (PRL) gene and its receptor (prolactin receptor, PRLR) in mammals. First we observed episodic evolution of the extracellular and intracellular domains of the PRLR, which is closely consistent with that seen in PRL. Correlated evolution was demonstrated both between PRL and its receptor and between the two domains of the PRLR using Pearson's correlation coefficient. On comparing the ratio of the nonsynonymous substitution rate to synonymous substitution rate (omega=d(N)/d(S)) for each branch of the star phylogeny of mammalian PRLRs, separately for the extracellular domain (ECD) and the transmembrane domain/intracellular domain (TMD/ICD), we observed a lower omega ratio for ECD than TMD/ICD along those branches leading to pig, dog and rabbit but a higher ratio for ECD than TMD/ICD on the branches leading to primates, rodents and ruminants, on which bursts of rapid evolution were observed. These observations can be best explained by coevolution between PRL and its receptor and between the two domains of the PRLR.

Molecular phylogenetics and biogeography of Lepus in Eastern Asia based on mitochondrial DNA sequences

In spite of several classification attempts among taxa of the genus Lepus, phylogenetic relationships still remain poorly understood. Here, we present molecular genetic evidence that may resolve some of the current incongruities in the phylogeny of the leporids. The complete mitochondrial cytb, 12S genes, and parts of ND4 and control region fragments were sequenced to examine phylogenetic relationships among Chinese hare taxa and other leporids throughout the World using maximum parsimony, maximum likelihood, and Bayesian phylogenetic reconstruction approaches. Using reconstructed phylogenies, we observed that the Chinese hare is not a single monophyletic group as originally thought. Instead, the data infers that the genus Lepus is monophyletic with three unique species groups: North American, Eurasian, and African. Ancestral area analysis indicated that ancestral Lepus arose in North America and then dispersed into Eurasia via the Bering Land Bridge eventually extending to Africa. Brooks Parsimony analysis showed that dispersal events followed by subsequent speciation have occurred in other geographic areas as well and resulted in the rapid radiation and speciation of Lepus. A Bayesian relaxed molecular clock approach based on the continuous autocorrelation of evolutionary rates along branches estimated the divergence time between the three major groups within Lepus. The genus appears to have arisen approximately 10.76 MYA (+/- 0.86 MYA), with most speciation events occurring during the Pliocene epoch (5.65 +/- 1.15 MYA similar to 1.12 +/- 10.47 MYA). (c) 2005 Elsevier Inc. All rights reserved.

Phylogenetic analyses of Fringillidae (Aves : Passeriformes) using mitochondrial tRNA gene sequences and secondary structure

Fringillidae is a large and diverse family of Passeriformes. So far, however, Fringillidae relationships deduced from morphological features and by a number of molecular approaches have remained unproven. Recently, much attention has been attracted to mitochondrial tRNA genes, whose sequence and secondary structural characteristics have shown to be useful for Acrodont Lizards and deep-branch phylogenetic studies. In order to identify useful phylogenetic markers and test Fringillidae relationships, we have sequenced three major clusters of mitochondrial tRNA genes from 15 Fringillidae, taxa. A coincident tree, with coturnix as outgroup, was obtained through Maximum-likelihood method using combined dataset of 11 mitochondrial tRNA gene sequences. The result was similar to that through Neighbor-joining but different from Maximum-parsimony methods. Phylogenetic trees constructed with stem-region sequences of 11 genes had many different topologies and lower confidence than with total sequences. On the other hand, some secondary structural characteristics may provide phylogenetic information on relatively short internal branches at under-genus level. In summary, our data indicate that mitochondrial tRNA genes can achieve high confidence on Fringillidae phylogeny at subfamily level, and stem-region sequences may be suitable only at above-family level. Secondary structural characteristics may also be useful to resolve phylogenetic relationship between different genera of Fringillidae with good performance.

A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae

Background: The Galliformes is a well-known and widely distributed Order in Aves. The phylogenetic relationships of galliform birds, especially the turkeys, grouse, chickens, quails, and pheasants, have been studied intensively, likely because of their close association with humans. Despite extensive studies, convergent morphological evolution and rapid radiation have resulted in conflicting hypotheses of phylogenetic relationships. Many internal nodes have remained ambiguous. Results: We analyzed the complete mitochondrial (mt) genomes from 34 galliform species, including 14 new mt genomes and 20 published mt genomes, and obtained a single, robust tree. Most of the internal branches were relatively short and the terminal branches long suggesting an ancient, rapid radiation. The Megapodiidae formed the sister group to all other galliforms, followed in sequence by the Cracidae, Odontophoridae and Numididae. The remaining clade included the Phasianidae, Tetraonidae and Meleagrididae. The genus Arborophila was the sister group of the remaining taxa followed by Polyplectron. This was followed by two major clades: ((((Gallus, Bambusicola) Francolinus) (Coturnix, Alectoris)) Pavo) and (((((((Chrysolophus, Phasianus) Lophura) Syrmaticus) Perdix) Pucrasia) (Meleagris, Bonasa)) ((Lophophorus, Tetraophasis) Tragopan))). Conclusions: The traditional hypothesis of monophyletic lineages of pheasants, partridges, peafowls and tragopans was not supported in this study. Mitogenomic analyses recovered robust phylogenetic relationships and suggested that the Galliformes formed a model group for the study of morphological and behavioral evolution.

Parallel and Convergent Evolution of the Dim-Light Vision Gene RH1 in Bats (Order: Chiroptera)

Rhodopsin, encoded by the gene Rhodopsin (RH1), is extremely sensitive to light, and is responsible for dim-light vision. Bats are nocturnal mammals that inhabit poor light environments. Megabats (Old-World fruit bats) generally have well-developed eyes, while microbats (insectivorous bats) have developed echolocation and in general their eyes were degraded, however, dramatic differences in the eyes, and their reliance on vision, exist in this group. In this study, we examined the rod opsin gene (RH1), and compared its evolution to that of two cone opsin genes (SWS1 and M/LWS). While phylogenetic reconstruction with the cone opsin genes SWS1 and M/LWS generated a species tree in accord with expectations, the RH1 gene tree united Pteropodidae (Old-World fruit bats) and Yangochiroptera, with very high bootstrap values, suggesting the possibility of convergent evolution. The hypothesis of convergent evolution was further supported when nonsynonymous sites or amino acid sequences were used to construct phylogenies. Reconstructed RH1 sequences at internal nodes of the bat species phylogeny showed that: (1) Old-World fruit bats share an amino acid change (S270G) with the tomb bat; (2) Miniopterus share two amino acid changes (V104I, M183L) with Rhinolophoidea; (3) the amino acid replacement I123V occurred independently on four branches, and the replacements L99M, L266V and I286V occurred each on two branches. The multiple parallel amino acid replacements that occurred in the evolution of bat RH1 suggest the possibility of multiple convergences of their ecological specialization (i.e., various photic environments) during adaptation for the nocturnal lifestyle, and suggest that further attention is needed on the study of the ecology and behavior of bats.