Evolutionary implications of multiple SINE insertions in an intronic region from diverse mammals

An analysis of the nuclear beta-fibrinogen intron 7 locus from 30 taxa representing 12 placental orders of mammals reveals the enriched occurrences of short interspersed clement (SINE) insertion events. Mammalian-wide interspersed repeats (MIRs) are present at orthologous sites of all examined species except those in the order Rodentia. The higher substitution rate in mouse and a rare MIR deletion from rat account for the absence of MIR in the rodents. A minimum of five lineage-specific SINE sequences are also found to have independently inserted into this intron in Carnivora, Artiodactyla and Lagomorpha. In the case of Carnivora, the unique amplification pattern of order-specific CAN SINE provides important evidence for the "pan-carnivore" hypothesis of this repeat element and reveals that the CAN SINE family may still be active today. Particularly interesting is the finding that all identified lineage-specific SINE elements show a strong tendency to insert within or in very close proximity to the preexisting MIRs for their efficient integrations, suggesting that the MIR clement is a hot spot for successive insertions of other SINEs. The unexpected MIR excision as a result of a random deletion in the rat intron locus and the non-random site targeting detected by this study indicate that SINEs actually have a greater insertional flexibility and regional specificity than had previously been recognized. Implications for SINE sequence evolution upon and following integration, as well as the fascinating interactions between retroposons and the host genomes are discussed.

Identification of novel SINEs from Cyprinidae and their evolutionary significance

Short interspersed nuclear elements (SINEs) are widespread among eukaryotic genomes. They are repetitive DNA sequences that have been amplified by retrotransposition. In this study, a class of SINEs were isolated from the Opsariichthys bidens genome, and named Opsar. Sequence analysis confirmed that Opsar is a new class of typical SINEs derived from tRNA molecules. With the tRNA-derived region of Opsar and through BLASTN search, we further identified Zb-SINEs from the zebrafish genome, which includes two groups: Zb-SINE-A and Zb-SINE-B. The Zb-SINE-A group comprises subfamilies of -Al--A5, and the Zb-SINE-B group is a dimer of the tRNA(Ala)-derived region and shares a similar dimeric composition to Alu. Zb-SINEs are composed of three distinct regions: a 5 end tRNA-derived region, a tRNA-unrelated region and a 3 end AT-rich region. The flanking regions are AT rich. The average length of Zb-SINEs elements is about 340 6p. Zb-SINEs account for as much as 0.1% of the whole zebrafish genome. About 70% of the Zb-SINEs are on chromosomes 11, 18, and 19. These Zb-SINEs were characterized by PCR and dot hybridization. The distribution pattern of Zb-SINEs in genome strongly supports the master genes model. The tRNA-derived regions of Opsar and Zb-SINEs were compared with the tRNA(Ala) gene, and they showed 76% similarity, indicating that Opsar and Zb-SINEs originated from an inactive tRNA(Ala) sequence or a tRNA(Ala)-like sequence. In view of the evolutionary status of zebrafish in the Cyprinidae, we deduced that Zb-SINEs were a very old class of interspersed sequences.

Retroposon analysis of major cetacean lineages: The monophyly of toothed whales and the paraphyly of river dolphins

SINE (short interspersed element) insertion analysis elucidates contentious aspects in the phylogeny of toothed whales and dolphins (Odontoceti), especially river dolphins. Here, we characterize 25 informative SINEs inserted into unique genomic loci during evolution of odontocetes to construct a cladogram. and determine a total of 2.8 kb per taxon of the flanking sequences of these SINE loci to estimate divergence times among lineages. We demonstrate that: (i) Odontocetes are monophyletic; (ii) Ganges River dolphins, beaked whales, and ocean dolphins diverged (in this order) after sperm whales; (iii) three other river dolphin taxa, namely the Amazon, La Plata, and Yangtze river dolphins, form a monophyletic group with Yangtze River dolphins being the most basal; and (iv) the rapid radiation of extant cetacean lineages occurred some 28-33 million years B.P., in strong accord with the fossil record. The combination of SINE and flanking sequence analysis suggests a topology and set of divergence times for odontocete relationships, offering alternative explanations for several long-standing problems in cetacean evolution.

Stiffness behaviour of injection moulded short glass fibre/impact modifier/polypropylene hybrid composites

The stiffness behaviour of injection moulded short glass fibre/impact modifier/polypropylene hybrid composites has been investigated in this work by theoretical predictions and experiments. Predictions from the self-consistent method were found to be in good agreement with test results for the impact modifier/polypropylene blends. By taking into account of the fibre orientation distributions in the skin and core layers, the values of Young's modulus for the skin and core layers were predicted by employing Eshelby's equivalent inclusion method and the average induced strain approach. The prediction of the values of Young's modulus for the whole sample was obtained by applying the simple mixture theory of laminated composites to the predicted results for the skin and core layers. Good correlation between predicted and experimental Young's modulus values were found.

Modeling and mesoscopic damage constitutive relation of brittle short-fiber-reinforced composites

Aimed at brittle composites reinforced by randomly distributed short-fibers with a relatively large aspect ratio, stiffness modulus and strength, a mesoscopic material model was proposed. Based on the statistical description, damage mechanisms, damage-induced anisotropy, damage rate effect and stress redistribution, the constitutive relation were derived. By taking glass fiber reinforced polypropylene polymers as an example, the effect of initial orientation distribution of fibers, damage-induced anisotropy, and damage-rate effect on macro-behaviors of composites were quantitatively analyzed. The theoretical predictions compared favorably with the experimental results.

An analysis on overall crack-number-density of short-fatigue-cracks

The evolution of dispersed short-fatigue-cracks is analysed based on the equilibrium of crack-number-density (CND). By separating the mean value and the stochastic fluctuation of local CND, the equilibrium equation of overall CND is derived. Comparing with the mean-field equilibrium equation, the equilibrium equation of overall CND has different forms in the expression of crack-nucleation-rate or crack-growth-rate. The simulation results are compared with experimental measurements showing the stochastic analyses provide consistent tendency with experiments. The discrepancy in simulation results between overall CND and mean-field CND is discussed.

An analysis of collective damage for short fatigue cracks based on equilibrium of crack numerical density

Collective damage of short fatigue cracks was analyzed in the light of equilibrium of crack numerical density. With the estimation of crack growth rate and crack nucleation rate, the solution of the equilibrium equation was studied to reveal the distinct feature of saturation distribution for crack numerical density. The critical time that characterized the transition of short and long-crack regimes was estimated, in which the influences of grain size and grain-boundary obstacle effect were investigated. Furthermore, the total number of cracks and the first order of damage moment were discussed.

Simulations and Experiments of Stochastic Characteristics for Collective Short Fatigue Cracks in Steels

Stochastic characteristics prevail in the process of short fatigue crack progression. This paper presents a method taking into account the balance of crack number density to describe the stochastic behaviour of short crack collective evolution. The results from the simulation illustrate the stochastic development of short cracks. The experiments on two types of steels show the random distribution for collective short cracks with the number of cracks and the maximum crack length as a function of different locations on specimen surface. The experiments also give the variation of total number of short cracks with fatigue cycles. The test results are consistent with numerical simulations.

Plastic constitutive behavior of short-fiber/particle reinforced composites

A cylindrical cell model based on continuum theory for plastic constitutive behavior of short-fiber/particle reinforced composites is proposed. The composite is idealized as uniformly distributed periodic arrays of aligned cells, and each cell consists of a cylindrical inclusion surrounded by a plastically deforming matrix. In the analysis, the non-uniform deformation field of the cell is decomposed into the sum of the first order approximate field and the trial additional deformation field. The precise deformation field are determined based on the minimum strain energy principle. Systematic calculation results are presented for the influence of reinforcement volume fraction and shape on the overall mechanical behavior of the composites. The results are in good agreement with the existing finite element analyses and the experimental results. This paper attempts to stimulate the work to get the analytical constitutive relation of short-fiber/particle reinforced composites.

Two-Phase Flow In Fuel Cells In Short-Term Microgravity Condition

A visual observation of liquid-gas two-phase flow in anode channels of a direct methanol proton exchange membrane fuel cells in microgravity has been carried out in a drop tower. The anode flow bed consisted of 2 manifolds and 11 parallel straight channels. The length, width and depth of single channel with rectangular cross section was 48.0 mm, 2.5 mm and 2.0 mm, respectively. The experimental results indicated that the size of bubbles in microgravity condition is bigger than that in normal gravity. The longer the time, the bigger the bubbles. The velocity of bubbles rising is slower than that in normal gravity because buoyancy lift is very weak in microgravity. The flow pattern in anode channels could change from bubbly flow in normal gravity to slug flow in microgravity. The gas slugs blocked supply of reactants from channels to anode catalyst layer through gas diffusion layer. When the weakened mass transfer causes concentration polarization, the output performance of fuel cells declines.

A theoretical analysis on stochastic behaviour of short cracks and fatigue damage of metals

In this paper, the closed form of solution to the stochastic differential equation for a fatigue crack evolution system is derived. and the relationship between metal fatigue damage and crack stochastic behaviour is investigated. It is found that the damage extent of metals is independent of crack stochastic behaviour ii the stochastic deviation of the crack growth rate is directly proportional to its mean value. The evolution of stochastic deviation of metal fatigue damage in the stage close to the transition point between short and long crack regimes is also discussed.

Regularity of strain distribution in short-fiber/whisker reinforced composites

Based on studies on the strain distribution in short-fiber/whisker reinforced metal matrix composites, a deformation characteristic parameter, lambda is defined as a ratio of root-mean-square strain of the reinforcers identically oriented to the macro-linear strain along the same direction. Quantitative relation between lambda and microstructure parameters of composites is obtained. By using lambda, the stiffness moduli of composites with arbitrary reinforcer orientation density function and under arbitrary loading condition are derived. The upper-bound and lower-bound of the present prediction are the same as those from the equal-strain theory and equal-stress theory, respectively. The present theory provides a physical explanation and theoretical base for the present commonly-used empirical formulae. Compared with the microscopic mechanical theories, the present theory is competent for stiffness modulus prediction of practical engineering composites in accuracy and simplicity.

Short-and resonant-range interactions between scales in turbulence and their applications

Interactions between different scales in turbulence were studied starting from the incompressible Navier-Stokes equations. The integral and differential formulae of the short-range viscous stresses, which express the short-range interactions between contiguous scales in turbulence, were given. A concept of the resonant-range interactions between extreme contiguous scales was introduced and the differential formula of the resonant-range viscous stresses was obtained. The short- and resonant-range viscous stresses were applied to deduce the large-eddy simulation (LES) equations as well as the multiscale equations, which are approximately closed and do not contain any empirical constants or relations. The properties and advantages of using the multiscale equations to compute turbulent flows were discussed. The short-range character of the interactions between the scales in turbulence means that the multiscale simulation is a very valuable technique for the calculation of turbulent flows. A few numerical examples were also given.

Collective evolution characteristics and computer simulation of short fatigue cracks

Fatigue testing was conducted using a kind of triangular isostress specimen to obtain the short-fatigue-crack behaviour of a weld low-carbon steel. The experimental results show that short cracks continuously initiate at slip bands within ferrite grain domains and the crack number per unit area gradually increases with increasing number of fatigue cycles. The dispersed short cracks possess an orientation preference, which is associated with the crystalline orientation of the relevant slip system. Based on the observed collective characteristics, computer modelling was carried out to simulate the evolution process of initiation, propagation and coalescence of short cracks. The simulation provides progressive displays which imitate the appearance of experimental observations. The results of simulation indicate that the crack path possesses a stable value of fractal dimension whereas the critical value of percolation covers a wide datum band, suggesting that the collective evolution process of short cracks is sensitive to the pattern of crack site distribution.