Positive selection on multiple antique allelic lineages of transferrin in the polyploid Carassius auratus

Transferrin polymorphism has been studied in the polyploid Carassius auratus by cloning and sequence analysis of cDNAs from its three subspecies C. auratus gibelio, C. auratus auratus, and C. auratus cuvieri. DNA polymorphism of extremely high extent was shown for the transferrin gene by the 248 segregation sites among coding region sequences of its alleles. The deduced amino acid sequences of the transferrin alleles showed variable theoretical physicochemical parameters, which might constitute molecular basis for their electrophoretic heterogeneity. Positive selection was inferred by the replacement/synonymous ratios larger than 1 in partial allelic lineages which was subsequently confirmed by likelihood simulation under neutral or selection models. Furthermore, the correspondent sites to these selected codons were collectively located at two planes in the crystallographic structure of rabbit transferrin, which suggested that the rapid evolution of C. auratus transferrin might correlate to its adaptation to variable environmental elements such as oxygen pressure. The minimal 26 recombination events were detected among coding sequences of C. auratus transferrin, with partial mosaic sequences and breakpoints identified by identity scanning and information site analyses. Phylogenetic analyses revealed multiple antique allelic lineages of transferrin, which was estimated to diverge fifteen to twenty MYA. All these features strongly suggested the role of balancing selection in long persistence of high transferrin polymorphism in C. auratus. Furthermore, owing to its particular evolutionary backgrounds, the silver crucian carp might possess a distinctive balancing selection mechanism.

Experimental Studies on Scramjet Tested in a Freejet Facility

Two different type scramjet models with side-wall compression and top-wall compression inlets have been tested in HPTF (Hypersonic Propulsion Test Facility) under the experimental conditions of Mach number 5.8, total temperature 1700K, total pressure 4.5MPa and mass flow rate 3.5kg/s. The liquid kerosene was used as main fuel for the scramjets. In order to get fast ignition in the combustor, a small amount of hydrogen was used as a pilot. A strut with alternative tail was employed for increasing the compression ratio and for mixing enhancement in the side-wall compression case. Recessed cavities were used as a flameholder for combustion stability. The combustion efficiency was estimated by one dimensional theory. The uniformity of the facility nozzle flow was verified by a scanning pitot rake. The experimental results showed that the kerosene fuel was successfully ignited and stable combustion was achieved for both scramjet models. However the thrusts were still less than the model drags due to the low combustion efficiencies.

Comparative studies on parallel and antiparallel duplex and triplex DNA

Parallel strand models for base sequences d(A)(10). d(T)(10), d(AT)(5) . d(TA)(5), d(G(5)C(5)). d(C(5)G(5)), d(GC)(5) . d(CG)(5) and d(CTATAGGGAT). d(GATATCCCTA), where reverse Watson-Crick A-T pairing with two H-bonds and reverse Watson-Crick G-C pairing with one H-bond or with two H-bonds were adopted, and three models of d(T)(14). d(A)(14). d(T)(14) triple helix with different strand orientations were built up by molecular architecture and energy minimization. Comparisons of parallel duplex models with their corresponding B-DNA models and comparisons among the three triple helices showed: (i) conformational energies of parallel AT duplex models were a little lower, while for GC duplex models they were about 8% higher than that of their corresponding B-DNA models; (ii) the energy differences between parallel and B-type duplex models and among the three triple helices arose mainly from base stacking energies, especially for GC base pairing; (iii) the parallel duplexes with one H-bond G-C pairs were less stable than those with two H-bonds G-C pairs. The present paper includes a brief discussion about the effect of base stacking and base sequences on DNA conformations. (C) 1997 Academic Press Limited.

Kinetic modeling of growth and biodegradation of phenol and m-cresol using Alcaligenes faecalis

A phenol-degrading. microorganism, Alcaligenes faecalis, was used to study the substrate interactions during cell growth on phenol and m-cresol dual substrates. Both phenol and m-cresol could be utilized by the bacteria as,the sole carbon and energy sources. When cells grew on the mixture of phenol and m-cresol, strong substrate interactions were observed. m-Cresol inhibited the degradation of phenol, on the other hand, phenol also inhibited the utilization of m-cresol, the overall cell growth rate was the co-action of phenol and m-cresol. In addition, the cell growth and substrate degradation kinetics of phenol, m-cresol as single and mixed substrates for A. faecalis in batch cultures were also investigated over a wide range of initial phenol concentrations (10-1400 mg L-1) and initial m-cresol concentrations (5-200 mg L-1). The single-substrate kinetics was described well using the Haldane-type kinetic models, with model constants of it mu(m1) = 0.15 h(-1), K-S1 = 2.22 mg L-1 and K-i1 = 245.37 mg L-1 for cell growth on phenol and mu(m2) = 0.0782 h(-1), K-S2 = 1.30 mg L-1 and K-i2 = 71.77 mgL(-1), K-i2' = 5480 (mg L-1)(2) for cell growth on m-cresol. Proposed cell growth kinetic model was used to characterize the substrates interactions in the dual substrates system, the obtained parameters representing interactions between phenol and m-cresol were, K = 1.8 x 10(-6), M = 5.5 x 10(-5), Q = 6.7 x 10(-4). The results received in the experiments demonstrated that these models adequately described the dynamic behaviors of phenol and m-cresol as single and mixed substrates by the strain of A. faecalis.

Properties of proton-implanted p-type Si: supports for the models explaining a novel p-n junction in Si

Proton-implanted and annealed p-type Si wafers were investigated by using both transmission electron microscopy and spreading resistivity probe. The novel pn junction [Li et al., Mat. Res. Sec. Symp, Proc. 396 (1996) 745], as obtained by using n-type Si subjected to the process as this work, was not observed in the p-type Si wafers in this work. A drop of superficial resistivity in the sample was found and is explained by the proposed models interpreting the novel pn junction. (C) 2000 Elsevier Science B.V. All rights reserved.

Statistical analysis of synthetic earthquake catalogs generated by models with various levels of fault zone disorder

The stress release model, a stochastic version of the elastic rebound theory, is applied to the large events from four synthetic earthquake catalogs generated by models with various levels of disorder in distribution of fault zone strength (Ben-Zion, 1996) They include models with uniform properties (U), a Parkfield-type asperity (A), fractal brittle properties (F), and multi-size-scale heterogeneities (M). The results show that the degree of regularity or predictability in the assumed fault properties, based on both the Akaike information criterion and simulations, follows the order U, F, A, and M, which is in good agreement with that obtained by pattern recognition techniques applied to the full set of synthetic data. Data simulated from the best fitting stress release models reproduce, both visually and in distributional terms, the main features of the original catalogs. The differences in character and the quality of prediction between the four cases are shown to be dependent on two main aspects: the parameter controlling the sensitivity to departures from the mean stress level and the frequency-magnitude distribution, which differs substantially between the four cases. In particular, it is shown that the predictability of the data is strongly affected by the form of frequency-magnitude distribution, being greatly reduced if a pure Gutenburg-Richter form is assumed to hold out to high magnitudes.

Long-range automaton models of earthquakes: Power-law accelerations, correlation evolution, and mode-switching

We introduce a conceptual model for the in-plane physics of an earthquake fault. The model employs cellular automaton techniques to simulate tectonic loading, earthquake rupture, and strain redistribution. The impact of a hypothetical crustal elastodynamic Green's function is approximated by a long-range strain redistribution law with a r(-p) dependance. We investigate the influence of the effective elastodynamic interaction range upon the dynamical behaviour of the model by conducting experiments with different values of the exponent (p). The results indicate that this model has two distinct, stable modes of behaviour. The first mode produces a characteristic earthquake distribution with moderate to large events preceeded by an interval of time in which the rate of energy release accelerates. A correlation function analysis reveals that accelerating sequences are associated with a systematic, global evolution of strain energy correlations within the system. The second stable mode produces Gutenberg-Richter statistics, with near-linear energy release and no significant global correlation evolution. A model with effectively short-range interactions preferentially displays Gutenberg-Richter behaviour. However, models with long-range interactions appear to switch between the characteristic and GR modes. As the range of elastodynamic interactions is increased, characteristic behaviour begins to dominate GR behaviour. These models demonstrate that evolution of strain energy correlations may occur within systems with a fixed elastodynamic interaction range. Supposing that similar mode-switching dynamical behaviour occurs within earthquake faults then intermediate-term forecasting of large earthquakes may be feasible for some earthquakes but not for others, in alignment with certain empirical seismological observations. Further numerical investigation of dynamical models of this type may lead to advances in earthquake forecasting research and theoretical seismology.

Study of three elastic-plastic constitutive models by non-proportional finite deformations of OFHC copper

Experimental stress-strain data of OFHC copper first under torsion to 13% and then under torsion-tension to about 10% are used to study the characteristics of three elastic-plastic constitutive models: Chaboche's super-positional nonlinear model, Dafalias and Popov's two surface model and Watanabe and Atluri's version of the endochronic model. The three models, originally oriented for infinitesimal deformation, have been extended for finite deformation. The results show (a) the Mises-type yield surface used in the three models brings about significant departure of the predictions from the experimental data; (b) Chaboche's and Dafalias' models are easier than Watanabe and Atluri's model in determining the material parameters in them, and (c) Chaboche's and Watanabe & Atluri's models produce almost the same prediction to the data, while Dafalias' model cannot accurately predict the plastic deformations when a loading path changes in its direction. Copyright (C) 1996 Elsevier Science Ltd

Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication

Background: Various evolutionary models have been proposed to interpret the fate of paralogous duplicates, which provides substrates on which evolution selection could act. In particular, domestication, as a special selection, has played important role in crop cultivation with divergence of many genes controlling important agronomic traits. Recent studies have indicated that a pair of duplicate genes was often sub-functionalized from their ancestral functions held by the parental genes. We previously demonstrated that the rice cell-wall invertase (CWI) gene GIF1 that plays an important role in the grain-filling process was most likely subjected to domestication selection in the promoter region. Here, we report that GIF1 and another CWI gene OsCIN1 constitute a pair of duplicate genes with differentiated expression and function through independent selection. Results: Through synteny analysis, we show that GIF1 and another cell-wall invertase gene OsCIN1 were paralogues derived from a segmental duplication originated during genome duplication of grasses. Results based on analyses of population genetics and gene phylogenetic tree of 25 cultivars and 25 wild rice sequences demonstrated that OsCIN1 was also artificially selected during rice domestication with a fixed mutation in the coding region, in contrast to GIF1 that was selected in the promoter region. GIF1 and OsCIN1 have evolved into different expression patterns and probable different kinetics parameters of enzymatic activity with the latter displaying less enzymatic activity. Overexpression of GIF1 and OsCIN1 also resulted in different phenotypes, suggesting that OsCIN1 might regulate other unrecognized biological process. Conclusion: How gene duplication and divergence contribute to genetic novelty and morphological adaptation has been an interesting issue to geneticists and biologists. Our discovery that the duplicated pair of GIF1 and OsCIN1 has experiencedsub-functionalization implies that selection could act independently on each duplicate towards different functional specificity, which provides a vivid example for evolution of genetic novelties in a model crop. Our results also further support the established hypothesis that gene duplication with sub-functionalization could be one solution for genetic adaptive conflict.

Relaxed purifying selection of rhodopsin gene within a Chinese endemic cavefish genus Sinocyclocheilus (Pisces: Cypriniformes)

The cyprinid fish genus Sinocyclocheilus, as the most cavefish rich genus, includes many species showing striking adaptation to caves and convergent reduction or even loss of eyes and pigmentation. RH1 is responsible for dim vision. In order to explore the evolution of RH1 gene in this genus, we sequenced the complete gene from 28 individuals of 16 representative species of Sinocyclocheilus, with cave and surface species included. Phylogenetic analyses supported the monophyly of Sinocyclocheilus and polyphyly of the cave species. Codon models implemented in PAML were used to infer the evolution of RH1. We found that Sinocyclocheilus had a significantly higher evolutionary rate for amino acids than other cyprinid fishes compared, which might be the result of relaxation of purifying selection and could be ascribed to cave habit of this genus. In contrast to previous hypotheses, both cave and surface lineages exhibited a similar rate of molecular evolution, so the RH1 of cave species may still be functional, although these species were highly adapted to cave environment. Two amino acid substitutions (D83G and E122V) that were not reported before were found, which may be useful for site-directed mutagenesis in the future.

Selection and ultrastructural observation of a high-CO2-requiring mutant of cyanobacterium Synechococcus sp PCC7942

A high-CO2-requiring mutant of Synechococcus sp. PCC7942 las been isolated after chemical mutagenesis of ethyl methane sulphonate (EMS). It was able to grow at 4% CO2, but not under ambient CO2. The initial screening of the mutant showed that the genetic reversion rate was about 10(-7) and death occurred 2 -3 days after being transferred from 4% CO2 to the ambient air. Its photosynthetic dependence on external dissolved inorganic carbon was higher than that of the wild type cells, but its carbonic anhydrase activity was comparatively low. In the ultrastructural level, various types of aberrant carboxysomes appeared in the mutant cells: rod-shaped carboxysomes, irregular carboxysomes and the "empty-inclusion carboxysomes" with increasing number of glycogen granules surrounding the thylakoids. All these alterations indicated that the mutant was defective in utilizing the external CO2. The induction of carboxysomes by lower levels of CO2 and the biogenesis of carboxysomes are herein discussed.

Pressure drops of single and two-phase flows through T-type microchannel mixers

In this paper, preliminary experimental results are presented on pressure drop characteristics of single and two-phase flows through two T-type rectangular microchannel mixers with hydraulic diameters of 528 and 333 mum, respectively. It is shown that both N-2 and water single-phase laminar flows in microchannels, with consideration of experimental uncertainties, are consistent with classic theory, if additional effects, such as entrance effects that will interfere with the interpretation of experimental results, are eliminated by carefully designing the experiments. The obtained pressure drop data of N-2-water two-phase flow in micromixers are analyzed and compared with existing flow pattern-independent models. It is found that the Lockhart-Martinelli method generally underpredicts the frictional pressure drop. Thereafter, a modified correlation of C value in the Chisholm's equation based on linear regression of experimental data is proposed to provide a better prediction of the two-phase frictional pressure drop. Also among the homogeneous flow models investigated, the viscosity correlation of McAdams indicates the best performance in correlating the frictional pressure drop data (mean deviations within +/-20% for two micromixers both). Finally it is suggested that systematic studies are still required to accurately predict two-phase frictional performance in microchannels. (C) 2004 Elsevier B.V. All rights reserved.

Heat-shock protein70 gene expression in four hatchery Pacific Abalone Haliotis discus hannai Ino populations using for marker-assisted selection

Heat shock proteins (Hsps) are molecular chaperones that help organisms cope with stressful conditions. Here, we report on the growth rates and Hsp70 expressions in inbred and hybrid populations of abalone Haliotis discus hannai Ino. In abalone, inbred populations expressed more Hsp70 than hybrid populations at all temperatures, except at very high temperatures close to the physiological limit. At benign temperatures, there was a clear trend towards higher Hsp70 expression in inbred than hybrid populations, whereas at higher temperatures, a trend in the opposite direction was observed. The temperature of maximal Hsp70 expression (T-peak) varied with the population type. The T-peak of inbred populations (26 degrees C) was lower than that of the hybrid populations (28 degrees C). The maximal inducible Hsp70 of inbred populations was higher than that of hybrid populations. The results showed a trend towards higher expression in inbred population at a lower temperature. These results provide direct experimental evidence that hybrids can cope with the intrinsic stress even at non-stressful temperatures. The constitutive Hsp70 may therefore be used for marker-assisted selection in a breeding programme.

复杂应力环境下断续节理岩体真三轴实验研究及其工程应用

The great deal of joints and faults , existing in the rock mass , are the leading cause of discontinuous rock mass. Structural planes not only destroy the integrality of rock mass, but also lead nonlinearity、heterogeneity、anisotropy and failure mode on mechanical properties of rock mass. Therefore the selection of strength and deformation parameters was very difficult. In practical rock mass engineering, equivalent parameters of rock mass were selected by the method of expert experience and engineering analogy. Based on the fine description of discontinuous joints in the type Ⅳ and Ⅴ rock mass and geological survey datum in situ, models was obtained by generalizing the structure of rock mass by the method of statistical analysis. Model intensity and deformation test were carried out on the true triaxial apparatus. Intermediate principle stress effect, anisotropy and dimension effect of discontinuous rock mass were considered in the model test. 3-D correction to Hoek-Brown empirical criterion was done by analysed the test datum. Detailed works were listed as follows: (1) The factors influenced intensity and deformation of discontinuous joints rock mass were the value of 、continuity, density and included angle of joints and anisotropy of joint plane. True triaxial intensity and deformation tests were carried out by considering above factors. The influence rule was obtained and corresponding relation formulary was established； (2) Based on the true triaxial tests under different stress path and load modes, we obtain intensity and deformation rule of rock mass； (3) Based on a great deal of true triaxial tests and other test datum, correction to the Hoek-Brown empirical criterion was done in the chapter 4. The intermediate principle stress was considered in the corrected formulary. It indicated that the formulary was applicable under a certain condition. In addition, the yield plane form of corrected Hoek-Brown empirical criterion under principle stress space was described in the paper. And the question of corner of yield plane was discussed； (4) Based on the single discontinuity theory, the three-dimensional intensity formulary of discontinuous joint rock mass was established. Correction to the intensity formulary was done considering intermediate principle stress effect. We may obtain the conclusion that the intensity of the discontinuous joint rock mass was influenced on compositive factors. They were 、 、continuity、internal frictional angle and cohesiveness of joint plane and rock； (5) The results of the true triaxial model test was applied into parameters evaluation of dam foundation rock mass of JinPing hydropower station. For there were abundant ophicalcite in the dam foundation, the interval of intensity and formation parameters influenced on continuity were determined based on test datum. (6) Especial mould for prismatic jointing model was designed. True triaxial intensity and deformation tests by Basalt with prismatic jointing were carried out. The influence of intermediate principle stress, stress path, anisotropy effect and dimensional effect to intensity and deformation was discussed in the chapter 6. The work of (3)、(4)、(6) was significative supplement and innovation to current test and theory.

改造型盆地油气成藏机理与油气预测－以银根－额济纳旗盆地为例

Reformed basin is a basin that underwent multiple immense reformation after the sedimentary stage, the major geologic elements of the petroleum system in the prototyped basin are destroyed to a certain extent, and their petroleum system has been reconstructed. This type of basin is frequently found in the course of exploration both home and abroad. In China, especially in the western and southern part of China, the basins in which oil explorations have been conducted are mostly reformed basins. The reformed basins from Paleozoic, Late Mesozoic to Cenozoic are widely distributed in West and South China. They are, and moreover, will be a challenge for oil and gas exploration. The conventional investigation and exploration techniques used in the slightly reconstructed basin just don't work well when facing the reformed basin. Therefore, the study on the reformed basin, especially the study on the pool-forming mechanism and reservoir prediction becomes a focus and one of difficulties for the geologists overseas and domestic. Yingen-Ejinaqi Basin is a typical case of the Late Mesozoic and Cenozoic reformed basins in China. It locates in West China and is a exploration frontier with difficulties and no break through is made for years. A comprehensive research on it will be of significance for oil and gas exploration in similar basins of China. The late research for reformed basin in China now is mainly concentrated on basin classification, formation mechanism, geologic features, and survey technique, distribution regularity of oil accumulation and its dominating factors, assessment of oil exploration prospect and target zones, etc. On the other hand, the study on the pool-forming mechanism and reservoir prediction seems insufficient in systematization, and the research is deficient in methodology and combination of qualitative and quantitative studies, as well as the application of the new theory and techniques. The current efforts are mainly directed to structures (faults), sedimentation, the relationship between reservoir evolution and oil accumulation, and some other relevant fields. However, the application of the new theory and techniques seems to be insufficient such as petroleum system, pool-forming dynamics, fluid pressure compartment, and basin simulation, etc. So is the dynamic and integrated research. As a result, incomplete knowledge and understandings derived from the research on pool-forming mechanism and reservoir prediction often do not accord with rea-lity of the basin. The study and exploration under the guidance of this knowledge will inevitably lead to errors and failure. This paper, based on the previous study of the other geologists on reformed basins, with emphasis on "wholeness or systematic, dynamic and integrated" research, presents a reverse thinking of beginning from conserved units in the basin and the combination of qualitative and quantitative study with new theory and technique by building a geological model. The paper also puts forward a new thought for studying the oil & gas accumulation and reservoir prediction , and establishes a new research system for reformed basin. It is verified by the known reservoir and oil accumulation area in the basin and has a practical value for use and reference. The new ideas and achievements in this research are as following: 1.This is the first time that the system for studying the reformed basin and its pool-forming mechanism and reservoir prediction is presented. A reverse thinking and combination of qualitative & quantitative are applied here with emphasis on "wholeness or systematic, dynamic and integrated" research, new theory, techniques & methods comprehensive use and geologic models building. 2. Identifying criterion and methods, classifying schemes, and denominating principles for the conserved units of reformed basins are presented in this paper. The geologic model of conserved units of Yingen-Ejinaqi Basin has been built. It is a practical method when combined with the traditional way for basin survey and the conserved units study. 3.The dynamic sources of basin deformation are believed to be stress, gravity and thermodynamics. The stress and gravity are key factors in basin deformation and pool forming, especially stress. Scientific proof is provided by classifying the functional type, style and range of the stress, gravity and thermodynamics. 4.The pool forming and reservoir distribution of Yingen-Ejinaqi Basin are controlled by multiple factors or geologic conditions or/and co-controlled by both of them. The qualitative and quantitative research on petroleum system and basin modeling will help us understand and determine the pool-forming period of the conserved unit (timing), the oil migrating direction (orientation), the oil accumulating region (location), the oil distributing border (bordering) and the size of oil accumulation (quantification). Thus the pool-forming and distribution zones can be predicted. 5.Three generating modes (reform-succession type, reform-destroyed type and reform-regenerating type or reform-newborn type) of pool forming for reformed basins are presented here, together with the inner relationships between basin deformation type, overlapping style and pool-forming modes. The pool-forming modes are determined by deformation type and overlapping style. Reservoir distribution will be predicted based on the modes and other concrete pool-forming conditions. 6.The evaluation methods of the conserved units and zones and the parameter selection are reliable in optimal selecting of target zones. The technical terms, new ideas and methods for the study of reformed basins, the pool-forming mechanism and reservoir prediction are presented in this paper. The concepts and terms, the identifying criterion, the denominating principles, the generating modes for pool forming, the methods of reservoir prediction, and the evaluation techniques for conserved units and zones can be used for reference in studies on the petroleum exploration of reformed basins in China and abroad. It serves as a typical example for further research of the reformed basins and the geologic regulations of oil accumulation. It has a practical value of use and reference. The future research in the field of pool-forming mechanism of the reformed basins may well be on the process simulation of pool-forming dynamics of the reformed basins. Experimental work has been conducted to simulate the processes by using quantitative and qualitative methods combined. The further study in this field calls for more efforts.