Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation

Background: Short and long interspersed elements (SINEs and LINEs, respectively), two types of retroposons, are active in shaping the architecture of genomes and powerful tools for studies of phylogeny and population biology. Here we developed special protocol to apply biotin-streptavidin bead system into isolation of interspersed repeated sequences rapidly and efficiently, in which SINEs and LINEs were captured directly from digested genomic DNA by hybridization to bead-probe complex in solution instead of traditional strategy including genomic library construction and screening. Results: A new couple of SINEs and LINEs that shared an almost identical 3'tail was isolated and characterized in silver carp and bighead carp of two closely related species. These SINEs (34 members), designated HAmo SINE family, were little divergent in sequence and flanked by obvious TSD indicated that HAmo SINE was very young family. The copy numbers of this family was estimated to 2 x 10(5) and 1.7 x 10(5) per haploid genome by Real-Time qPCR, respectively. The LINEs, identified as the homologs of LINE2 in other fishes, had a conserved primary sequence and secondary structures of the 3'tail region that was almost identical to that of HAmo SINE. These evidences suggest that HAmo SINEs are active and amplified recently utilizing the enzymatic machinery for retroposition of HAmoL2 through the recognition of higher-order structures of the conserved 42-tail region. We analyzed the possible structures of HAmo SINE that lead to successful amplification in genome and then deduced that HAmo SINE, SmaI SINE and FokI SINE that were similar in sequence each other, were probably generated independently and created by LINE family within the same lineage of a LINE phylogeny in the genomes of different hosts. Conclusion: The presented results show the advantage of the novel method for retroposons isolation and a pair of young SINE family and its partner LINE family in two carp fishes, which strengthened the hypotheses containing the slippage model for initiation of reverse transcription, retropositional parasitism of SINEs on LINEs, the formation of the stem loop structure in 3'tail region of some SINEs and LINEs and the mechanism of template switching in generating new SINE family.

职业倦怠与自我和谐、人际信任的关系研究：中学校长与一般教师的对比

Job Burnout has been a focus of the Occupational Stress Research. As a typical,helping occupation, teacher has attracted widely attention and researches in the areas of pedagogy and psychology. The special subgroup of teacher, headmasters who are the elites of the Basic Education, is ignored. The research about principals’ Job Burnout is nearly blank after analyzing related documents and information. With the development of the society, people pay more and more attention to the education and put more demands on the headmasters, especially middle-school principals. They are required not only to be good educators, who are equipped with all the inner qualities as a teacher, but also good managers. So the main purpose of this research was to compare the principal group with ordinary teacher group, and reveal underling factors, such as background variables and psychological protection variables. A representative sample of Wenzhou middle school principals sized 192 and a sample of middle school teacher sized 302 were sampled from various schools. The educational version of burnout inventory, self consistency scale, and interpersonal trust scale were administrated to the two samples, together with some demographic variables of interest. The applicability and equivalence of the three instruments used in this study were checked. Based on well-established reliability and cross-sample congruence of measures, the difference between principals and teachers was test. Then the contributing factors were analysis gradually. The five background variables were examined one by one in the two samples separately. A multiple covariance analysis was conducted to test whether there remained any difference between these two samples on the variables of interest. Regression analysis was used to further control the effect of self harmony and interpersonal trust to test the difference between two samples. Mediating analysis was conducted to build the relationship among the three constructs. The main results of the research were stated as following: 1. The internal consistency coefficients of all the scales were good, and no difference exited between the two groups. The measurement equivalence of three instruments was established well. The measures could be applied to and comparing the two samples. 2. The self-harmony, and interpersonal trust of principals were better than the ordinary middle-school teachers. Job Burnout of principals was significant lower than teachers. 3. Demographic variables like the gender, age groups, income levels, disricts, and the type of school, were important influencing factors. The difference patterns of the variables on these five variables in two samples had similarity and distinction. 4. After controlling the background variables, there remained significant difference between principals and teachers on the variables of interest. 5. Job Burnout negatively correlated with self-harmony and interpersonal trust. That is to say，the lower the degree of self-harmony and interpersonal are, the serious of the Job Burnout is, The correlation between the self-harmony and the interpersonal trust was positive. 6. After statistically controlling the background variables and psychological variables, there still exited significant difference between two groups of this study. Also, self harmony and interpersonal trust were significant protection predictors to different aspect of job burnout. 7. Mediating analysis was conducted to the residual score of the three constructs after controlling the five variables and group membership. Self harmony partially mediated the relationship between interpersonal trust and job burnout. That is, interpersonal trust had indirect effect to burnout mediated by self harmony, also had direct effect to burnout.

Effects of physical parameter range on dimensionless variable sensitivity in water flooding reservoirs

The similarity criterion for water flooding reservoir flows is concerned with in the present paper. When finding out all the dimensionless variables governing this kind of flow, their physical meanings are subsequently elucidated. Then, a numerical approach of sensitivity analysis is adopted to quantify their corresponding dominance degree among the similarity parameters. In this way, we may finally identify major scaling law in different parameter range and demonstrate the respective effects of viscosity, permeability and injection rate.

Crack tip behavior and crack-propagation in ductile materials

Dilatational plastic equations, which can include the effects of ductile damage, are derived based on the equivalency in expressions for dissipated plastic work. Void damage developed internally at the large-strain stage is represented by an effective continuum being strain-softened and plastically dilated. Accumulation of this local damage leads to progressive failure in materials. With regard to this microstructural background, the constitutive parameters included for characterizing material behaviour have the sense of internal variables. They are not able to be determined explicitly by macroscopic testing but rather through computer simulation of experimental curves and data. Application of this constitutive model to mode-I cracking examples demonstrates that a huge strain concentration accompanied by a substantial drop of stress does occur near the crack tip. Eventually, crack propagation is simulated by using finite elements in computations. Two numerical examples show good accordance with experimental data. The whole procedure of study serves as a justification of the constitutive formulation proposed in the text.

A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features

As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue–residue correlations better. Based on a coarse-grained approach, the hydrophobic force between each pair of residues is written out from protein sequence. It results in the construction of an intramolecular hydrophobic force network that describes the whole residue–residue interactions of each protein molecule, and characterizes protein's biological properties in the hydrophobic aspect. A former work has suggested that such network can characterize the top weighted feature regarding hydrophobicity. Moreover, for each homologous protein of a family, the corresponding network shares some common and representative family characters that eventually govern the conservation of biological properties during protein evolution. In present work, we score such family representative characters of a protein by the deviation of its intramolecular hydrophobic force network from that of background. Such score can assist the existing scoring schemes/algorithms, and boost up the ability of multiple sequences alignment, e.g. achieving a prominent increase (50%) in searching the structurally alike residue segments at a low identity level. As the theoretical basis is different, the present scheme can assist most existing algorithms, and improve their efficiency remarkably.

Analysis of complete mitochondrial genome sequences increases phylogenetic resolution of bears (Ursidae), a mammalian family that experienced rapid speciation

Background: Despite the small number of ursid species, bear phylogeny has long been a focus of study due to their conservation value, as all bear genera have been classified as endangered at either the species or subspecies level. The Ursidae family repre

Molecular evolution of the keratin associated protein gene family in mammals, role in the evolution of mammalian hair

Background: Hair is unique to mammals. Keratin associated proteins (KRTAPs), which contain two major groups: high/ultrahigh cysteine and high glycine-tyrosine, are one of the major components of hair and play essential roles in the formation of rigid and

The evolution of YidC/Oxa/Alb3 family in the three domains of life: a phylogenomic analysis

Background: YidC/Oxa/Alb3 family includes a group of conserved translocases that are essential for protein insertion into inner membranes of bacteria and mitochondria, and thylakoid membranes of chloroplasts. Because mitochondria and chloroplasts are of b

Origin and evolution of the RIG-I like RNA helicase gene family

Background: The DExD/H domain containing RNA helicases such as retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5) are key cytosolic pattern recognition receptors (PRRs) for detecting nucleotide pathogen associated molecular patterns (PAMPs) of invading viruses. The RIG-I and MDA5 proteins differentially recognise conserved PAMPs in double stranded or single stranded viral RNA molecules, leading to activation of the interferon system in vertebrates. They share three core protein domains including a RNA helicase domain near the C terminus (HELICc), one or more caspase activation and recruitment domains (CARDs) and an ATP dependent DExD/H domain. The RIG-I/MDA5 directed interferon response is negatively regulated by laboratory of genetics and physiology 2 (LGP2) and is believed to be controlled by the mitochondria antiviral signalling protein (MAVS), a CARD containing protein associated with mitochondria. Results: The DExD/H containing RNA helicases including RIG-I, MDA5 and LGP2 were analysed in silico in a wide spectrum of invertebrate and vertebrate genomes. The gene synteny of MDA5 and LGP2 is well conserved among vertebrates whilst conservation of the gene synteny of RIG-I is less apparent. Invertebrate homologues had a closer phylogenetic relationship with the vertebrate RIG-Is than the MDA5/LGP2 molecules, suggesting the RIG-I homologues may have emerged earlier in evolution, possibly prior to the appearance of vertebrates. Our data suggest that the RIG-I like helicases possibly originated from three distinct genes coding for the core domains including the HELICc, CARD and ATP dependent DExD/H domains through gene fusion and gene/domain duplication. Furthermore, presence of domains similar to a prokaryotic DNA restriction enzyme III domain (Res III), and a zinc finger domain of transcription factor (TF) IIS have been detected by bioinformatic analysis. Conclusion: The RIG-I/MDA5 viral surveillance system is conserved in vertebrates. The RIG-I like helicase family appears to have evolved from a common ancestor that originated from genes encoding different core functional domains. Diversification of core functional domains might be fundamental to their functional divergence in terms of recognition of different viral PAMPs.