Origin and evolution of new genes

Organisms have variable genome sizes and contain different numbers of genes. This difference demonstrates that new gene origination is a fundamental process in evolutionary biology. Though the study of the origination of new genes dated back more than hal

Origin and evolution of new exons in the rodent zinc finger protein 39 gene

The origin of new structures and functions is an important process in evolution. In the past decades, we have obtained some preliminary knowledge of the origin and evolution of new genes. However, as the basic unit of genes, the origin and evolution of exons remain unclear. Because young exons retain the footprints of origination, they can be good materials for studying origin and evolution of new exons. In this paper, we report two young exons in a zinc finger protein gene of rodents. Since they are unique sequences in mouse and rat genome and no homologous sequences were found in the orthologous genes of human and pig, the young exons might originate after the divergence of primates and rodents through exonization of intronic sequences. Strong positive selection was detected in the new exons between mouse and rat, suggesting that these exons have undergone significant functional divergence after the separation of the two species. On the other hand, population genetics data of mouse demonstrate that the new exons have been subject to functional constraint, indicating an important function of the new exons in mouse. Functional analyses suggest that these new exons encode a nuclear localization signal peptide, which may mediate new ways of nuclear protein transport. To our knowledge, this is the first example of the origin and evolution of young exons.

Origin and evolution of new exons in rodents

Gene number difference among organisms demonstrates that new gene origination is a fundamental biological process in evolution. Exon shuffling has been universally observed in the formation of new genes. Yet to be learned are the ways new exons originate and evolve, and how often new exons appear. To address these questions, we identified 2695 newly evolved exons in the mouse and rat by comparing the expressed sequences of 12,419 orthologous genes between human and mouse, using 743,856 pig ESTs as the outgroup. The new exon origination rate is about 2.71 x 10(-3) per gene per million years. These new exons have markedly accelerated rates both of nonsynonymous substitutions and of insertions/ deletions (indels). A much higher proportion of new exons have Kappa(a)/Kappa(s) ratios > 1 (where K-a is the nonsynonymous substitution rate and K-s is the synonymous substitution rate) than K do the old exons shared by human and mouse, implying a role of positive selection in the rapid evolution. The majority of these new exons have sequences unique in the genome, suggesting that most new exons might originate through "exonization" of intronic sequences. Most of the new exons appear to be alternative exons that are expressed at low levels.

On the origin and evolution of new genes-a genomic and experimental perspective

The inherent interest on the origin of genetic novelties can be traced back to Darwin. But it was not until recently that we were allowed to investigate the fundamental process of origin of new genes by the studies on newly evolved Young genes. Two indisp

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.

Identification of one intron loss and phylogenetic evolution of Dfak gene in the Drosophila melanogaster species group

Intron loss and its evolutionary significance have been noted in Drosophila. The current study provides another example of intron loss within a single-copy Dfak gene in Drosophila. By using polymerase chain reaction (PCR), we amplified about 1.3 kb fragment spanning intron 5-10, located in the position of Tyr kinase (TyK) domain of Dfak gene from Drosophila melanogaster species group, and observed size difference among the amplified DNA fragments from different species. Further sequencing analysis revealed that D. melanogaster and D. simulans deleted an about 60 bp of DNA fragment relative to other 7 Drosophila species, such as D. elegans, D. ficusphila, D. biarmipes, D. takahashii, D. jambulina, D. prostipennis and D. pseudoobscura, and the deleted fragment located precisely in the position of one intron. The data suggested that intron loss might have occurred in the Dfak gene evolutionary process of D. melanogaster and D. simulans of Drosophila melanogaster species group. In addition, the constructed phylogenetic tree based on the Dfak TyK domains clearly revealed the evolutionary relationships between subgroups of Drosophila melanogaster species group, and the intron loss identified from D. melanogaster and D. simulans provides a unique diagnostic tool for taxonomic classification of the melanogaster subgroup from other group of genus Drosophila.

Defect evolution and accompanied change of electrical properties during the GaN growth by metalorganic chemical vapor deposition

The defect evolution and its correlation with electrical properties of GaN films grown by metalorganic chemical vapor deposition are investigated. It is found that the dislocation density decreases gradually during the growth process, and the dislocation reduction rate in the island coalescence process is especially rapid. The changes in electron mobility of GaN with the increase of growth time are mainly dependent on the dislocations acting as scattering centers. Furthermore, the variation of carrier concentration in GaN may be related with the point defects and their clusters. The quality of GaN could be improved by suitably increasing the film thickness. (C) 2009 Elsevier B.V. All rights reserved.

Origin and evolution of photoluminescence from Si nanocrystals embedded in a SiO2 matrix

A detailed analysis of the photoluminescence (PL) from Si nanocrystals (NCs) embedded in a silicon-rich SiO2 matrix is reported. The PL spectra consist of three Gaussian bands (peaks A,B, and C), originated from the quantum confinement effect of Si NCs, the interface state effect between a Si NC and a SiO2 matrix, and the localized state transitions of amorphous Si clusters, respectively. The size and the surface chemistry of Si NCs are two major factors affecting the transition of the dominant PL origin from the quantum confinement effect to the interface state recombination. The larger the size of Si NCs and the higher the interface state density (in particular, Si = O bonds), the more beneficial for the interface state recombination process to surpass the quantum confinement process, in good agreement with Qin's prediction in Qin and Li [Phys. Rev. B 68, 85309 (2003)]. The realistic model of Si NCs embedded in a SiO2 matrix provides a firm theoretical support to explain the transition trend.

Influence of AlN thickness on strain evolution of GaN layer grown on high-temperature AlN interlayer

The strain evolution of a GaN layer grown on a high- temperature AlN interlayer with varying AlN thickness by metalorganic chemical vapour deposition is investigated. In the growth process, the growth strain changes from compression to tension in the top GaN layer, and the thickness at which the compressive- to- tensile strain transition takes place is strongly influenced by the thickness of the AlN interlayer. It is confirmed from the x- ray diffraction results that the AlN interlayer has a remarkable effect on introducing relative compressive strain to the top GaN layer. The strain transition process during the growth of the top GaN layer can be explained by the threading dislocation inclination in the top GaN layer. Adjusting the AlN interlayer thickness could change the density of the threading dislocations in the top GaN layer and then change the stress evolution during the top GaN layer's growth.

Influences of reactor pressure of GaN buffer layers on morphological evolution of GaN grown by MOCVD

The morphological evolution of GaN thin films grown on sapphire by metalorganic chemical vapor deposition was demonstrated to depend strongly on the growth pressure of GaN nucleation layer (NL). For the commonly used two-step growth process, a change in deposition pressure of NL greatly influences the growth mode and morphological evolution of the following GaN epitaxy. By means of atomic force microscopy and scanning electron microscope, it is shown that the initial density and the spacing of nucleation sites on the NL and subsequently the growth mode of FIT GaN epilayer may be directly controlled by tailoring the initial low temperature NL growth pressure. A mode is proposed to explain the TD reduction for NL grown at relatively high reactor pressure. (C) 2003 Elsevier B.V. All rights reserved.

Mechanisms of the sidewall facet evolution in lateral epitaxial overgrowth of GaN by MOCVD

The lateral epitaxial overgrowth of GaN was carried out by low-pressure metalorganic chemical vapor deposition, and the cross section shape of the stripes was characterized by scanning electron microscopy. Inclined {11-2n} facets (n approximate to 1-2.5) were observed in the initial growth, and they changed gradually into the vertical {11-20} sidewalls in accordance with the process of the lateral overgrowth. A model was proposed utilizing diffusion equations and boundary conditions to simulate the concentration of the Ga species constituent throughout the concentration boundary layer. Solutions to these equations are found using the two-dimensional, finite element method. We suggest that the observed evolution of sidewall facets results from the variation of the local V/III ratio during the process of lateral overgrowth induced by the lateral supply of the Ga species from the SiNx mask regions to the growing GaN regions.

Carbonization process of Si(100) by ion-beam bombardment

The evolution of carbonization process on Si as a function of ion dose has been carried out by mass-selected ion-beam deposition technique. 3C-SiC layer has been obtained at low ion dose, which has been observed by reflection high energy electron diffraction and X-ray photoelectron spectroscopy (XPS). The chemical states of Si and carbon have also been examined as a function of ion dose by XPS. Carbon enrichment was found regardless of the used ion dose here, which may be due to the high deposition rate. The formation mechanism of SiC has also been discussed based on the subplantation process. The work will also provide further understanding of the ion-bombardment effect. (C) 2001 Published by Elsevier Science B.V.

processline: visualizing time-series data in process industry

In modern process industry, it is often difficult to analyze a manufacture process due to its umerous time-series data. Analysts wish to not only interpret the evolution of data over time in a working procedure, but also examine the changes in the whole production process through time. To meet such analytic requirements, we have developed ProcessLine, an interactive visualization tool for a large amount of time-series data in process industry. The data are displayed in a fisheye timeline. ProcessLine provides good overviews for the whole production process and details for the focused working procedure. A preliminary user study using beer industry production data has shown that the tool is effective.

A kinetic model for nanocrystal morphology evolution

A kinetic model is developed with the goal of understanding and predicting the morphology evolution of nonocrystals in nonequilibrium growth conditions. The model is based on the assumption that under such conditions, different crystal planes have different kinetic parameters. This model focuses on the morphology-developing stage and is successfully related to the nucleation process and other crystal evolution mechanisms. It is believed to be a universal model and is applied to discuss the morphology evolution of CdSe nanocrystals, including the aspect ratio, injection I schemes, ligands effect and morphology distribution.

Evolution of Localized Damage Zone in Heterogeneous Media

Evolution of localized damage zone is a key to catastrophic rupture in heterogeneous materials. In the present article, the evolutions of strain fields of rock specimens are investigated experimentally. The observed evolution of fluctuations and autocorrelations of strain fields under uniaxial compression demonstrates that the localization of deformation always appears ahead of catastrophic rupture. In particular, the localization evolves pronouncedly with increasing deformation in the rock experiments. By means of the definition of the zone with high strain rate and likely damage localization, it is found that the size of the localized zone decreases from the sample size at peak load to an eventual value. Actually, the deformation field beyond peak load is bound to suffer bifurcation, namely an elastic unloading part and a continuing but localized damage part will co-exist in series in a specimen. To describe this continuous bifurcation and localization process observed in experiments, a model on continuum mechanics is developed. The model can explain why the decreasing width of localized zone can lead stable deformation to unstable, but it still has not provided the complete equations governing the evolution of the localized zone.