Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey

Although the complete genome sequences of over 50 representative species have revealed the many duplicated genes in all three domains of life(1-4), the roles of gene duplication in organismal adaptation and biodiversity are poorly understood. In addition,

Adaptive diversification of bitter taste receptor genes in mammalian evolution

The diversity and evolution of bitter taste perception in mammals is not well understood. Recent discoveries of bitter taste receptor (T2R) genes provide an opportunity for a genetic approach to this question. We here report the identification of 10 and 30 putative T2R genes from the draft human and mouse genome sequences, respectively, in addition to the 23 and 6 previously known T2R genes from the two species. A phylogenetic analysis of the T2R genes suggests that they can be classified into three main groups, which are designated A, B, and C. Interestingly, while the one-to-one gene orthology between the human and mouse is common to group B and C genes, group A genes show a pattern of species- or lineage-specific duplication. It is possible that group B and C genes are necessary for detecting bitter tastants common to both humans and mice, whereas group A genes are used for species-specific bitter tastants. The analysis also reveals that phylogenetically closely related T2R genes are close in their chromosomal locations, demonstrating tandem gene duplication as the primary source of new T2Rs. For closely related paralogous genes, a rate of nonsynonymous nucleotide substitution significantly higher than the rate of synonymous substitution was observed in the extracellular regions of T2Rs, which are presumably involved in tastant-binding. This suggests the role of positive selection in the diversification of newly duplicated T2R genes. Because many natural poisonous substances are bitter, we conjecture that the mammalian T2R genes are under diversifying selection for the ability to recognize a diverse array of poisons that the organisms may encounter in exploring new habitats and diets.

Adaptive diversification of vomeronasal receptor 1 genes in rodents

The vomeronasal receptor 1 (V1R) are believed to be pheromone receptors in rodents. Here we used computational methods to identify 95 and 62 new putative V1R genes from the draft rat and mouse genome sequence, respectively. The rat V1R repertoire consists of 11 subfamilies, 10 of which are shared with the mouse, while rat appears to lack the H and I subfamilies found in mouse and possesses one unique subfamily (M). The estimations of the relative divergence times suggest that many subfamilies originated after the split of rodents and primates. The analysis also reveals that these clusters underwent an expansion very close to the split of mouse and rat. In addition, maximum likelihood analysis showed that the nonsynonymous and synonymous rate ratio for most of these clusters was much higher than one, suggesting the role of positive selection in the diversification of these duplicated V1R genes. Because V1R are thought to mediate the process of signal transduction in response to pheromone detection, we speculate that the V1R genes have evolved under positive Darwinian selection to maintain the ability to discriminate between large and complex pheromonal mixtures.

The unusual adaptive expansion of pancreatic ribonuclease gene in carnivora

Pancreatic ribonuclease (RNASE1) is a digestive enzyme that has been recognized to be one of the most attractive model systems for molecular evolutionary studies. The contribution of RNASE1 gene duplication to the functional adaptation of digestive physio

Adaptive evolution of energy metabolism genes and the origin of flight in bats

Bat flight poses intriguing questions about how flight independently developed in mammals. Flight is among the most energy-consuming activities. Thus, we deduced that changes in energy metabolism must be a primary factor in the origin of flight in bats. The respiratory chain of the mitochondrial produces 95% of the adenosine triphosphate (ATP) needed for locomotion. Because the respiratory chain has a dual genetic foundation, with genes encoded by both the mitochondrial and nuclear genomes, we examined both genomes to gain insights into the evolution of flight within mammals. Evidence for positive selection was detected in 23.08% of the mitochondrial-encoded and 4.90% of nuclear-encoded oxidative phosphorylation (OXPHOS) genes, but in only 2.25% of the nuclear-encoded nonrespiratory genes that function in mitochondria or 1.005% of other nuclear genes in bats. To address the caveat that the two available bat genomes are of only draft quality, we resequenced 77 OXPHOS genes from four species of bats. The analysis of the resequenced gene data are in agreement with our conclusion that a significantly higher proportion of genes involved in energy metabolism, compared with background genes, show evidence of adaptive evolution specific on the common ancestral bat lineage. Both mitochondrial and nuclear-encoded OXPHOS genes display evidence of adaptive evolution along the common ancestral branch of bats, supporting our hypothesis that genes involved in energy metabolism were targets of natural selection and allowed adaptation to the huge change in energy demand that were required during the origin of flight.

Adaptive Evolution of Digestive RNASE1 Genes in Leaf-Eating Monkeys Revisited: New Insights from Ten Additional Colobines

Pancreatic RNase genes implicated in the adaptation of the colobine monkeys to leaf eating have long intrigued evolutionary biologists since the identification of a duplicated RNASE1 gene with enhanced digestive efficiencies in Pygathrix nemaeus. The recent emergence of two contrasting hypotheses, that is, independent duplication and one-duplication event hypotheses, make it into focus again. Current understanding of Colobine RNASE1 gene evolution of colobine monkeys largely depends on the analyses of few colobine species. The present study with more intensive taxonomic and character sampling not only provides a clearer picture of Colobine RNASE1 gene evolution but also allows to have a more thorough understanding about the molecular basis underlying the adaptation of Colobinae to the unique leaf-feeding lifestyle. The present broader and detailed phylogenetic analyses yielded two important findings: 1) All trees based on the analyses of coding, noncoding, and both regions provided consistent evidence, indicating RNASE1 duplication occurred after Asian and African colobines speciation, that is, independent duplication hypothesis; 2) No obvious evidence of gene conversion in RNASE1 gene was found, favoring independent evolution of Colobine RNASE1 gene duplicates. The conclusion drawn from previous studies that gene conversion has played a significant role in the evolution of Colobine RNASE1 was not supported. Our selective constraint analyses also provided interesting insights, with significant evidence of positive selection detected on ancestor lineages leading to duplicated gene copies. The identification of a handful of new adaptive sites and amino acid changes that have not been characterized previously also provide a necessary foundation for further experimental investigations of RNASE1 functional evolution in Colobinae.

Large Gene Family Expansions and Adaptive Evolution for Odorant and Gustatory Receptors in the Pea Aphid, Acyrthosiphon pisum

Gaining insight into the mechanisms of chemoreception in aphids is of primary importance for both integrative studies on the evolution of host plant specialization and applied research in pest control management because aphids rely on their sense of smell

Coherence loss and recovery of an electron spin coupled inhomogeneously to a one-dimensional interacting spin bath: An adaptive time-dependent density-matrix renormalization group study

Coherence evolution and echo effect of an electron spin, which is coupled inhomogeneously to an interacting one-dimensional finite spin bath via hyperfine-type interaction, are studied using the adaptive time-dependent density-matrix renormalization group method. It is found that the interplay of the coupling inhomogeneity and the transverse intrabath interactions results in two qualitatively different coherence evolutions, namely, a coherence-preserving evolution characterized by periodic oscillation and a complete decoherence evolution. Correspondingly, the echo effects induced by an electron-spin flip at time tau exhibit stable recoherence pulse sequence for the periodic evolution and a single peak at root 2 tau for the decoherence evolution, respectively. With the diagonal intrabath interaction included, the specific feature of the periodic regime is kept, while the root 2 tau-type echo effect in the decoherence regime is significantly affected. To render the experimental verifications possible, the Hahn echo envelope as a function of tau is calculated, which eliminates the inhomogeneous broadening effect and serves for the identification of the different status of the dynamic coherence evolution, periodic versus decoherence.

Planar refractive microlens arrays in indium phosphide and quartz substrates

Large-area concave refractive microlens arrays, or concave template structures, and then the non-refractive-index-gradient type of planar refractive microlens arrays in InP and quartz substrates, are fabricated utilizing the method consisting of conventional UV photolithography, thermal shaping of concave photoresist microlenses, etching with an argon ion beam of large diameter, and filling or growing optical medium structures onto the curved surfaces of preshaped concave templates. Several key conditions for fabricating concave and also planar microlenses are discussed in detail. The concave structures obtained are characterized by scanning electron microscope and surface profile measurements. The far-field optical characteristics of quartz/ZrO2 planar refractive microlens arrays have been acquired experimentally. (c) 2008 Society of Photo-Optical Instrumentation Engineers.

Development of solar-blind AlGaN 128x128 ultraviolet focal plane arrays

This paper reports the development of solar-blind aluminum gallium nitride (AlGaN) 128x128 UV Focal Plane Arrays (FPAs). The back-illuminated hybrid FPA architecture consists of an 128x128 back-illuminated AlGaN PIN detector array that is bump-mounted to a matching 128x128 silicon CMOS readout integrated circuit (ROIC) chip. The 128x128 p-i-n photodiode arrays with cuton and cutoff wavelengths of 233 and 258 nm, with a sharp reduction in response to UVB (280-320 nm) light. Several examples of solar-blind images are provided. This solar-blind band FPA has much better application prospect.

Composition deviation of arrays of FePt nanoparticles starting from poly(styrene)-poly(4-vinylpyridine) micelles

Ordered arrays of FePt nanoparticles were prepared using a diblock polymer micellar method combined with plasma treatment. Rutherford backscattering spectroscopy analyses reveal that the molar ratios of Fe to Pt in metal-salt-loaded micelles deviate from those when metal precursors are added, and that the plasma treatment processes have little influence upon the compositions of the resulting FePt nanoparticles. The results from Fourier transform infrared spectroscopy show that the maximum loadings of FeCl3 and H2PtCl6 inside poly( styrene)-poly(4-vinylpyridine) micelles are different. The composition deviation of FePt nanoparticles is attributed to the fact that one FeCl3 molecule coordinates with a single 4-vinylpyridine (4VP) unit, while two neighboring and uncomplexed 4VP units are required for one H2PtCl6 molecule. Additionally, we demonstrate that the center-to-center distances of the neighboring FePt nanoparticles can also be tuned by varying the drawing velocity.

Quasi-hexagonal ordered arrays of FePt nanoparticles prepared by a micellar method

Hexagonally ordered arrays of magnetic FePt nanoparticles on Si substrates are prepared by a self assembly of diblock copolymer PS-b-P2VP in toluene, a dip coating process and finally plasma treatment. The as-treated FePt nanoparticles are covered by an oxide layer that can be removed by a 40 s Ar+ sputtering. The effects of the sequence of adding salts on the composition distribution are revealed by x-ray photoelectron spectroscopy measurements. No particle agglomeration is observed after 600 degrees C annealing for the present ordered array of FePt nanoparticles, which exhibits advantages in patterning FePt nanoparticles by a micellar method. Moreover, magnetic properties of the annealed FePt nanoparticles at room temperature are investigated by a vibrating sample magnetometer.

Optical properties of highly ordered AlN nanowire arrays grown on sapphire substrate

Highly ordered AlN nanowire arrays were synthesized via a simple physical vapor deposition method on sapphire substrate. The nanowires have an extremely sharp tip < 10 nm, with the average length around 3 mu m. Raman spectroscopy analysis on the AlN nanowire arrays revealed that the lifetime of the phonons is shorter than that in bulk AlN. The transmission spectra of the AlN nanowires showed a blueshift similar to 0.27 eV at the absorption edge with that of the bulk AlN, which is closely related to the small size of the nanowires. (c) 2005 American Institute of Physics.

Structural, photoluminescence, and field emission properties of vertically well-aligned ZnO nanorod arrays

The self-assembled growth of vertically well-aligned ZnO nanorod arrays with uniform length and diameter on Si substrate has been demonstrated via thermal evaporation and vapor-phase transport. The structural, photoluminescence (PL), and field emission properties of the as-prepared nanorod arrays were investigated. The PL spectrum at 10 K shows a strong and sharp near-band gap emission (NBE) peak ( full width at half-maximum (FWHM) = 4.7 meV) and a weak neglectable deep-level emission (DL) peak (I-NBE/I-DL= 220), which implies its good crystallinity and high optical quality. The room-temperature NBE peak was deduced to the composition of free exciton and its first-order replicas emissions by temperature-dependent PL spectra. The field emission measurements indicate that, with a vacuum gap of 400 Am, the turn-on field and threshold field is as low as 2.3 and 4.2 V/mu m. The field enhancement factor beta and vacuum gap d follows a universal equation.

Enhanced infrared absorption of spatially ordered quantum dot arrays

We have investigated the intersubband absorption for spatially ordered and non-ordered quantum dots (QDs). It is found that the intersubband absorption of spatially ordered QDs is much stronger than that of non-ordered QDs. The enhanced absorption is attributed to the improved size uniformity concurrent with the spatial ordering for the growth condition employed. For the FTIR measurement under normal incidence geometry, using a undoped sample as reference can remove the interference effect due to multiple reflections. (c) 2006 Elsevier B.V. All rights reserved.