Values and actions in aversion

Model-based and model-free controllers can, in principle, learn arbitrary actions to optimize their behavior, at least those actions that can be expressed and explored. Indeed, these are often referred to as instrumental controllers because their choices are learned to be instrumental for the delivery of desired outcomes. Although this flexibility is very powerful, it comes with an attendant cost of learning. Evolution appears to have endowed everything from the simplest organisms to us with powerful, pre-specified, but inflexible alternatives. These responses are termed Pavlovian, after the famous Russian physiologist and psychologist Pavlov. The responses of the Pavlovian controller are determined by evolutionary (phylogenetic) considerations rather than (ontogenetic) aspects of the contingent development or learning of an individual. These responses directly interact with instrumental choices arising from goal-directed and habitual controllers. This interaction has been studied in a wealth of animal paradigms, and can be helpful, neutral, or harmful, according to circumstance. Although there has been less careful or analytical study of it in humans, it can be interpreted as underpinning a wealth of behavioral aberrations. © 2009 Elsevier Inc. All rights reserved.

The evolution of a stratified turbulent cloud

Localized regions of turbulence, or turbulent clouds, in a stratified fluid are the subject of this study, which focuses on the edge dynamics occurring between the turbulence and the surrounding quiescent region. Through laboratory experiments and numerical simulations of stratified turbulent clouds, we confirm that the edge dynamics can be subdivided into materially driven intrusions and horizontally travelling internal wave-packets. Three-dimensional visualizations show that the internal gravity wave-packets are in fact large-scale pancake structures that grow out of the turbulent cloud into the adjacent quiescent region. The wave-packets were tracked in time, and it is found that their speed obeys the group speed relation for linear internal gravity waves. The energetics of the propagating waves, which include waveforms that are inclined with respect to the horizontal, are also considered and it is found that, after a period of two eddy turnover times, the internal gravity waves carry up to 16 % of the cloud kinetic energy into the initially quiescent region. Turbulent events in nature are often in the form of decaying turbulent clouds, and it is therefore suggested that internal gravity waves radiated from an initial cloud could play a significant role in the reorganization of energy and momentum in the atmosphere and oceans.©2013 Cambridge University Press.

Sox genes evolution in closely related young tetraploid cyprinid fishes and their diploid relative

Previous study and analysis of cytochrome b suggested that polyploidization event in the genus Tor occurred about 10 Mya ago. In order to understand evolutionary fates of Sox gene in the early stage of genome duplication at the nucleotide level, PCR surveys for Sox genes in three closely related cyprinid fishes T douronensis (2n = 100), T qiaojiensis (2n = ?), T sinensis (2n = 100) and their relative T brevifilis (2n = 50) were performed. Totally, 52 distinct Sox genes were obtained in these four species, representing SoxB, SoxC, and SoxE group. As expected, isoforms of some Sox genes correspond with the ploidy of species, such as two copies of Sox9a exist in tetraploid species. Analysis indicated that duplicated Sox gene pairs caused by polyploidization evolved independently of each other within polyploid species. Results of substitution rate showed nearly equal rate of nonsynonymous substitution of duplicated Sox orthologs among different polyploid species and their diploid relative orthologs, suggesting at the early stage of genome duplicated Sox orthologs are under similar selective constraints in different polyploidy species and their diploid relative at the amino acid level. All PCR fragments of Sox genes obtained in this study are not accompanied by obvious increase in mutations and pseudogene formation which means that they are under strong purifying selection, suggesting that they are functional at the DNA level. Cenealogical analysis revealed that T qiaojiensis was tetraploid, and T douronensis, T qiaojiensis as well as T sinensis had an allotetraploid ancestor. (C) 2009 Elsevier B.V. All rights reserved.

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.

Light-directed writing of chemically tunable narrow-band holographic sensors

This tunable holographic sensor offers interrogation and a reporting transducer as well as an analyte-responsive hydrogel, rendering it label-free and reusable. A single 6 ns laser pulse is used to fabricate holographic sensors consisting of silver nanoparticles arranged periodically within a polymer film. The tunability of the sensor is demonstrated through pH sensing of artificial urine and validated through computational modeling. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular evolution of connective tissue growth factor in Cyprinidae (Teleostei : Cypriniformes)

Connective tissue growth factor (CTGF) plays an important role in regulation of cell growth, differentiation, apoptosis and individual development in animals. The study of sequences variation and molecular evolution of CTGF gene across various species of the cyprinid could be helpful for understanding of speciation and gene divergence in this kind of fish. In this study, 19 novel sequences of CTGF gene were obtained from the representative species of the family Cyprinidae using PCR amplification, cloning and sequencing. Phylogenetic relationships of Cyprinidae were reconstructed by neighbor-joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian method. Oryzias latipes from the family Cyprinodontidae was assigned to be the outgroup taxon. Leuciscini and Barbini were clustered into the monophyletic lineages, respectively, with the high nodal supports. The estimation of the ratio of non-synonymous to synonymous substitution (dN/dS) for the various branches indicated that there stood the different evolution rates between the Leuciscini and the Barbini. With the ratio of dN/dS of the Leuciscini being lower than that of the Barbini, species within the Barbini were demonstrated to be subjected to the relatively less selection pressure and under the relaxable evolution background. A 6 by indel (insertion/deletion) was found at the 5' end of CTGF gene of Cyprinidae, and this 6 by deletion only appeared in the Leuciscini, which is a typical characteristic of the Leuciscini and provides evidence for the monophylogeny of the Leuciscini. For the amino acid sequences of CTGF protein, the most variations and indels were distributed in the signal region and IGFBP region of this protein, implying that these variations were correlated with the regulation of the CTGF gene expression and protein activity. (c) 2007 National Natural Science Foundation of China and Chinese Academy of Sciences. Published by Elsevier Limited and Science in China Press. All rights reserved.

Evolution of vertical phase separation in P3HT:PCBM thin films induced by thermal annealing

The achievement of the desirable morphology at the nanometer scale of bulk heterojunctions consisting of a conjugated polymer with fullerene derivatives is a prerequisite in order to optimize the power conversion efficiency of organic solar cells. The various experimental conditions such as the choice of solvent, drying rates and annealing have been found to significantly affect the blend morphology and the final performance of the photovoltaic device. In this work, we focus on the effects of post deposition thermal annealing at 140 °C on the blend morphology, the optical and structural properties of bulk heterojunctions that consist of poly(3-hexylthiophene) (P3HT) and a methanofullerene derivative (PCBM). The post thermal annealing modifies the distribution of the P3HT and the PCBM inside the blend films, as it has been found by Spectroscopic Ellipsometry studies in the visible to far-ultraviolet spectral range. Phase separation was identified by AFM and GIXRD as a result of a slow drying process which took place after the spin coating process. The increase of the annealing time resulted to a significant increase of the P3HT crystallinity at the top regions of the blend films. © 2011 Elsevier B.V. All rights reserved.

Site-directed gene integration in transgenic zebrafish mediated by cre recombinase using a combination of mutant Lox sites

With current gene-transfer techniques in fish, insertion of DNA into the genome occurs randomly and in many instances at multiple sites. Associated position effects, copy number differences, and multiple gene interactions make gene expression experiments difficult to interpret and fish phenotype less predictable. To meet different fish engineering needs, we describe here a gene targeting model in zebrafish. At first, four target zebrafish lines, each harboring a single genomic lox71 target site, were generated by zebrafish transgenesis. The zygotes of transgenic zebrafish lines were coinjected with capped Cre mRNA and a knockin vector pZklox66RFP. Site-specific integration event happened from one target zebrafish line. In this line two integrant zebrafish were obtained from more than 80,000 targeted embryos (integrating efficiency about 10(-4) to 10(-5)) and confirmed to have a sole copy of the integrating DNA at the target genome site. Genomic polymerase chain reaction analysis and DNA sequencing verified the correct gene target events where lox71 and lox66 have accurately recombined into double mutant lox72 and wild-type loxP. Each integrant zebrafish chosen for analysis harbored the transgene rfp at the designated egfp concatenates. Although the Cre-mediated recombination is site specific, it is dependent on a randomly placed target site. That is, a genomic target cannot be preselected for integration based solely on its sequence. Conclusively, an rfp reporter gene was successfully inserted into the egfp target locus of zebrafish genome by Cre-lox-mediated recombination. This site-directed knockin system using the lox71/lox66 combination should be a promising gene-targeting platform serving various purposes in fish genetic engineering.

The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii : Cyprinifonnes) and an altemative pattem of mitogenomic evolution in vertebrate

The complete mitochondrial genome sequence of the Chinese hook snout carp, Opsariichthys bidens, was newly determined using the long and accurate polymerase chain reaction method. The 16,611-nucleotide mitogenome contains 13 protein-coding genes, two rRNA genes (12S, 16S) 22 tRNA genes, and a noncoding control region. We use these data and homologous sequence data from multiple other ostariophysan fishes in a phylogenetic evaluation to test hypothesis pertaining to codon usage pattern of O. bidens mitochondrial protein genes as well as to re-examine the ostariophysan phylogeny. The mitochondrial genome of O. bidens reveals an alternative pattern of vertebrate mitochondrial evolution. For the mitochondrial protein genes of O. bidens, the most frequently used codon generally ends with either A or C, with C preferred over A for most fourfold degenerate codon families; the relative synonymous codon usage of G-ending codons is greatly elevated in all categories. The codon usage pattern of O. bidens mitochondrial protein genes is remarkably different from the general pattern found previously in the relatively closely 9 related zebrafish and most other vertebrate mitochondria. Nucleotide bias at third codon positions is the main cause of codon bias in the mitochondrial protein genes of O. bidens, as it is biased particularly in favor of C over A. Bayesian analysis of 12 concatenated mitochondrial protein sequences for O. bidens and 46 other teleostean taxa supports the monophyly of Cypriniformes and Otophysi and results in a robust estimate of the otophysan phylogeny. (C) 2007 Published by Elsevier B.V.

Sox genes in grass carp (Ctenopharyngodon idella) with their implications for genome duplication and evolution

The Sox gene family is found in a broad range of animal taxa and encodes important gene regulatory proteins involved in a variety of developmental processes. We have obtained clones representing the HMG boxes of twelve Sox genes from grass carp (Ctenopharyngodon idella), one of the four major domestic carps in China. The cloned Sox genes belong to group B1, B2 and C. Our analyses show that whereas the human genome contains a single copy of Sox4, Sox11 and Sox14, each of these genes has two co-orthologs in grass carp, and the duplication of Sox4 and Sox11 occurred before the divergence of grass carp and zebrafish, which support the "fish-specific whole-genome duplication" theory. An estimation for the origin of grass carp based on the molecular clock using Sox1, Sox3 and Sox11 genes as markers indicates that grass carp (subfamily Leuciscinae) and zebrafish (subfamily Danioninae) diverged approximately 60 million years ago. The potential uses of Sox genes as markers in revealing the evolutionary history of grass carp are discussed.

Integration of double-fluorescence expression vectors into zebrafish genome for the selection of site-directed knockout/knockin

Production of zebrafish by modifying endogenous growth hormone (GH) gene through homologous recombination is described here. We first constructed the targeting vectors pGHT1.7k and pGHT2.8k, which were used for the knockout/knockin of the endogenous GH gene of zebrafish, and injected these two vectors into the embryos of zebrafish. Overall, the rate of targeted integration with the characteristic of germ line transmission in zebrafish was 1.7x10(-6). In one experimental patch, the integrating efficiency of pGHT2.8k was higher than that of pGHT1.7k, but the lethal effect of pGHT2.8k was stronger than that of pGHT1.7k. The clones with the correct integration of target genes were identified by a simple screening procedure based on green fluorescent protein (GFP) and RFP dual selection, which corresponded to homologous recombination and random insertion, respectively. The potential homologous recombination zebrafish was further bred to produce a heterozygous F-1 generation, selected based on the presence of GFP. The potential targeted integration of exogenous GH genes into a zebrafish genome at the P-0 generation was further verified by polymerase chain reaction and Southern blot analysis. Approximately 2.5% of potential founder knockout and knockin zebrafish had the characteristic of germ line transmission. In this study, we developed an efficient method for producing the targeted gene modification in zebrafish for future studies on genetic modifications and gene functions using this model organism.

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.

Structural evolution of mechanically alloyed nanocrystalline FeAl intermetallics

Nanostructured FeAl intermetallics were prepared directly by mechanical alloying (MA) in a high-energy planetary ball-mill. The phase transformations and structural changes occurring in the studied material during mechanical alloying were investigated by X-ray diffraction (XRD). Transmission electron microscopy (TEM) was employed to examine the morphology of the powders. Thermal behavior of the milled powders was examined by differential scanning calorimetry (DSC). Disordered Fe(Al) solid solution was formed at the early stage. After 30 h of milling, Fe(Al) solid solution transformed into an ordered FeAl phase. The average crystallite size reduction down to about 12 nm was accompanied by the introduction of the average lattice strain up to 1.7%. The TEM picture showed that the size of milled powders was less than 30 nm. (c) 2007 Elsevier B.V. All rights reserved.

Evolution of structural defects in SiOx films fabricated by electron cyclotron resonance plasma chemical vapour deposition upon annealing treatment

We study the structural defects in the SiOx film prepared by electron cyclotron resonance plasma chemical vapour deposition and annealing recovery evolution. The photoluminescence property is observed in the as-deposited and annealed samples. [-SiO3](2-) defects are the luminescence centres of the ultraviolet photoluminescence (PL) from the Fourier transform infrared spectroscopy and PL measurements. [-SiO3](2-) is observed by positron annihilation spectroscopy, and this defect can make the S parameters increase. After 1000 degrees C annealing, [-SiO3](2-) defects still exist in the films.

Evolution of Ge and SiGe quantum dots under excimer laser annealing

We present different relaxation mechanisms of Ge and SiGe quantum dots under excimer laser annealing. Investigation of the coarsening and relaxation of the dots shows that the strain in Ge dots on Ge films is relaxed by dislocation since there is no interface between the Ge dots and the Ge layer, while the SiGe dots on Si0.77Ge0.23 film relax by lattice distortion to coherent clots, which results from the obvious interface between the SiGe clots and the Si0.77Ge0.23 film. The results are suggested and sustained by Vanderbilt and Wickham's theory, and also demonstrate that no bulk diffusion oGeurs during the excimer laser annealing.