Comprehensive Transcriptome Analysis Reveals Accelerated Genic Evolution in a Tibet Fish, Gymnodiptychus pachycheilus

Elucidating the genetic mechanisms of organismal adaptation to the Tibetan Plateau at a genomic scale can provide insights into the process of adaptive evolution. Many highland species have been investigated and various candidate genes that may be responsible for highland adaptation have been identified. However, we know little about the genomic basis of adaptation to Tibet in fishes. Here, we performed transcriptome sequencing of a schizothoracine fish (Gymnodiptychus pachycheilus) and used it to identify potential genetic mechanisms of highland adaptation. We obtained totally 66,105 assembled unigenes, of which 7,232 were assigned as putative one-to-one orthologs in zebrafish. Comparative gene annotations from several species indicated that at least 350 genes lost and 41 gained since the divergence between G. pachycheilus and zebrafish. An analysis of 6,324 orthologs among zebrafish, fugu, medaka, and spotted gar identified consistent evidence for genome-wide accelerated evolution in G. pachycheilus and only the terminal branch of G. pachycheilus had an elevated Ka/Ks ratio than the ancestral branch. Many functional categories related to hypoxia and energy metabolism exhibited rapid evolution in G. pachycheilus relative to zebrafish. Genes showing signature of rapid evolution and positive selection in the G. pachycheilus lineage were also enriched in functions associated with energy metabolism and hypoxia. The first genomic resources for fish in the Tibetan Plateau and evolutionary analyses provided some novel insights into highland adaptation in fishes and served as a foundation for future studies aiming to identify candidate genes underlying the genetic bases of adaptation to Tibet in fishes

The complete mitochondrial genome of Leiocassis crassilabris (Teleostei, Siluriformes: Bagridae)

The Leiocassis crassilabris is an important economic fish in China, and is widely distributed in south China, e.g. Yangtze River, Pearl River, and Min River, so it is a good model to study population genetics and geological changes of these regions. In this study, the complete mitochondrial genome sequence of L. crassilabris has been obtained with PCR. The gene arrangement and composition L. crassilabris of mitochondrial genome sequence are similar to most of the other vertebrates', which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region with the total length of 16,530 bp. Except for eight tRNA and ND6 genes, other genes are encoded on heavy-strand (H-strand). Similar to most other vertebrates, the bias of G and C have universality in different region (genes). The complete mitochondrial genome sequence of L. crassilabris would contribute to better understand population genetics, conservation, biogeography, evolution of this lineage.The Leiocassis crassilabris is an important economic fish in China, and is widely distributed in south China, e.g. Yangtze River, Pearl River, and Min River, so it is a good model to study population genetics and geological changes of these regions. In this study, the complete mitochondrial genome sequence of L. crassilabris has been obtained with PCR. The gene arrangement and composition L. crassilabris of mitochondrial genome sequence are similar to most of the other vertebrates', which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region with the total length of 16,530 bp. Except for eight tRNA and ND6 genes, other genes are encoded on heavy-strand (H-strand). Similar to most other vertebrates, the bias of G and C have universality in different region (genes). The complete mitochondrial genome sequence of L. crassilabris would contribute to better understand population genetics, conservation, biogeography, evolution of this lineage

Cyprinid phylogeny based on Bayesian and maximum likelihood analyses of partitioned data: implications for Cyprinidae systematics

Cyprinidae is the biggest family of freshwater fish, but the phylogenetic relationships among its higher-level taxa are not yet fully resolved. In this study, we used the nuclear recombination activating gene 2 and the mitochondrial 16S ribosomal RNA and cytochrome b genes to reconstruct cyprinid phylogeny. Our aims were to (i) demonstrate the effects of partitioned phylogenetic analyses on phylogeny reconstruction of cyprinid fishes; (ii) provide new insights into the phylogeny of cyprinids. Our study indicated that unpartitioned strategy was optimal for our analyses; partitioned analyses did not provide better-resolved or -supported estimates of cyprinid phylogeny. Bayesian analyses support the following relationships among the major monophyletic groups within Cyprinidae: (Cyprininae, Labeoninae), ((Acheilognathinae, ((Leuciscinae, Tincinae), Gobioninae)), Xenocyprininae). The placement of Danioninae was poorly resolved. Estimates of divergence dates within the family showed that radiation of the major cyprinid groups occurred during the Late Oligocene through the Late Miocene. Our phylogenetic analyses improved our understanding of the evolutionary history of this important fish family.Cyprinidae is the biggest family of freshwater fish, but the phylogenetic relationships among its higher-level taxa are not yet fully resolved. In this study, we used the nuclear recombination activating gene 2 and the mitochondrial 16S ribosomal RNA and cytochrome b genes to reconstruct cyprinid phylogeny. Our aims were to (i) demonstrate the effects of partitioned phylogenetic analyses on phylogeny reconstruction of cyprinid fishes; (ii) provide new insights into the phylogeny of cyprinids. Our study indicated that unpartitioned strategy was optimal for our analyses; partitioned analyses did not provide better-resolved or -supported estimates of cyprinid phylogeny. Bayesian analyses support the following relationships among the major monophyletic groups within Cyprinidae: (Cyprininae, Labeoninae), ((Acheilognathinae, ((Leuciscinae, Tincinae), Gobioninae)), Xenocyprininae). The placement of Danioninae was poorly resolved. Estimates of divergence dates within the family showed that radiation of the major cyprinid groups occurred during the Late Oligocene through the Late Miocene. Our phylogenetic analyses improved our understanding of the evolutionary history of this important fish family

Perceptual Grouping without Awareness: Superiority of Kanizsa Triangle in Breaking Interocular Suppression

Much information could be processed unconsciously. However, there is no direct evidence on whether perceptual grouping could occur without awareness. To answer this question, we investigated whether a Kanizsa triangle (an example of perceptual grouping) is processed differently from stimuli with the same local components but are ungrouped or weakly grouped. Specifically, using a suppression time paradigm we tested whether a Kanizsa triangle would emerge from interocular continuous flash suppression sooner than control stimuli. Results show a significant advantage of the Kanizsa triangle: the Kanizsa triangle emerged from suppression noise significantly faster than the control stimulus with the local Pacmen randomly rotated (t(9) = −2.78, p = 0.02); and also faster than the control stimulus with all Pacmen rotated 180° (t(11) = −3.20, p<0.01). Additional results demonstrated that the advantage of the grouped Kanizsa triangle could not be accounted for by the faster detection speed at the conscious level for the Kanizsa figures on a dynamic noise background. Our results indicate that certain properties supporting perceptual grouping could be processed in the absence of awareness

Growth disturbance of extracts from several crops straw (residue) on Ageratina adenophora and biological-control implications in hazardous weed invasion for eco-restoration

Laboratory biological simulation experiment was conducted to investigate growth disturbance of high, moderate, low concentration of aqueous extracts (i.e. the original extracts with a solid liquid ratio of 1:40 g mL-1 and its 5 times diluents and 25 times diluents) from several crops straw (residue) on Ageratina adenophora, a worldwide notorious invasive weed. The results showed: (a) aqueous extracts from several crops straw (residue) brought about different impacts on the single index for germination and growth of A. adenophora, e.g., high concentration of aqueous extracts from Brassica oleracea waste leaves showed a strong inhibition against the germination rate (GR) and germination index (GI) of A. adenophora, while high concentration of aqueous extracts from Vicia cracca straw showed a strong inhibition against radicle length (RL) and hypocotyl length (HL) of A. adenophora; (b) high concentration of aqueous extracts from B. oleracea waste leaves and high, moderate and low concentration of aqueous extracts from Oryza sativa straw and Triticum aestivum straw showed rather strong synthetic effects (inhibition) on GR and GI of A. adenophora, which could be chosen for the control over the seeds germination of A. adenophora; (c) high and moderate concentrations of aqueous extracts from V. cracca straw, high concentration of aqueous extracts from B. campestris waste leaves, and moderate and low concentrations of aqueous extracts from O. sativa straw and T. aestivum straw showed rather strong synthetic effects (inhibition) on RL and HL of A. adenophora, which could be selected as ideal materials for the control over the seedlings growth of A. adenophora; and (d) high concentrations of aqueous extracts from V. cracca straw, B. oleracea waste leaves and B. campestris waste leaves, and high, moderate and low concentrations of aqueous extracts from O. sativa straw and T. aestivum straw showed rather strong synthetic effects (inhibition) on GR, GI, RL and HL of A. adenophora, which could be selected as ideal materials for the control over the seeds germination and seedlings growth of A. adenophora. Thus, this study would provide a theoretic guidance and technical support for the resources utilization of crops straw (residue) and the prevention and control over invasive weeds as well. (C) 2013 Elsevier B.V. All rights reserved.Laboratory biological simulation experiment was conducted to investigate growth disturbance of high, moderate, low concentration of aqueous extracts (i.e. the original extracts with a solid liquid ratio of 1:40 g mL-1 and its 5 times diluents and 25 times diluents) from several crops straw (residue) on Ageratina adenophora, a worldwide notorious invasive weed. The results showed: (a) aqueous extracts from several crops straw (residue) brought about different impacts on the single index for germination and growth of A. adenophora, e.g., high concentration of aqueous extracts from Brassica oleracea waste leaves showed a strong inhibition against the germination rate (GR) and germination index (GI) of A. adenophora, while high concentration of aqueous extracts from Vicia cracca straw showed a strong inhibition against radicle length (RL) and hypocotyl length (HL) of A. adenophora; (b) high concentration of aqueous extracts from B. oleracea waste leaves and high, moderate and low concentration of aqueous extracts from Oryza sativa straw and Triticum aestivum straw showed rather strong synthetic effects (inhibition) on GR and GI of A. adenophora, which could be chosen for the control over the seeds germination of A. adenophora; (c) high and moderate concentrations of aqueous extracts from V. cracca straw, high concentration of aqueous extracts from B. campestris waste leaves, and moderate and low concentrations of aqueous extracts from O. sativa straw and T. aestivum straw showed rather strong synthetic effects (inhibition) on RL and HL of A. adenophora, which could be selected as ideal materials for the control over the seedlings growth of A. adenophora; and (d) high concentrations of aqueous extracts from V. cracca straw, B. oleracea waste leaves and B. campestris waste leaves, and high, moderate and low concentrations of aqueous extracts from O. sativa straw and T. aestivum straw showed rather strong synthetic effects (inhibition) on GR, GI, RL and HL of A. adenophora, which could be selected as ideal materials for the control over the seeds germination and seedlings growth of A. adenophora. Thus, this study would provide a theoretic guidance and technical support for the resources utilization of crops straw (residue) and the prevention and control over invasive weeds as well. (C) 2013 Elsevier B.V. All rights reserved

RpaA Regulates the Accumulation of Monomeric Photosystem I and PsbA under High Light Conditions in Synechocystis sp PCC 6803

The response regulator RpaA was examined by targeted mutagenesis under high light conditions in Synechocystis sp. PCC 6803. A significant reduction in chlorophyll fluorescence from photosystem I at 77 K was observed in the RpaA mutant cells under high light conditions. Interestingly, the chlorophyll fluorescence emission from the photosystem I trimers at 77 K are similar to that of the wild type, while the chlorophyll fluorescence from the photosystem I monomers was at a much lower level in the mutant than in the wild type under high light conditions. The RpaA inactivation resulted in a dramatic reduction in the monomeric photosystem I and the D1 protein but not the CP47 content. However, there is no significant difference in the transcript levels of psaA or psbA or other genes examined, most of which are involved in photosynthesis, pigment biosynthesis, or stress responses. Under high light conditions, the growth of the mutant was affected, and both the chlorophyll content and the whole-chain oxygen evolution capability of the mutant were found to be significantly lower than those of the wild type, respectively. We propose that RpaA regulates the accumulation of the monomeric photosystem I and the D1 protein under high light conditions. This is the first report demonstrating that inactivation of a stress response regulator has specifically reduced the monomeric photosystem I. It suggests that PS I monomers and PS I trimers can be regulated independently for acclimation of cells to high light stress.The response regulator RpaA was examined by targeted mutagenesis under high light conditions in Synechocystis sp. PCC 6803. A significant reduction in chlorophyll fluorescence from photosystem I at 77 K was observed in the RpaA mutant cells under high light conditions. Interestingly, the chlorophyll fluorescence emission from the photosystem I trimers at 77 K are similar to that of the wild type, while the chlorophyll fluorescence from the photosystem I monomers was at a much lower level in the mutant than in the wild type under high light conditions. The RpaA inactivation resulted in a dramatic reduction in the monomeric photosystem I and the D1 protein but not the CP47 content. However, there is no significant difference in the transcript levels of psaA or psbA or other genes examined, most of which are involved in photosynthesis, pigment biosynthesis, or stress responses. Under high light conditions, the growth of the mutant was affected, and both the chlorophyll content and the whole-chain oxygen evolution capability of the mutant were found to be significantly lower than those of the wild type, respectively. We propose that RpaA regulates the accumulation of the monomeric photosystem I and the D1 protein under high light conditions. This is the first report demonstrating that inactivation of a stress response regulator has specifically reduced the monomeric photosystem I. It suggests that PS I monomers and PS I trimers can be regulated independently for acclimation of cells to high light stress

Isolation and expression of grass carp toll-like receptor 5a (CiTLR5a) and 5b (CiTLR5b) gene involved in the response to flagellin stimulation and grass carp reovirus infection

Toll-like receptor 5 (TLR5), a member of Toll-like receptors (TLRs) family and is responsible for the bacterial flagellin recognition in vertebrates, play an important role in innate immunity. In the study, two TLR5 genes of grass carp (Ctenopharyngodon idellus), named CiTLR5a and CiTLR5b, were cloned and analyzed. Both CiTLR5a and CiTLR5b are typical TLR proteins, including LRR motif, transmembrane region and TIR domain. The full-length cDNA of CiTLR5a is 3054 bp long, with a 2646 bp open reading frame (ORF), 78 bp 5' untranslated regions (UTR), and 330 bp 3' UTR. The full-length cDNA of CiTLR5b is 3326 bp, with a 2627 bp ORF, 95 bp 5' UTR, and 594 bp 3' UTR. Phylogenetic analysis showed that CiTLR5a and CiTLR5b were closed to the TLR5 of cirrhinus mrigala, cyprinus_carpio, and danio redo. Subcellular localization indicated that CiTLR5a and CiTLR5b shared similar localization pattern and may locate in the plasma membrane of transfected cells. Real-time quantitative PCR revealed CiTLR5a and CiTLR5b were constitutively expressed in all examined tissues, whereas the highest expressed tissue differed. Following exposure to flagellin and GCRV, CiTLR5a and CiTLR5b were up-regulated significantly. Moreover, the downstream genes of TLR5 signal pathway such as MyD88, NF-kappa B, IRF7, IL-1 beta, and TNF-alpha also up-regulated significantly, whereas the I kappa B gene was down-regulated, suggesting that CiTLR5a and CiTLR5b involved in response to flagellin stimulation and GCRV infection. The results obtained in the study would provide a new insight for further understand the function of TLR5 in teleost fish. (C) 2015 Elsevier Ltd. All rights reserved

A dynamic coupling model for hybrid atomistic-continuum computations

A dynamic coupling model is developed for a hybrid atomistic-continuum computation in micro- and nano-fluidics. In the hybrid atomistic-continuum computation, a molecular dynamics (MD) simulation is utilized in one region where the continuum assumption breaks down and the Navier-Stokes (NS) equations are used in another region where the continuum assumption holds. In the overlapping part of these two regions, a constrained particle dynamics is needed to couple the MD simulation and the NS equations. The currently existing coupling models for the constrained particle dynamics have a coupling parameter, which has to be empirically determined. In the present work, a novel dynamic coupling model is introduced where the coupling parameter can be calculated as the computation progresses rather than inputing a priori. The dynamic coupling model is based on the momentum constraint and exhibits a correct relaxation rate. The results from the hybrid simulation on the Couette flow and the Stokes flow are in good agreement with the data from the full MD simulation and the solutions of the NS equations, respectively. (c) 2007 Elsevier Ltd. All rights reserved

Spatial variability of soil salinity in Bohai Sea coastal wetlands, China: Partition into four management zones

Soil salinization constitutes an environmental hazard worldwide. The Bohai Sea coastal wetland area is experiencing dramatic soil salinization, which is affecting its economic development. This study focused on the spatial variation and distribution characteristics of soil salinity in this area using geostatistical analysis combined with the kriging interpolation method, based on a large-scale field investigation and layered soil sampling (0-30, 30-60 and 60-100cm). The results revealed that soil salinity in these layers demonstrated strong variability, obvious spatial structure characteristics and strong spatial autocorrelation. Soil salinity displayed a significant zonal distribution, gradually decreasing with increasing distance from the coastline. Apart from the northern part of the study area, which appeared to be not affected by soil salinization, there were varying degrees of soil salinization in nearly 70% of the total area. With increasing soil depth, the areas of non-salinized and mild salinized soil gradually decreased, while those of moderate salinized and strong salinized soils increased. The area of saline soil first decreased and then increased. The study area could be divided into four management zones according to soil salinities in the top 1-m soil body, and utilization measures, adapted to local conditions, were proposed for each zone. The results of our study present an important theoretical basis for the improvement of saline soils, for wetland re-vegetation and for the sustainable utilization of soil resources in the Bohai Sea coastal wetland.Soil salinization constitutes an environmental hazard worldwide. The Bohai Sea coastal wetland area is experiencing dramatic soil salinization, which is affecting its economic development. This study focused on the spatial variation and distribution characteristics of soil salinity in this area using geostatistical analysis combined with the kriging interpolation method, based on a large-scale field investigation and layered soil sampling (0-30, 30-60 and 60-100cm). The results revealed that soil salinity in these layers demonstrated strong variability, obvious spatial structure characteristics and strong spatial autocorrelation. Soil salinity displayed a significant zonal distribution, gradually decreasing with increasing distance from the coastline. Apart from the northern part of the study area, which appeared to be not affected by soil salinization, there were varying degrees of soil salinization in nearly 70% of the total area. With increasing soil depth, the areas of non-salinized and mild salinized soil gradually decreased, while those of moderate salinized and strong salinized soils increased. The area of saline soil first decreased and then increased. The study area could be divided into four management zones according to soil salinities in the top 1-m soil body, and utilization measures, adapted to local conditions, were proposed for each zone. The results of our study present an important theoretical basis for the improvement of saline soils, for wetland re-vegetation and for the sustainable utilization of soil resources in the Bohai Sea coastal wetland

Piezoresistive Sensitivity, Linearity and Resistance Time Drift of Polysilicon Nanofilms with Different Deposition Temperatures

Our previous research work indicated that highly boron doped polysilicon nanofilms (≤100 nm in thickness) have higher gauge factor (the maximum is ∼34 for 80 nm-thick films) and better temperature stability than common polysilicon films (≥ 200nm in thickness) at the same doping levels. Therefore, in order to further analyze the influence of deposition temperature on the film structure and piezoresistance performance, the piezoresistive sensitivity, piezoresistive linearity (PRL) and resistance time drift (RTD) of 80 nm-thick highly boron doped polysilicon nanofilms (PSNFs) with different deposition temperatures were studied here. The tunneling piezoresistive model was established to explain the relationship between the measured gauge factors (GFs) and deposition temperature. It was seen that the piezoresistance coefficient (PRC) of composite grain boundaries is higher than that of grains and the magnitude of GF is dependent on the resistivity of grain boundary (GB) barriers and the weight of the resistivity of composite GBs in the film resistivity. In the investigations on PRL and RTD, the interstitial-vacancy (IV) model was established to model GBs as the accumulation of IV pairs. And the recrystallization of metastable IV pairs caused by material deformation or current excitation is considered as the prime reason for piezoresistive nonlinearity (PRNL) and RTD. Finally, the optimal deposition temperature for the improvement of film performance and reliability is about 620 °C and the high temperature annealing is not very effective in improving the piezoresistive performance of PSNFs deposited at lower temperatures