Cloning and characterization of interferon stimulated genes Viperin and ISG15, and their promoters from snakehead Channa argus

By suppression subtractive hybridization, rapid amplification of cDNA ends and gene walking methods, interferon stimulated genes (ISGs), Viperin and ISG15, and their promoters have been cloned and characterized from snakehead Channa argus. The Viperin cDNA was found to be 1474 nt and contain an open reading frame (ORF) of 1059 nt that translates into a putative peptide of 352 amino acid (aa). The putative peptide of Viperin shows high identity to that in teleosts and mammals except for the N-terminal 70 aa. The ISG15 cDNA was found to be 758 nt and contain an ORF of 468 nt that translates into a putative peptide of 155 aa. The putative peptide of ISG15 is composed of two tandem repeats of ubiquitin-like (UBL) domains, and a canonical conjugation motif (LRGG) at C-terminal. Viperin and ISG15 promoter regions were characterized by the presence of interferon stimulating response elements (ISRE) and gamma-IFN activation sites (GAS). ISRE is a feature of IFN-induced gene promoter and partially overlaps interferon regulatory factor (IRF) 1 and IRF2 recognition sites. GAS is responsible for the gamma-IFN mediated transcription. One conserved site for NF-kappa B was found in the promoter region of Viperin. This is the first report of conservative binding motif for NF-kappa B in accordance with the consensus sequence (GGGRN-NYYCC) among teleost ISG promoters. Moreover, there were also TATA, CAAT and Sp1 transcription factor sites in Viperin and ISG15 promoters. In 5' untranslated region (UTR), snakehead ISG15 gene contains a single intron, which differs from Viperin gene. The transcripts of Vipeirn and ISG15 mRNA were mainly expressed in head kidney, posterior kidney, spleen and gill. The expression levels in liver were found to increase obviously in response to induction by IFN-inducer poly I : C.By suppression subtractive hybridization, rapid amplification of cDNA ends and gene walking methods, interferon stimulated genes (ISGs), Viperin and ISG15, and their promoters have been cloned and characterized from snakehead Channa argus. The Viperin cDNA was found to be 1474 nt and contain an open reading frame (ORF) of 1059 nt that translates into a putative peptide of 352 amino acid (aa). The putative peptide of Viperin shows high identity to that in teleosts and mammals except for the N-terminal 70 aa. The ISG15 cDNA was found to be 758 nt and contain an ORF of 468 nt that translates into a putative peptide of 155 aa. The putative peptide of ISG15 is composed of two tandem repeats of ubiquitin-like (UBL) domains, and a canonical conjugation motif (LRGG) at C-terminal. Viperin and ISG15 promoter regions were characterized by the presence of interferon stimulating response elements (ISRE) and gamma-IFN activation sites (GAS). ISRE is a feature of IFN-induced gene promoter and partially overlaps interferon regulatory factor (IRF) 1 and IRF2 recognition sites. GAS is responsible for the gamma-IFN mediated transcription. One conserved site for NF-kappa B was found in the promoter region of Viperin. This is the first report of conservative binding motif for NF-kappa B in accordance with the consensus sequence (GGGRN-NYYCC) among teleost ISG promoters. Moreover, there were also TATA, CAAT and Sp1 transcription factor sites in Viperin and ISG15 promoters. In 5' untranslated region (UTR), snakehead ISG15 gene contains a single intron, which differs from Viperin gene. The transcripts of Vipeirn and ISG15 mRNA were mainly expressed in head kidney, posterior kidney, spleen and gill. The expression levels in liver were found to increase obviously in response to induction by IFN-inducer poly I : C

Effect of Pyrolysis Temperature on the Characterisation of Dissolved Organic Matter from Pyroligneous Acid

Dissolved organic matter (DOM) greatly influences the transformation of nutrients and pollutants in the environment. To investigate the effects of pyrolysis temperatures on the composition and evolution of pyroligneous acid (PA)-derived DOM, DOM solutions extracted from a series of PA derived from eucalyptus at five pyrolysis temperature ranges (240–420 °C) were analysed with Fourier transform infrared spectroscopy, gas chromatography–mass spectroscopy, and fluorescence spectroscopy. Results showed that the dissolved organic carbon content sharply increased (p 370 °C). The results of two-dimensional correlation spectroscopic analysis suggested that with increasing pyrolysis temperatures, the humic-acid-like substances became more sensitive than other fluorescent components. This study provides valuable information on the characteristic evolution of PA-derived DOM

Experimental realization of a highly secure chaos communication under strong channel noise

A one-way coupled spatiotemporally chaotic map lattice is used to contruct cryptosystem. With the combinatorial applications of both chaotic computations and conventional algebraic operations, our system has optimal cryptographic properties much better than the separative applications of known chaotic and conventional methods. We have realized experiments to pratice duplex voice secure communications in realistic Wired Public Switched Telephone Network by applying our chaotic system and the system of Advanced Encryption Standard (AES), respectively, for cryptography. Our system can work stably against strong channel noise when AES fails to work.Comment: 15 pages, 5 figure

Identification and characterization of common carp (Cyprinus carpio L.) granzyme A/K, a cytotoxic cell granule-associated serine protease

Granzyme (Gzm) is an important member of serine protease family, and key component in the specific and non-specific cell-mediated cytotoxicity Partial GzmA/K cDNA sequence of common carp (Cyprinus carpi L) was isolated from thymus cDNA library by the method of suppression subtractive hybridization (SSH). Subsequently, the full length cDNA of carp GzmA/K was obtained by means of 3' RACE and 5' RACE, respectively The full length cDNA of carp GzmA/K was 1053 bp, consisting of a 5'-terminal untranslated region (UTR) of 65 bp, a 3'-terminal UTR of 214 bp, and an open reading frame of 774 bp Amino acid sequence analysis indicated the existence of a signal peptide, eight consensus cysteine residues, one conserved IIGG motif and three conserved residues as central elements of the GzmA/K active site. Carp GzmA/K shared 36% and 39% amino acid identity to human GzmA and K, respectively, and was phylogenetically related to the granzyme A and K subgroups Then, a genomic DNA, which covers the promoter region and entire coding region of carp GzmA/K, was obtained by PCR. In the 5.4 k-long genomic sequence, five exons and four introns were identified. Real-time RT-PCR analysis showed that carp GzmA/K transcript was predominantly detected in the immune-related tissues, and after SVCV infection, was up-regulated in most immune-related tissues in a time-dependent manner Real-time RT-PCR results also showed that carp GzmA/K transcript was up-regulated in thymus tissue of GH transgenic carp These results will help to understand the molecular characterization and the potential role of teleost GzmA/K, a cytotoxic cell granule-associated serine protease Crown Copyright (C) 2010 Published by Elsevier Ltd. All rights reserve

Structural and functional insight into the mechanism of an alkaline exonuclease from Laribacter hongkongensis

Alkaline exonuclease and single-strand DNA (ssDNA) annealing proteins (SSAPs) are key components of DNA recombination and repair systems within many prokaryotes, bacteriophages and virus-like genetic elements. The recently sequenced β-proteobacterium Laribacter hongkongensis (strain HLHK9) encodes putative homologs of alkaline exonuclease (LHK-Exo) and SSAP (LHK-Bet) proteins on its 3.17 Mb genome. Here, we report the biophysical, biochemical and structural characterization of recombinant LHK-Exo protein. LHK-Exo digests linear double-stranded DNA molecules from their 5′-termini in a highly processive manner. Exonuclease activities are optimum at pH 8.2 and essentially require Mg2+ or Mn2+ ions. 5′-phosphorylated DNA substrates are preferred over dephosphorylated ones. The crystal structure of LHK-Exo was resolved to 1.9 Å, revealing a ‘doughnut-shaped’ toroidal trimeric arrangement with a central tapered channel, analogous to that of λ-exonuclease (Exo) from bacteriophage-λ. Active sites containing two bound Mg2+ ions on each of the three monomers were located in clefts exposed to this central channel. Crystal structures of LHK-Exo in complex with dAMP and ssDNA were determined to elucidate the structural basis for substrate recognition and binding. Through structure-guided mutational analysis, we discuss the roles played by various active site residues. A conserved two metal ion catalytic mechanism is proposed for this class of alkaline exonucleases

The effects of conformity-driven teaching ability on opinion consensus

Opinion dynamics based on evolutionary game provides a new theoretical method to investigate opinion consensus. Yang (EPL, 115 (2016) 40007) proposed a concise model to address this issue. By introducing game theory into opinion dynamics, the benefits (costs) caused by agreement (disagreement) during the evolution of opinions can be considered conveniently. Motivated by this work, we introduce conformity-driven teaching ability into the opinion dynamics based on evolutionary game. In the model, we use a sensitive factor H to characterize the dependence of the teaching ability on the conformity of individuals. The results show that the consensus time could be shortened by small H, which corresponds to the teaching ability strongly depending on the conformity. Moreover, there exists a threshold, Hth, for achieving the shortest consensus time. When H is below Hth, the consensus time is insensitive to the variation of H and remains at the minimum. However, once H exceeds Hth, the consensus time increases significantly with the increase of H. Furthermore, we provide a microscopic explanation for the results by monitoring the opinion clusters during the evolution. Besides, we study the roles of leaders in the opinion dynamics and find that the leaders holding the same opinion could effectively lead to the consensus on that opinion

Leaders should be more persistent in evolutionary social dilemmas

Strategy persistence has been found to play an important role in the emergence and maintenance of cooperation. In this work, we propose a spatial prisoner's dilemma game in which there are two types of individuals, P-individuals with nonzero strategy persistence level and NP-individuals without strategy persistence. We concern with the question: Who should P-individuals be if the goal is to achieve a high level of cooperation? By investigating four different schemes, i.e., uniform, inversely degree-related, degree-related, and collective influence schemes, we find that highly cooperative outcomes emerge if P-individuals are played by leaders with high degrees regardless of the structures of the underlying networks. In contrast, if the masses with low degrees act as P-individuals where leaders change their strategies frequently, cooperation cannot be promoted and, instead, it can even be weakened

Aspiration-dependent strategy persistence promotes cooperation in spatial prisoner's dilemma game

In this paper, we introduce an aspiration-dependent persistence into the spatial prisoner's dilemma game aimed at promoting cooperation in a population. Based on aspiration, a player could adjust his/her strategy persistence level during the evolutionary process. In particular, he/she will hold a strategy longer if it brings him/her a satisfactory payoff, otherwise he/she will decrease the time duration of keeping the present choice. We also introduce a tunable parameter to characterize the sensitivity of strategy persistence to aspiration and investigate the effects of the sensitivity on the evolution of cooperation. The results show that aspiration-dependent strategy persistence could effectively promote cooperation. At an intermediate aspiration, diverse strategy persistence levels among population could be formed during the evolution, which ultimately results in the highest cooperation level. Then, we present intuitive explanations for the existence of optimal aspiration by scrutinizing the microscopic evolution of cooperation. Moreover, we find that, in the population where individuals are more sensitive to aspiration, cooperation could be further promoted by assembling greater cooperator clusters with the help of diverse strategy persistence distribution. Our results highlight the more realistic scenario where aspiration-dependent persistence is involved in the spatial prisoner's dilemma game

The effects of the conformity threshold on cooperation in spatial prisoner's dilemma games

Conformity is a common phenomenon existing both in humans and in social animals, which has strong impact on collective behaviors. The effects of conformity on cooperation in a population have been widely explored in evolutionary games. Conformity-driven individuals tend to follow the strategy adopted by the majority of their neighbors. In most previous studies, the individuals take the half-number of their neighbors as the threshold for identifying the majority. However, in reality, the individuals may determine the majority based on a different threshold. For example, they might not conform unless the proportion of the majority reaches three-quarters. In contrast, it is also possible that the individuals have a lower reference than the half for majority. Here, we study the effects of the conformity threshold on cooperation in spatial prisoner's dilemma games. Our results show that there always exists an optimal conformity threshold for the population to maximize the cooperation level. Moreover, we find that the optimal conformity threshold depends on the payoff parameter of the game. Besides, the robustness of the results has been checked and we find that the simulation results are qualitatively unchanged when the different network scheme is used

Preferential selection based on degree difference in the spatial prisoner's dilemma games

Strategy evolution in spatial evolutionary games is generally implemented through imitation processes between individuals. In most previous studies, it is assumed that individuals pick up one of their neighbors randomly to learn from. However, by considering the heterogeneity of individuals' influence in the real society, preferential selection is more realistic. Here, we introduce a preferential selection mechanism based on degree difference into spatial prisoner's dilemma games on Erdös-Rényi networks and Barabási-Albert scale-free networks and investigate the effects of the preferential selection on cooperation. The results show that, when the individuals prefer to choose the neighbors who have small degree difference with themselves to imitate, cooperation is hurt by the preferential selection. In contrast, when the individuals prefer to choose those large degree difference neighbors to learn from, there exists optimal preference strength resulting in the maximal cooperation level no matter what the network structure is. In addition, we investigate the robustness of the results against variations of the noise, the average degree and the size of network in the model, and find that the qualitative features of the results are unchanged