A Full-automatic Sequence Design Algorithm for Branched DNA Structures

Abstract

Production of various structures by self-assembling single stranded DNA molecules is a widely used technology in the filed of DNA nanotechnology. Base sequences of single strands do predict the shape of the resulting nanostructure. Therefore, sequence design is crucial for the successful structure fabrication. This paper presents a sequence design algorithm based on mismatch minimization that can be applied to every desired DNA structure. With this algorithm, junctions, loops, single as well as double stranded regions, and very large structures up to several thousand base pairs can be handled. Thereby, the algorithm is fast for the most structures. Algorithm is Java-implemented. Its implementation is called Seed and is available publicly. As an example for a successful sequence generation, this paper presents the fabrication of DNA chain molecules consisting of double-crossover (DX) tiles as well.     

The role of the cannabinoid type 1 receptor and down-stream cAMP/DARPP-32 signal in the nucleus accumbens of methamphetamine-sensitized rats

Blockade of the cannabinoid type 1 (CB(1)) receptor could suppress methamphetamine self-administration; however, the cellular mechanism remains unclear. In this study, we intended to investigate the significance of brain CB(1) receptors on the development of behavioral sensitization to methamphetamine. Male Sprague-Dawley rats treated with chronic methamphetamine (4 mg/kg, i.p.) for either 7 or 14 days developed behavioral sensitization to methamphetamine (1 mg/kg) at withdrawal day 7. A progressive decrease in numbers of CB(1) receptor (both Bmax and mRNA) but increase in binding affinity (Kd) was noticed during withdrawal days 3 to 7. Microinjection of CB(1) antagonist [5-(4-bromophenyl)-1-(2,4-dichlorophenyl)-4-ethyl-N-(1-piperidinyl)-1H-pyrazole-3-carboxamide] into the nucleus accumbens (NAc) at withdrawal day 7, significantly suppressed the behavioral sensitization to methamphetamine. In NAc brain slices preparation, acute incubation with CB(1) agonist (1R,3R,4R)-3-[2-hydroxy-4-(1,1-dimethylheptyl)phenyl]-4-(3-hydroxypropyl)cyclohexan-1-ol (CP 55940) dose-dependently enhanced cAMP accumulation in sensitized rats; no change was noticed in control groups. Consequently, treatment of CP 55940 induced a dose-dependent (10 nmol/L-10 micromol/L) phosphorylation on down-stream dopamine and cAMP-regulated phosphoprotein of Mr 32 000 (DARPP-32)/Thr34 in sensitized rats, while only 10 micromol/L CP 55940 was able to enhance the phosphoDARPP-32/T34 in control groups. Alternatively, both basal activity of calcineurin (PP-2B) and CP 55940-induced changes in the amount of PP-2B in the NAc were both decreased in sensitized rats, but not in controls. Overall, we demonstrated that brain CB(1) receptor and its down-stream cAMP/DARPP-32/T34/PP-2B signaling are profoundly altered in methamphetamine-sensitized animals.     

Dual alteration of limbic dopamine D1 receptor-mediated signalling and the Akt/GSK3 pathway in dopamine D3 receptor mutants during the development of methamphetamine sensitization

The central dopamine system plays significant roles in motor activity and drug-induced behavioural sensitization. Our goal was to determine the significance of dopamine D(3) receptors in the development of behavioural sensitization to methamphetamine, assessed with D(3) receptor mutant mice. The absence of D(3) receptors significantly increased the behavioural responses to acute methamphetamine and evoked a faster rate of behavioural sensitization to chronic methamphetamine. In addition, both D(3) receptor protein and mRNA levels in the limbic forebrain decreased in sensitized wild-type mice. Further analyses indicated that D(1)-dependent behavioural sensitization and the number of limbic D(1) receptors increased in sensitized D(3) mutants as compared with sensitized wild-type mice. Consistent with this finding, we observed higher levels of D(1) receptor-evoked cAMP accumulation and basal phosphoDARPP-32/Thr34 in the limbic forebrain of D(3) mutants than wild-type mice and the difference was more pronounced after chronic methamphetamine treatment. We also observed an increase in phospho-extracellular signal-regulated kinase 2 but a decrease in phosphoAkt/Ser473 and phosphoglycogen synthase kinase 3 (GSK3)-alpha/beta in the limbic forebrain of D(3) mutants compared with wild-type mice after methamphetamine treatment. The convergent results implicate D(3) receptors as a negative regulator of the development of methamphetamine sensitization. A compensatory up-regulation of D(1) receptor-mediated signals, in addition to an altered Akt/GSK3 pathway, could contribute to the accelerated development of behavioural sensitization.     

20S proteasome-dependent generation of an IEpp89 murine cytomegalovirus-derived H-2L(d) epitope from a recombinant protein

The majority of MHC class I epitopes is generated through the ubiquitin-proteasome system. In the present study, we have analyzed the proteasome-dependent generation of the IE pp89 MCMV-derived H-2L(d) epitope by both in vitro and in vivo experiments. As revealed by cytotoxic T-cell assays, the pp89 9mer epitope was generated with high fidelity from the recombinant IE pp89 by 20S proteasomes. In vitro processing showed that the recombinant pp89 was rapidly degraded by 20S proteasomes. Analysis of cell lysates under conditions that allowed detection of polyubiquitinated proteins provided no evidence for the presence of ubiquitin-pp89-conjugates in vivo. These findings suggest a ubiquitin-independent mechanism of proteasomal degradation for pp89.     

An anti-interferon activity shared by paramyxovirus C proteins: Inhibition of Toll-like receptor 7/9-dependent alpha interferon induction

Paramyxovirus C protein targets the host interferon (IFN) system for virus immune evasion. To identify its unknown anti-IFN activity, we examined the effect of Sendai virus C protein on activation of the IFN-α promoter via various signaling pathways. This study uncovers a novel ability of C protein to block Toll-like receptor (TLR) 7- and TLR9-dependent IFN-α induction, which is specific to plasmacytoid dendritic cells. C protein interacts with a serine/threonine kinase IKKα and inhibits phosphorylation of IRF7. This anti-IFN activity of C protein is shared across genera of the Paramyxovirinae, and thus appears to play an important role in paramyxovirus immune evasion.     

Characterizing phosphoproteins and phosphoproteomes using mass spectrometry.

The reversible phosphorylation of proteins plays a major role in many vital cellular processes by modulating protein function and transmitting signals within cellular pathways and networks. Because phosphorylation is dynamic and the sites of modification cannot be predicted by an organism's genome, proteomic measurements are required to identify sites of and changes in the phosphorylation state of proteins. The low stoichiometry of phosphorylation sites that accompany the multifarious nature of protein phosphorylation in biological systems continues to challenge the dynamic range of present mass spectrometry (MS) technologies and proteomic measurements, despite the preponderance of research and analytical methods devoted to this area. This review addresses some of the strategies and limitations involving the use of MS to map and quantify changes in protein phosphorylation sites for samples that range from a single protein to an entire proteome, and presents several compelling reasons as to why comprehensive phosphorylation site analysis has proven to be so elusive without a hypothesis-driven experimental approach to elicit more meaningful and confident results.     

PIAS1对PRRSV N蛋白SUMO化修饰及病毒复制的影响

【目的】猪繁殖与呼吸综合征病毒(PRRSV)是一种危害全球养猪业的重要病原。SUMO(Small ubiquitin-like modifier)化修饰作为一种可逆的翻译后修饰在调节病毒复制方面发挥着重要功能。PIAS1(Protein inhibitor of activated STAT1)是SUMO E3连接酶PIAS家族的一员,可以促进靶蛋白的SUMO化修饰,进而影响靶蛋白的功能,参与基因转录调控过程。探究PIAS1与PRRSV N蛋白相互作用的机制及其对N蛋白SUMO化修饰和病毒复制的影响,为进一步阐明PRRSV复制调控和致病的分子机制提供科学依据。【方法】利用酵母回复杂交、免疫共沉淀和激光共聚焦技术验证N蛋白与PIAS1的相互作用;以递增剂量外源性转染PIAS1观察其是否介导N蛋白SUMO化修饰;采用RNA干扰和慢病毒转导技术测定PIAS1对PRRSV复制的影响。【结果】PIAS1能与N蛋白相互作用,而且两者主要共定位于胞浆中;外源转染PIAS1并未增加N蛋白SUMO化修饰水平;在MARC-145细胞中,PIAS1的表达有利于PRRSV的复制。【结论】PIAS1可促进PRRSV的复制。     

鼠冠状病毒核衣壳蛋白的抗体制备与抗原决定簇分析

核衣壳(nucleocapsid,N)蛋白有稳定病毒基因组、调控病毒复制及细胞状态的特殊作用。鼠肝炎病毒(murine hepatitis virus,MHV)为乙型冠状病毒属的原型病毒,是研究冠状病毒N蛋白功能的经典模型。本研究用去污剂处理鼠冠状病毒粒子暴露N蛋白,另用原核表达纯化的重组N蛋白分别免疫小鼠,制备多克隆及单克隆抗体。酶联免疫吸附试验(enzyme-linked immunosorbent assay,ELISA)和蛋白免疫印迹分析结果显示两类抗体均具有高灵敏度和特异度,与甲型冠状病毒猪传染性胃肠炎病毒(porcine transmissible gastroenteritis virus,TGEV)的N蛋白无交叉反应。原核表达缺失突变的N蛋白分析结果显示,多克隆抗体与单克隆抗体2E6识别的鼠冠状病毒N蛋白抗原决定簇完全一致,位于N端结构域(N-terminal domain,NTD)C端与SR之间的58个氨基酸残基内。此外,基于单克隆抗体2E6的ELISA及免疫荧光法能检测到感染细胞中和培养上清液中的N蛋白组分,且其含量与病毒复制的滴度一致。这些结果表明,鼠冠状病毒复制过程中粒子与细胞中的N蛋白可能维持相似的结构,使NTD与SR之间的部分氨基酸残基一直暴露在表面,从而形成了优势抗原决定簇。