88 Comparison of monovalent and divalent ion distributions around a DNA duplex with molecular dynamic simulation and Poisson–Boltzmann approach

Ion interactions with nucleic acids (both DNA and RNA) are an important and evolving field of investigation. Positively charged cations may interact with highly negatively charged nucleic acids via simple electrostatic interactions to help screen the electrostatic repulsion along the nucleic acids and assist their folding and/or compaction. Cations may also bind at specific sites and become integral parts of the structures, possibly playing important enzymatic roles. Two popular methods for computationally exploring a nucleic acid’s ion atmosphere are atomistic molecular dynamics (MD) simulations and the Poisson–Boltzmann (PB) equation. In general, monovalent ion results obtained from MD simulations and the PB equation agree well with experiment. However, Bai et al. (2007) observed discrepancies between experiment and the PB equation while examining the competitive binding of monovalent and divalent ions, with more significant discrepancies for divalent ions. The goal of this project was to thoroughly investigate monovalent (Na⁺) and divalent (Mg²⁺) ion distributions formed around a DNA duplex with MD simulations and the PB equation. We simulated three different cation concentrations, and matched the equilibrated bulk ion concentration for our theoretical calculations with the PB equation. Based on previous work, our Mg²⁺ ions were fully solvated, the expected state of Mg²⁺ ions when interacting with a duplex, when the production simulations began and remained throughout the simulations (Kirmizialtin, 2010; Robbins, 2012). Na⁺ ion distributions and number of Na⁺ ions within 10?Å of the DNA obtained from our two methods agreed well. However, results differed for Mg²⁺ ions, with a lower number of ions within the cut-off distance obtained from the PB equation when compared to MD simulations. The Mg²⁺ ion distributions around the DNA obtained via the two methods also differed. Based on our results, we conclude that the PB equation will systematically underestimate Mg²⁺ ions bound to DNA, and much of this deviation is attributed to dielectric saturation associated with high valency ions.     

The comparison of immune-enhancing activity of sulfated polysaccharidses from Tremella and Condonpsis pilosula

Based on our previous research, four sulfated polysaccharide (sPSs) from Tremella and Condonpsis pilosula, sTPS_tp, sTPS_70c, sCPPS_tp and sCPPS_50c, were prepared and their effects on splenic lymphocytes proliferation in vitro and the immune response of ND vaccine in chicken were compared taking the unmodified polysaccharide (uPS) TPS_tp as control. The results showed that four sPSs could significantly or numerically stimulate splenic lymphocyte proliferation singly or synergistically with LPS in vitro, sTPS_70c and sCPPS_tp demonstrated better effect; promote peripheral lymphocytes proliferation and enhance serum HI antibody titer in chickens vaccinated with ND vaccine, the actions of sPSs were stronger than that of uPS, and sTPS_70c at medium dosage presented the best efficacy. These indicated that sulfation modification could improve the immune-enhancing activity of TPS and CPPS, sTPS_70c possessed the strongest activity and would be expected as a component of new-type immunopotentiator.     

河漫滩湿地生态阈值——以二卡自然保护区为例

以典型河漫滩湿地 —— 二卡自然保护区为研究区域,进行生态阈值研究。根据湿地补给河流 —— 海拉尔河的月均流量频率分布特征,选取58.72 m³/s(P=74.6%)、119.26 m³/s(P=44.4%)、190.35 m³/s(P=23.8%)分别代表河流的低、中、高径流期,分析各径流期湿地分布特征。结果表明,低、中径流期内草本沼泽及盐化沼泽所占比例较高,而高径流期则以季节性河流湿地及湖泊湿地为主。低径流期内,作为湿地中心区的湖泊湿地景观破碎度出现一个较明显的跃变,由中径流期的0.57增加到1.37。此时的湿地状态可近似的作为区域的生态阈值,即维持湿地面积占全区域面积的43.03%。而中、高径流期湿地面积比例可近似作为保护区湿地面积的适宜值和理想值,分别为53.66%和69.53%。其研究结果为二卡自然保护区的管理及保护提供支持,并为河漫滩湿地研究提供思路。     

门诊患者医疗服务感受度影响因素研究

??????? 目的 了解门诊患者对就医服务感受度影响因素,以期提高患者满意度。 方法 现场问卷调查法、专家访谈法。 结果 患者在门诊过程中最为关注的就诊流程、等候时间、就医环境、医德医风四个因素,非常看重医护人员服务规范,服务流程便捷流畅。病情不同患者对等候时间要求不同,对医院熟悉程度与就诊环境感受度不同。结论 在门诊服务中为患者提供便捷流畅、规范化的服务,同时应注重患者的不同服务需求。     

Bt水稻田重要非靶标节肢动物权露于Cry2Aa蛋白的程度分析

根据风险=危险×机露的原理,在实验室条件下评价转基因作物对非靶标节肢动物影响时,所选择的代表性非靶标生物通常是在农田系统中较高地关露于转基因外源杀虫蛋白的节肢动物种.为了弄清Bt稻田主要节肢动物暴露于Cry蛋白的程度,选择合适的非靶标节肢动物,用于转基因抗虫水稻的风险评价,本文采用酶联免疫技术检测了水稻不同生长期从转cry2Aa基因水稻田采集的不同节肢动物体内Cry2Aa蛋白的含量.结果表明:不同节肢动物种体内的Cry蛋白含量差异显著.一些节肢动物体内不合Cry蛋白,而一些节肢动物体内含有较高的Cry蛋白;相对于花期后采集的节肢动物,在Bt水稻花期采集的节肢动物,特别是捕食性节肢动物体内的Cry蛋白含量较高;寄生性节肢动物体内未检测到Cry蛋白.这为在实验室条件下评价转基因水稻对农田非靶标节肢动物的影响奠定了基础.     

Topological persistency found in aggregations of coastal sea skater,Halobates japonicus Esaki, 1924 (Hemiptera: Gerridae), based on genetic relationships amongst three aggregations in Ishigaki Island,Japan

Sea skaters, genus Halobates Eschscholtz, 1822, are the only marine insects living in mangrove beds and the tide pools of coral reefs, both of which provide dramatically variable habitats daily by virtue of tide-driven changes in surface level. Females of H. japonicus Esaki, 1924 were collected from three distinct aggregations in a single bay (24°27′5″N, 124°8′40″E) on 1–5 November 2006. Two aggregations were formed in respective tide pools of the coral reef and one was formed in the mangrove beds. Amplified fragment length polymorphism markers were used to detect the persistency of each aggregation at a mesoscale. The results suggested that H. japonicus repeatedly immigrated from outside the bay to establish a meta-population of several deme groups. Aggregations along the coastline had some persistency to the line itself and had little tendency to cross to the opposite shore, even when the distance was short.     

基于扩展起始节点和加权融合策略预测肺癌风险致病基因

肺癌风险致病基因预测有助于了解疾病发病机制、提高临床治疗效果.目前,以重启游走为框架的风险致病基因预测算法,普遍存在起始节点少、节点转移概率相同、信息源单一的问题.为此,本文提出一种基于扩展起始节点和加权融合策略的风险致病基因预测算法(命名为AFMFSC),并在肺癌中验证算法有效性.首先,基于增广模糊测量思想,计算疾病表型近似基因间的增广功能相似得分,从中选出重要基因与致病基因作为扩展起始节点;其次,采用节点拓扑相似度转移矩阵及基因表达差异相关性转移矩阵,分别在蛋白质网络中重启随机游走,并将两种结果加权融合排序;最后,通过富集分析排名靠前基因,得到有显著意义的风险致病基因.AFMFSC算法预测的73个肺癌风险致病基因,均与肺癌发生、发展有密切联系,生物学意义显著.与其他排序算法相比,AFMFSC算法的Top 1%、Top 5%和AUC值比较大,平均排名和受拓扑特性偏差影响程度小;融合策略排名性能优于单一转移矩阵或普通邻接矩阵游走排名.AFMFSC算法不仅能准确有效地预测肺癌风险致病基因,而且可推广预测其他疾病风险致病基因,为探索癌症致病机理提供新视角及依据.