Blue Moon Approach to Rare Events

The "Blue Moon" ensemble is a computationally efficient molecular dynamics method to estimate the rate constants of rare activated events when the process can be described by a reaction coordinate ξ(r), a well-defined function in configuration space. By means of holonomic constraints a number of values of ξ(r) can be prescribed along the relevant path to identify the "bottleneck" region first and to sample an ensemble of starting conditions to generate activated trajectories. These MD trajectories sample phase space according to a biased configurational distribution. With a suitable re-weighting of averages from such ensemble of trajectories one can characterize completely rare events.     

The Solution Structure of a Locked Nucleic Acid (LNA) Hybridized to DNA

Abstract

LNA (Locked Nucleic Acids) is a novel oligonucleotide analogue containing a conformationally restricted nucleotide with a 2′-0, 4′-C-methylene bridge that induces unprecedented thermal affinities when mixed with complementary single stranded DNA and RNA. We have used two-dimensional'H NMR spectroscopy obtained at 750 and 500 MHz to determine a high resolution solution structure of an LNA oligonucleotide hybridized to the complementary DNA strand. The determination of the structure was based on a complete relaxation matrix analysis of the NOESY cross peaks followed by restrained molecular dynamics calculations. Forty final structures were generated for the duplex from A-type and B-type dsDNA starting structures. The root-mean-square deviation (RMSD) of the coordinates for the forty structures of the complex was 0.32Å. The structures were analysed by use of calculated helix parameters. This showed that the values for rise and buckle in the LNA duplex is markedly different from canonical B-DNA at the modification site. A value of twist similar to A-DNA is also observed at the modification site. The overall length of the helix which is 27.3Å. The average twist over the sequence are 35.9° ± 0.3°. Consequently, the modification does not cause the helix to unwind. The bis-intercalation of the thiazole orange dye TOTO to the LNA duplex was also investigated by ¹H NMR spectroscopy to sense the structural change from the unmodified oligonucleotide. We observed that the bis-intercalation of TOTO is much less favourable in the 5′-CT^LAG-3′ site than in the unmodified 5′-CT^LAG-3′ site. This was related to the change in the base stacking of the LNA duplex compared to the unmodified duplex.     

Morningness-eveningness preferences,learning approach and academic achievement of undergraduate medical students

ABSTRACT

Several studies have focused on determining the effect of chronotype and learning approach on academic achievement separately indicating that morning types have an academic advantage over the evening types and so have the deep learners over the surface learners. But, surprisingly none have assessed the possible relationship between chronotype and learning approach. So, the current study aimed to evaluate this association and their individual influence on academic performance as indicated by the Cumulative Grade Point Average (CGPA) as well as the effect of their interaction on academic performance. The study included 345 undergraduate medical students who responded to reduced Morningness-Eveningness Questionnaire and Biggs Revised Two-Factor Study Process Questionnaire. Morning types indulged in deep learning while evening types in surface learning. Morning and evening types did not differ on academic performance but deep learners had better academic outcomes than their counterparts. The interaction between chronotype and learning approach was significant on determining academic achievement. Our findings gave the impression that chronotype could have an impact on academic performance not directly but indirectly through learning approaches.     

Integration and religiosity among the Turkish second generation in Europe: a comparative analysis across four capital cities

Drawing on recent cross-national surveys of the Turkish second generation, we test hypotheses of secularization and of religious vitality for Muslim minorities in Europe. Secularization predicts an inverse relationship between structural integration and religiosity, such that the Turkish second generation would be less religious with higher levels of educational attainment and intermarriage. The religious vitality hypothesis predicts the maintenance of religion in the second generation, highlighting the role of religious socialization within immigrant families and communities. Taking a comparative approach, these hypotheses are tested in the context of different national approaches to the institutionalization of Islam as a minority religion in four European capital cities: Amsterdam, Berlin, Brussels and Stockholm. Across contexts, religious socialization strongly predicts second-generation religiosity, in line with religious vitality. The secularization hypothesis finds support only among the second generation in Berlin, however, where Islam is least accommodated.     

On the limitations of standard statistical modeling in biological systems: A full Bayesian approach for biology

One of the most important scientific challenges today is the quantitative and predictive understanding of biological function. Classical mathematical and computational approaches have been enormously successful in modeling inert matter, but they may be inadequate to address inherent features of biological systems. We address the conceptual and methodological obstacles that lie in the inverse problem in biological systems modeling. We introduce a full Bayesian approach (FBA), a theoretical framework to study biological function, in which probability distributions are conditional on biophysical information that physically resides in the biological system that is studied by the scientist.     

藏鹀的自然历史、威胁和保护

藏鹀(Emberiza koslowi)是我国青藏高原东部的特有珍稀鸟种,目前关于它的资料非常匮乏.为了解藏鹀的分布、数量和基本生活史特征,促进对于该物种的有效保护,自2005年起以青海省果洛州久治县白玉乡为中心对藏鹀进行了持续6年的观察,并针对其面临的威胁采取了相应的保护措施.结果显示,藏鹀主要分布在青海的玉树、果洛和四川的阿坝一带海拔3 500～4 700 m范围内的适宜栖息地,该分布区比原有认知更靠东北,更为狭小且海拔更高.用样线法开展的藏鹀数量监测,在7.4 km2的调查范围内记录到一个18 ～33只的稳定种群.此外,还对藏鹀的筑巢、育雏和争斗等行为进行了详细描述.食肉动物的捕食、冬季食物缺乏和牲畜踩踏鸟卵是藏鹀面临的最直接威胁.通过持续监测、与当地牧民协商、建立保护小区并开展有针对性的保护,藏鹀种群趋于稳定.     

The diagnostic value of reproductive organs in some genera of articulated Coralline red algae

Clearcut differences exist between the reproductive organs of Corallina and Jania. Fully formed spermatangial conceptacles in Corallina have low ceillings and pronounced beaks whereas in Jania they have high ceilings and lack beaks. Fusion cells in carposporophytic conceptacles are thin and broad in the former genus and thick and narrow in the latter. Tetrasporangial conceptacles have less capacity in Jania than in Corallina and the fertile areas in young conceptacles cover a smaller area.

Haliptylon is changed from group to generic status and Corallina subulata is transferred to this genus. Haliptylon is characterised by conceptacles similar in all known respects to those of Jania, but the branching is pinnate, as in Corallina.

From the available evidence it appears possible that organisms having Corallina-type conceptacles diverged phylogenetically long ago from those having Jania-type conceptacles.     

广谱流感疫苗的研究进展

流行性感冒(简称流感)的频频暴发严重危害人类健康和公共卫生,已引起全球范围内的高度关注。预防流感最有效和经济的措施是接种疫苗,但流感病毒的持续变异可逃逸人群已有的免疫应答,目前使用的季节性流感疫苗仅对亚型内抗原匹配较好的毒株产生免疫保护作用,难以有效应对因抗原漂移或抗原转换而产生的无法预料的流感大流行。因此,研发对流感病毒不同亚型均具有交叉免疫保护作用的广谱流感疫苗具有重要意义。近年来,流感病毒广谱中和抗体的发现、对流感病毒抗原保守区域及细胞免疫机制的深入研究、疫苗免疫策略的优化等都为广谱流感疫苗的研发提供了新思路。本文简述了近几年基于血凝素、基质蛋白、核蛋白等多种流感靶抗原的广谱流感疫苗的研究进展。