Optimisation of data locality in energy calculations for large-scale molecular dynamics simulations

The main bottleneck of molecular dynamic simulations is the estimation of nonbonded pairwise interaction, which often employs neighbour search algorithms to find out interacting atom pairs. These methods have some drawbacks in fulfilling data locality principle, which is unable to take full advantage of modern computer architecture. In this article, we developed a new method by introducing a temporary list to reduce the sparsity in data access. This list permits to obtain a compact and sequential data structure which benefits to efficiently fulfil the data locality principle. We tested and compared the performance of the new method with that of the extensively used reordering method. The new method based on linked cell list is shown to increase 13% of computation speed and have better parallelism in comparison with reordering method. The increase in parallel efficiency makes the new method a promising option for large-scale molecular simulations.     

On the progressive enrichment of the oxygen isotopic composition of water along a leaf

A model has been derived for the enrichment of heavy isotopes of water in leaves, including progressive enrichment along the leaf. In the model, lighter water is preferentially transpired leaving heavier water to diffuse back into the xylem and be carried further along the leaf. For this pattern to be pronounced, the ratio of advection to diffusion (Péclet number) has to be large in the longitudinal direction, and small in the radial direction. The progressive enrichment along the xylem is less than that occurring at the sites of evaporation in the mesophyll, depending on the isolation afforded by the radial Péclet number. There is an upper bound on enrichment, and effects of ground tissue associated with major veins are included. When transpiration rate is spatially nonuniform, averaging of enrichment occurs more naturally with transpiration weighting than with area-based weighting. This gives zero average enrichment of transpired water, the modified Craig-Gordon equation for average enrichment at the sites of evaporation and the Farquhar and Lloyd (In Stable Isotopes and Plant Carbon-Water Relations, pp. 47-70. Academic Press, New York, USA, 1993) prediction for mesophyll water. Earlier results on the isotopic composition of evolved oxygen and of retro-diffused carbon dioxide are preserved if these processes vary in parallel with transpiration rate. Parallel variation should be indicated approximately by uniform carbon isotope discrimination across the leaf.     

Rapid Identification of Probiotic Lactobacillus Biosurfactant Proteins by ProteinChip Tandem Mass Spectrometry Tryptic Peptide Sequencing

A novel ProteinChip-interfaced tandem mass spectrometer was employed to identify collagen binding proteins from biosurfactant produced by Lactobacillus fermentum RC-14. On-chip tryptic digestion of the captured collagen binding proteins resulted in rapid sequence identification of five novel tryptic peptide sequences via collision-induced dissociation tandem mass spectrometry.     

老芒麦遗传多样性及育种研究进展

老芒麦（Elymus sibiricus）的研究对我国北方草原及青藏高原高寒草甸的退化草地改良、发展草地畜牧业具有重要意义。本文综述了老芒麦在形态学、细胞学、蛋白质和DNA分子水平上的遗传多样性研究概况,并总结了国内老芒麦的育种研究进展。目前国内外专门针对不同老芒麦种质材料（accession）或居群（populations）遗传多样性的研究鲜见报道,相关研究主要集中在与披碱草属（Elymus）及其近缘小麦族物种的系统进化研究方面;其次,我国仅有6个老芒麦国家审定品种,且育种手段较单一、落后,育成品种优势集中在产量和适应性上,缺乏对抗逆性种质的筛选培育。     

在子宫颈上皮内瘤变和鳞癌组织中CyclinE、Rb基因表达的研究

目的 探讨细胞周期素E（CyclinE）、视网膜母细胞瘤（Rb）基因与上皮内瘤变（CIN）和宫颈鳞癌的关系,及其在癌变过程中的意义。方法 应用免疫组化技术（S-P法）,检测CyclinE和Rb基因产物在各级别CIN77例和宫颈鳞癌40例中的表达状况,并以正常子宫颈鳞状上皮20例做对照。结果 在正常宫颈鳞状上皮、CINⅠ、CINⅡ、CINⅢ及宫颈鳞癌中,CyclinE的阳性表达率呈逐渐增强趋势,分别为：0．0％、30．0％、75．0％、65．0％、60．0％。正常宫颈鳞状上皮与各级别CIN和宫颈鳞癌之间差异均有显著性（P〈0．01或〈0．005）,CINⅠ与CINⅡ、CINⅢ、宫颈鳞癌组间差异均有显著性（P〈0．005或〈0．01）;Rb基因蛋白的表达率逐渐下调,分别为：100．0％、55．0％、20．0%、24．3%、23．5％,在正常宫颈鳞状上皮与各级别CIN和宫颈鳞癌组间差异均有显著性（P〈0．005）;CINI与CINHI、宫颈鳞癌组间差异有显著性（P〈O．005）。结论CyclinE在正常子宫颈鳞状上皮表达阴性,随着发生CIN从轻到重至宫颈鳞癌,表达呈逐渐增强趋势;表明CyclinE在子宫颈癌变过程中起到重要作用,CyclinE参与CIN的进展及子宫颈癌癌变机制。Rb基因蛋白在正常子宫颈鳞状上皮100％阳性,随着发生CIN从轻到重至宫颈鳞癌,表达呈逐渐下调趋势,甚至消失;表明Rb基因可能主要通过功能性失活参与宫颈鳞癌的发生,并且其在癌变过程中起重要作用。发现CyclinE表达增强和RB基因表达下调或消失,有助于宫颈鳞癌发生的判断及CIN程度和级别的确定。     

A novel set of 223 EST-SSR markers in <Emphasis Type="Italic">Casuarina</Emphasis> L. ex Adans.: polymorphisms,cross-species transferability,and utility for commercial clone genotyping

Simple sequence repeat (SSR) markers are very useful for genetic applications in plants, but SSR resource for the important tree genus Casuarina L. ex Adans. is still limited. In this study, we report a novel set of 223 SSR markers in Casuarina developed from expressed sequence tag (EST) resource of GenBank. The 223 EST-SSR markers were polymorphic among 10 unrelated individuals of C. equisetifolia L. Johnson, with the number of alleles per locus (N_a), observed heterozygosity (H_o), expected heterozygosity (H_e), and polymorphic information content (PIC) averaging at 5.5, 0.72, 0.86, and 0.63, respectively. The rates of cross-species transferability ranged from 96.9% (C. glauca Sieber ex Sprengel) through 97.8% (C. cunninghamiana Miquel) to 99.1% (C. junghuhniana Miquel). Fifty-five C. equisetifolia clones widely planted in China were successfully genotyped with a subset of 20 EST-SSRs. These newly developed markers will have a great potential for genetic and breeding applications in Casuarina species and related taxa.     

伸展素在黄瓜胞壁中的转化及其与羟脯氨酸和异联酪氨酸的关系

用~(14)C-Pro和~3H_2-Tyr离体暗培养黄瓜子叶,发现细胞质、SECW和RCW中的Hyp/Pro和Idt/Tyr都随时间呈线性增加。这两种比值后两者高于前者,而两种比值增加速度之比在胞质部分最大、RCW中最小。表明在胞质和胞壁中都有Pro羟化和Tyr异联化过程,但羟化作用主要发生在胞质中,异联化主要在RCW中。 理化处理(高渗溶液和CHM)和放射性示踪证明胞质中存在HRGP库;它被分泌到胞壁后,先以离子键与壁结合,后转变为共价键与壁结合的伸展素。     

脂肪酶在微乳液和微乳液凝胶中催化辛酸辛醇的酯化反应

脂肪酶在合成反应中具有很高的区域选择性和立体选择性 ,已广泛用于食品工业和药物工业[1,2 ] ,在有机介质中的脂肪酶催化反应已有较多研究[3 ,4 ] 。微乳液一般由表面活性剂、助表面活性剂、油和水等组份组成 ,它是一种热力学稳定、光学透明、宏观均匀而微观不均匀的体系 ,能提供酶催化所需要的巨大油 /水界面[5] 。而将脂肪酶增溶于油包水(Ｗ /Ｏ)微乳液中的纳米级“水池”中 ,可使酶以分子水平分散[6] ,图 1(ａ) ,从而可用来模拟细胞微环境中的反应。油包水微乳液中的酶可通过加入明胶而制成固定化酶 ,含明胶的微乳液凝胶 (ＭＢＧｓ)最早…