流溪河水库的盔形溞和舌状叶镖水蚤对浮游植物的牧食影响研究(英文)

盔形溞 Daphnia galeata 和舌状叶镖 Phyllodiaptomus tunguidus 是流溪河水库的两种大型的滤食物性的浮游动物,P. tunguidus 也是中国特有种,他们的牧食直接影响浮游植物种类组成和群落结构。为了解这两种浮游动物在自然水体中对浮游植物牧食的作用及营养盐水平对牧食作用的影响,将 D. galeata 和 P. tunguidus 以 4.4 ind.L-1 的密度,分别在两个营养水平(不添加与添加营养盐)中用 4.5L 的透明塑料瓶培养 10 天(2008 年 3 月 28-4 月 8 日)。在不添加营养盐的实验中,水样为用 64um 孔径的筛绢过滤后的水库水,在添加营养盐的实验中,为过滤后的水样再加入 KH2PO4 和 NaNO3,使 TN:TP=16:1(TN=34.86 μ mol?L-1,TP=2.18 μ mol?L-1)。10 天后,计数和分析浮游植物四个粒径级别(<20μm, 20-30μm, 30-50μm, >50μm)和各门类及优势种类的生物量组成,比较两组动物在两种营养状态中对浮游植物生物量的影响。在不添加营养盐的实验中,两种浮游动物对浮游植物总生物量的抑制均不明显,但<30μm的浮游植物生物量均下降,且 D. galeata 处理组中,小于 20μm的浮游植物生物量低于 P. tunguidus 处理组,P. tunguidus 处理组中20-30μm的浮游植物生物量低于 D. galeata 组,说明两种浮游动物对<30μm的浮游植物均有抑制作用,但 D. galeata 对<20μm的浮游植物抑制强于 P. tunguidus 而 P. tunguidus 对 20-30μm的浮游植物抑制强于 D. galeata。在添加营养盐的实验中,营养盐对浮游植物生物量,尤其对<20μm的浮游植物生物量的促进作用明显。但两种浮游动物对浮游植物的抑制作用在不同种类之间产生差异。D. galeataa 处理组的浮游植物总生物量明显高于P. tunguidus 组,表明P. tunguidus 对浮游植物的抑制作用强于D. galeata。D. galeata 处理组中,蓝藻生物量比例(15%)远低于绿藻(41%)和硅藻(37%),但在P. tunguidus 组蓝藻生物量比例(36%)远高于绿藻(18%)和硅藻(32%),与不添加营养盐实验的t检验表明D. galeata 对绿藻和蓝藻抑制明显,而P. tunguidus对绿藻和硅藻的抑制明显(t-test,p>0.05)。D. galeata 对衣藻chlamydomonas sp.,绿球藻chlorococcum sp.,单细胞蓝藻抑制作用明显,而P. tunguidus对小球藻chlorella sp.,衣藻chlamydomonas sp.,绿球藻 chlorococcum sp.,小环藻 cyclotella sp.,曲壳藻 achnanthes sp.,针杆藻 Synedra sp.的抑制明显。实验结果表明两种浮游动物影响不同的浮游植物种类,对浮游植物的群落结构的影响具有差异。     

流溪河水库的盔形滔和舌状叶镖水蚤对浮游植物的牧食影响研究

盔形涵Daphnia galeata和舌状叶镖Phyllodiaptomus tunguidus是流溪河水库的两种大型的滤食物性的浮游动物,Ptunguidus也是中国特有种,他们的牧食直接影响浮游植物种类组成和群落结构。为了解这两种浮游动物在自然水体中对浮游植物牧食的作用及营养盐水平对牧食作用的影响,将D．galeata和Ptunguidus以4．4ind．L^-1的密度,分别在两个营养水平（不添加与添加营养盐）中用4．5L的透明塑料瓶培养10天（2008年3月28-4月8日）。在不添加营养盐的实验中,水样为用64um孔径的筛绢过滤后的水库水,在添加营养盐的实验中,为过滤后的水样再加入KH2P04和NaNO3,使TN：TP=16：1（TN=34．86μmol&#183;L^-1,TP=2．18μmol&#183;L^-1）。10天后,计数和分析浮游植物四个粒径级别（〈20μm,20—30μm,30．50μm,〉50μm）和各门类及优势种类的生物量组成,比较两组动物在两种营养状态中对浮游植物生物量的影响。在不添加营养盐的实验中,两种浮游动物对浮游植物总生物量的抑制均不明显,但〈30μm的浮游植物生物量均下降,且D．galeata处理组中,小于20μm的浮游植物生物量低于Ptunguidus处理组,Ptunguidus处理组中20-30μm的浮游植物生物量低于D．galeata组,说明两种浮游动物对〈30Ixm的浮游植物均有抑制作用,但D．galeata对〈20μm的浮游植物抑制强于Ptunguidus而Ptunguidus对20．30μm的浮游植物抑制强于D．galeata。在添加营养盐的实验中,营养盐对浮游植物生物量,尤其对〈20μm的浮游植物生物量的促进作用明显。但两种浮游动物对浮游植物的抑制作用在不同种类之间产生差异。Dgaleataa处理组的浮游植物总生物量明显高于Ptunguidus组,表明Ptunguidus对浮游植物的抑制作用强于Dgaleata。Dgaleata处理组中,蓝藻生物量比例（15％）远低于绿藻（41％）和硅藻（37％）,但在Ptunguidus组蓝藻生物量比例（36％）远高于绿藻（18％）和硅藻（32％）,与不添加营养盐实验的t检验表明Dgaleata对绿藻和蓝藻抑制明显,而Ptunguidus对绿藻和硅藻的抑制明显（t-test,p〉0．05）。Dgaleata对衣藻chlamydomonassp．,绿球藻chlorococcumsp．,单细胞蓝藻抑制作用明显,而Ptunguidus对小球藻chlorellasp．,衣藻chlamydomonassp．,绿球藻chlorococcumsp．,小环藻cyclotellasp．,曲壳藻achnanthessp．,针杆藻Synedrasp．的抑制明显。实验结果表明两种浮游动物影响不同的浮游植物种类,对浮游植物的群落结构的影响具有差异。     

南亚热带磷限制水库中浮游植物群落对氮磷比变化的响应

为了解P限制水体中浮游植物群落对N、P营养盐的响应,通过添加N、P营养盐设置N/P梯度,对广东省流溪河水库中的浮游植物群落进行了研究。结果表明,添加N、P显著促进浮游植物的生长,浮游植物群落受P盐的影响比N盐显著;藻类的种属特异性导致浮游植物群落对氮磷营养盐的响应不一致,浮游植物总丰度与N/P比值不相关,其中隐球藻(Aphanocapsa sp.)、拟柱胞藻(Cylindrospermopsis raciborskii)和假鱼腥藻(Pseudanabaena sp.)等蓝藻适合在高N高P条件下生长,双对栅藻(Scenedesmus bijuga)等绿藻优势种偏好中N高P环境,而曲壳藻(Achnanthes sp.)、小环藻(Cyclotella sp.)等硅藻在低N低P的环境下占据优势;P浓度为0.8～2.0μmol/L时存在诱导浮游植物碱性磷酸酶活性的阈值,当P浓度大于2.0μmol/L时则抑制酶活性; P浓度为2.0μmol/L可能是浮游植物维持生长的最适浓度,浮游植物N/P维持动态平衡;藻细胞N/P、C/P与水体P浓度、N/P呈显著正相关,而藻细胞C/N受N影响更明显(P0.05)。这为热带亚热带水库的水质管理提供了理论参考。     

南亚热带大型贫营养水库浮游植物群落结构与季节变化——以新丰江水库为例

新丰江水库是我国第四大的水库,也是广东省最大的水库和重要的水源地。于2004～2005年2月一次调查了新丰江水库水文、水质和浮游植物分布,分析了浮游植物群落季节动态特征。新丰江水库浮游植物生物量比较低,在0．037—1．497mg&#183;L^-1之间变化。浮游植物种类较多,11次采样共检到158种。在丰度上,水库浮游植物主要以小环藻、蓝纤维藻、小球藻和纤维藻等优势种为主,而在生物量上则以微小多甲藻为优势。浮游植物组成随季节变化而不同,春季以硅藻、甲藻和绿藻为优势类群;夏季以蓝藻、绿藻和硅藻为优势类群;秋季蓝、绿藻减少而硅藻和甲藻增加。2004年的浮游植物季节性变化更为明显,有从硅藻-绿藻优势（2月和4月份）,到蓝藻-绿藻优势（6月和8月份）,到混合优势（10月份）和金藻优势（12月份）这样一个变化过程。2005年硅藻的相对丰度比2004年高出很多。两年浮游植物组成的差异与两年的降水量有关。水动力学对丰水期（6～8月份）浮游植物组成结构有较大影响,导致硅藻和绿藻相对丰度的增加。与温带贫营养型水库相比,新丰江水库的浮游植物群落具有春季和秋季种类多、夏季的蓝藻种类丰富的特点。从细胞大小分布上看,小于20μm浮游植物是生物量的主要贡献者,其次是大于45μm的浮游植物。在粒径小于20μm的浮游植物中,微小多甲藻是最主要的贡献者。浮游植物群落的大小分布受水动力学条件和营养盐浓度动态的影响。     

抚仙湖浮游植物群落结构、分布及其影响因子

云南抚仙湖是我国典型的高原深水湖泊,为揭示该湖浮游植物群落特征及其对生态系统变化的响应,2005年6～7月对浮游植物及环境因子进行了调查.调查期间共采集浮游植物80种,隶属于7门32科56属,以绿藻、蓝藻和硅藻为主,种类数绿藻(46.0%)＞蓝藻门(25.0%)＞硅藻门(15.0%),密度绿藻(61.6%)＞硅藻(16.1%)＞蓝藻(9.1%).群落平均密度为87.58 ×104 ind./L, 转板藻(Mougeotia sp.)占绝对优势,其相对密度为35.9%.在水平分布上,浮游植物平均密度北区大于南区(P＜0.05),沿岸区大于湖心区(P＜0.01).在垂直分布上,浮游植物分层明显,主要分布在0～30 m水层,不同水层绿藻均占绝对优势.环境分析表明:抚仙湖浮游植物密度水平分布主要受营养盐的影响,而垂直分布主要受物理因子的影响.不同时期的调查结果比较表明,抚仙湖浮游植物种类数和密度呈增长趋势,与水体营养水平升高有关.20世纪90年代中期以来,大型丝状藻类转板藻发展成为绝对优势种,与其较强的竞争优势及太湖新银鱼摄食引发的下行效应有关.     

放养鲢鱼(Hypophthalmichys molitrix C et V)对水库围隔浮游生物群落的影响

本文研究在水库围隔实验生态系统中鲢鱼对浮游生物群落的影响。结果表明,放养鲢鱼后,浮游动物生物量、浮游植物生物量、叶绿素a和浮游植物毛产量分别下降了58.7％、63.6％、52.5％和65.0％;透明度、浮游植物群落多样性指数分别提高了18.2％、32.5％;铜绿微囊藻数量减少了90.6％“水华”得到明显抑制。但小型绿藻(<20μm)数量未出现显著变化,因而其在藻类生物量中所占比例反而提高了82.3％。围隔内可被鲢鱼滤食的大型藻类(硅藻、甲藻、隐藻和绿藻(>20μm))占藻类生物量的85.8％,因此鲢鱼的存在能明显限制浮游植物的生物量。此外,放养鲢鱼还显著降低了水体中的COD,TP,DO和pH值,这表明鲢鱼对水质有净化作用。     

太湖梅梁湾湖岸带浮游植物群落演替及其与水华形成的关系

利用2009～2010年周年观测数据,结合江苏太湖湖泊生态系统研究站15年监测数据,分析了太湖梅梁湾湖岸带浮游植物群落演替及其与蓝藻水华形成的关系.50次周监测结果表明:蓝藻门(Cyanophyta)、绿藻门(Chlorophyta)、硅藻门(Bacillariophyta)分别占浮游植物总生物量的60%、16%和22%.冬春季绿藻、硅藻为主要优势种,夏秋季蓝藻门的微囊藻占绝对优势.4月下旬～6月初,平均温度低于20℃,蓝藻没有大规模生长,硅藻门、绿藻门生物量急剧降低,总生物量小于1mg·L^-1;随后温度超过25℃,蓝藻迅速增长并很快成为绝对优势,蓝藻增加滞后于绿藻、硅藻的减少.在营养盐充足、物理因素合适的条件下,浮游植物群落结构自然演替是蓝藻水华形成的主要原因之一.     

应用光合色素研究广西钦州湾丰水期浮游植物群落结构

通过2010年6月现场航次19个站点的调查,应用反相高效液相色谱(RP - HPLC) 并结合二极管阵列检测器分析技术,分析了丰水期广西钦州湾浮游植物光合色素组成,进而由CHEMTAX 软件估算全粒级浮游植物的群落结构。结果表明,钦州湾浮游植物光合色素含量以叶绿素a最高,其次为岩藻黄素;浮游植物的优势类群为硅藻,其次为蓝藻和青绿藻,它们分别平均占据了浮游植物生物量的70.2%、12.6%和9.4%,而其它藻类除了绿藻茅岭江河口占据较高的比例(40.2%)之外在其它站点所占比例很低。钦州湾浮游植物群落结构形成了茅岭江口、内湾、外湾和湾外近海共四种类型,茅岭江口以绿藻为优势类群,内湾以硅藻、蓝藻和青绿藻为主要优势类群,外湾以硅藻为单一优势类群,湾外相对于外湾硅藻比重略为下降。主要光合色素含量及浮游植物类群生物量的分布特征与盐度、营养盐关系密切,浮游植物群落结构的分布变化主要受径流及其输入导致的营养盐变化的影响,而这种影响导致了内湾和外湾之间浮游植物主要类群的生物量多寡及浮游植物群落结构的差异。     

南亚热带河流型水库浮游植物群落的季节变化：以广东飞来峡水库为例

于2003年4-12月调查了广东省飞来峡水库的水文、营养盐分布状况和浮游植物种类与数量,分析了浮游植物群落的种类及数量组成与动态特征,探讨了其动态变化的驱动因子。结果表明,飞来峡水库是一个典型的河流型大型水库,水力滞留时间短,年均值低于15 d;降雨量主要集中于夏季,最短水力滞留时间只有8 d。水温全年没有分层现象。丰水期营养盐和叶绿素a高于枯水期。浮游植物生物量低,细胞密度在21.7×103-808×103 cells L-1之间变化,没有超过106 cells L-1,叶绿素a的平均浓度为2μg L-1。浮游植物种类较多,4次采样共检到140种。种类组成上有较大变化,4月份有83种,以硅藻为主;7月和9月超过90种,以绿藻为主;12月有51种,蓝藻、绿藻和硅藻种类数量相当。优势种类的构成上与温带水库不同,硅藻仅在低水温时期为优势类群,而在丰水期则以蓝藻、绿藻和硅藻共同占优势。硅藻的主要优势种是变异直链藻(Melosira varians)、梅尼小环藻(Cyclotella menighiniana)和针杆藻(Synedra spp.)。绿藻种类组成季节变化较大,没有明显的优势种类。丰度相对较高的有美丽胶网藻(Dictyosphaerium pulchellum)、集星藻(Actinastrum hantzschii)和空球藻(Eudorina elegans)等。蓝藻的优势种以粘球藻(Gloeocapsa sp.)、优美平列藻(Merismopedia elegans)和伪鱼腥藻(Pseudoanabaena sp.)为主。与绿藻不同的是蓝藻的优势种在全年均可出现。隐藻只在水力滞留时间较长、温度较低的12月份占优势,主要优势种为啮蚀隐藻(Cryptomonas erosa)、尖尾蓝隐藻(Chroomonas acuta)。     

滇池北部湖区浮游植物时空格局及相关环境因子

为研究滇池北部湖区浮游植物的时空格局,探讨影响格局形成的关键影响因子,2008年12月至2009年6月,在滇池北部湖区选择6个点位,共开展了24次采样,调查并分析了浮游植物群落及其相关理化参数。通过比对滇池全湖周年监测数据,研究发现,北部湖区叶绿素a浓度从12月中旬开始下降,2月中旬降至最低值26.5μg/L,5月中旬达到最大值530.5μg/L。调查期间共鉴定出浮游植物74属97种,其中绿藻53种,蓝藻20种,硅藻17种,隐藻2种,金藻2种,甲藻1种,裸藻2种。蓝藻生物量在12月、3月至6月期间占优势,12月份优势种为绿色微囊藻(Microcystis viridis),3月至5月为水华束丝藻(Aphanizomenonflos-aquae),6月为惠氏微囊藻(Microcystis wesenbergii)。硅藻在1月占优势,优势种为颗粒直链藻最窄变种(Melosira granulata var.angustissima)。研究结果表明,水温高于14℃以上,微囊藻生物量迅速增加;束丝藻生物量随温度增加而增加,高于22℃时迅速减少。北部湖区6个点位浮游植物的空间差异显著,D1、D4号点微囊藻、束丝藻生物量显著高于其他四个点(P<0.01),D2、D5号点广缘小环藻生物量显著高于其他四个点(P<0.01)。研究结果显示,在富营养化严重的滇池北部湖区,水温可能为影响浮游植物种类组成及生物量的关键因子,浮游植物水平分布的差异主要由气象因素和水体营养盐共同决定。     

Extended secondary structures in proteins

Supersecondary structures of proteins have been systematically searched and classified, but not enough attention has been devoted to such large edifices beyond the basic identification of secondary structures. The objective of the present study is to show that the association of secondary structures that share some of their backbone residues is a commonplace in globular proteins, and that such deeper fusion of secondary structures, namely extended secondary structures (ESSs), helps stabilize the original secondary structures and the resulting tertiary structures. For statistical purposes, a set of 163 proteins from the protein databank was randomly selected and a few specific cases are structurally analyzed and characterized in more detail. The results point that about 30% of the residues from each protein, on average, participate in ESS. Alternatively, for the specific cases considered, our results were based on the secondary structures produced after extensive Molecular Dynamics simulation of a protein–aqueous solvent system. Based on the very small width of the time distribution of the root mean squared deviations, between the ESS taken along the simulation and the ESS from the mean structure of the protein, for each ESS, we conclude that the ESSs significantly increase the conformational stability by forming very stable aggregates. The ubiquity and specificity of the ESS suggest that the role they play in the structure of proteins, including the domains formation, deserves to be thoroughly investigated.     

Sequence-similar, structure-dissimilar protein pairs in the PDB

It is often assumed that in the Protein Data Bank (PDB), two proteins with similar sequences will also have similar structures. Accordingly, it has proved useful to develop subsets of the PDB from which "redundant" structures have been removed, based on a sequence-based criterion for similarity. Similarly, when predicting protein structure using homology modeling, if a template structure for modeling a target sequence is selected by sequence alone, this implicitly assumes that all sequence-similar templates are equivalent. Here, we show that this assumption is often not correct and that standard approaches to create subsets of the PDB can lead to the loss of structurally and functionally important information. We have carried out sequence-based structural superpositions and geometry-based structural alignments of a large number of protein pairs to determine the extent to which sequence similarity ensures structural similarity. We find many examples where two proteins that are similar in sequence have structures that differ significantly from one another. The source of the structural differences usually has a functional basis. The number of such proteins pairs that are identified and the magnitude of the dissimilarity depend on the approach that is used to calculate the differences; in particular sequence-based structure superpositioning will identify a larger number of structurally dissimilar pairs than geometry-based structural alignments. When two sequences can be aligned in a statistically meaningful way, sequence-based structural superpositioning provides a meaningful measure of structural differences. This approach and geometry-based structure alignments reveal somewhat different information and one or the other might be preferable in a given application. Our results suggest that in some cases, notably homology modeling, the common use of nonredundant datasets, culled from the PDB based on sequence, may mask important structural and functional information. We have established a data base of sequence-similar, structurally dissimilar protein pairs that will help address this problem (http://luna.bioc.columbia.edu/rachel/seqsimstrdiff.htm).     

遗传算法在蛋白质结构预测中的应用

遗传算法(geneticalgorithm,GA)作为一种自适应启发式概率性迭代式全局搜索算法,具有不依赖于问题模型的特性、全局最优性、隐含并行性、高效性、解决不同非线性问题的鲁棒性特点,目前已经广泛应用于自动控制、机器人学、计算机科学、模式识别、模糊人工神经和工程优化等设计领域。本文首先介绍了GA的基本原理,即搜索的基本过程;随后总结了GA与传统算法相比所具有的优点;第三部分则分别综述了GA在蛋白质结构预测中主要使用的模型、设计和执行策略,以及使用GA与其他算法相互结合预测蛋白质结构的研究进展;最后提出了作者对GA研究中存在问题的认识和研究展望。     

Patterns of protein-fold usage in eight microbial genomes: A comprehensive structural census

Eight microbial genomes are compared in terms of protein structure. Specifically, yeast, H. influenzae, M. genitalium, M. jannaschii, Synechocystis, M. pneumoniae, H. pylori, and E. coli are compared in terms of patterns of fold usage—whether a given fold occurs in a particular organism. Of the ∼340 soluble protein folds currently in the structure databank (PDB), 240 occur in at least one of the eight genomes, and 30 are shared amongst all eight. The shared folds are depleted in all-helical structure and enriched in mixed helix-sheet structure compared to the folds in the PDB. The top-10 most common of the shared 30 are enriched in superfolds, uniting many non-homologous sequence families, and are especially similar in overall architecture—eight having helices packed onto a central sheet. They are also very different from the common folds in the PBD, highlighting databank biases. Folds can be ranked in terms of expression as well as genome duplication. In yeast the top-10 most highly expressed folds are considerably different from the most highly duplicated folds. A tree can be constructed grouping genomes in terms of their shared folds. This has a remarkably similar topology to more conventional classifications, based on very different measures of relatedness. Finally, folds of membrane proteins can be analyzed through transmembrane-helix (TM) prediction. All the genomes appear to have similar usage patterns for these folds, with the occurrence of a particular fold falling off rapidly with increasing numbers of TM-elements, according to a “Zipf-like” law. This implies there are no marked preferences for proteins with particular numbers of TM-helices (e.g. 7-TM) in microbial genomes. Further information pertinent to this analysis is available at http://bioinfo.mbb.yale.edu/genome. Proteins 33:518–534, 1998. © 1998 Wiley-Liss, Inc.     

A use of Ramachandran potentials in protein solution structure determinations

A strategy is developed to use database-derived - constraints during simulated annealing procedures for protein solution structure determination in order to improve the Ramachandran plot statistics, while maintaining the agreement with the experimental constraints as the sole criterion for the selection of the family. The procedure, fully automated, consists of two consecutive simulated annealing runs. In the first run, the database-derived - constraints are enforced for all aminoacids (but prolines and glycines). A family of structures is then selected on the ground of the lowest violations of the experimental constraints only, and the - values for each residue are examined. In the second and final run, the database-derived - constraints are enforced only for those residues which in the first run have ended in one and the same favored - region. For residues which are either spread over different favored regions or concentrated in disallowed regions, the constraints are not enforced. The final family is then selected, after the second run, again only based on the agreement with the experimental constraints. This automated approach was implemented in DYANA and was tested on as many as 12 proteins, including some containing paramagnetic metals, whose structures had been previously solved in our laboratory. The quality of the structures, and of Ramachandran plot statistics in particular, was notably improved while preserving the agreement with the experimental constraints.     

农田防护林生态系统结构研究进展

农田防护林生态系统结构决定着生态功能,其时空结构是该领域研究的核心,旨在探讨形成结构的完整性、稳定性、持久性的组件间的相互关系,将其分为树体结构、林带结构、林网结构、景观结构4个层次,针对各层次中结构研究的原理、方法及成果进行了综述,通过树木个体的形态、质态结构研究,应用分形图形学的手段可实现动态结构的可视化,以研究林带树体结构的生成机理;精确界定林带结构的分维疏透度。探讨农田防护林带最佳结构理论,以构建防护林带最佳结构计算机生成模型;确立多物种、多层次的窄林带小网格的林网优化模式;评价农田防护林景观的合理性、稳定性、持续性,是今后的重要研究方向。     

Using multiple templates to improve quality of homology models in automated homology modeling

When researchers build high-quality models of protein structure from sequence homology, it is today common to use several alternative target-template alignments. Several methods can, at least in theory, utilize information from multiple templates, and many examples of improved model quality have been reported. However, to our knowledge, thus far no study has shown that automatic inclusion of multiple alignments is guaranteed to improve models without artifacts. Here, we have carried out a systematic investigation of the potential of multiple templates to improving homology model quality. We have used test sets consisting of targets from both recent CASP experiments and a larger reference set. In addition to Modeller and Nest, a new method (Pfrag) for multiple template-based modeling is used, based on the segment-matching algorithm from Levitt's SegMod program. Our results show that all programs can produce multi-template models better than any of the single-template models, but a large part of the improvement is simply due to extension of the models. Most of the remaining improved cases were produced by Modeller. The most important factor is the existence of high-quality single-sequence input alignments. Because of the existence of models that are worse than any of the top single-template models, the average model quality does not improve significantly. However, by ranking models with a model quality assessment program such as ProQ, the average quality is improved by approximately 5% in the CASP7 test set.     

On the “coloring problem” in YMgZn and related phases

During exploration in the Y-Mg-Zn system for quasicrystal approximants, three new phases, YMg_1−xZn_1+x (0 ? x ? 0.17) adopting the hexagonal ZrNiAl structure type, have been discovered. In these structures, the elements are completely ordered to minimize both the site energies and the bond energies as calculated by tight-binding calculations. Evaluation of the electron density in YMgZn suggests that Mg-Zn and Y-Zn bonding coupled with maximizing the Zn?Zn separations is the main factor influencing the atomic arrangements. Analysis of the electronic density of states of YMgZn indicates an optimized bonding situation for eight valence electrons per formula unit, e.g., as in YMgGa. Subsequently, YMgAl, YMgGa, and YMgIn were successfully prepared and structurally characterized. Their structures show relationships to both densely-packed structures common for intermetallics as well as three-dimensional networks common for valence compounds.     

Evolution of protein 3D structures as diffusion in multidimensional conformational space

A theory of protein spatial-structure evolution in terms of random walks in multidimensional conformational space is proposed. It is shown that the spatial divergence in pairs of homologous proteins depends only on their sequence similarity and is independent of the protein size. X-ray data are reasonably well described in terms of the theory developed. Correspondence to: A.M. Gutin