Integrating Molecular Models Into CryoEM Heterogeneity Analysis Using Scalable High-resolution Deep Gaussian Mixture Models

Resolving the structural variability of proteins is often key to understanding the structure–function relationship of those macromolecular machines. Single particle analysis using Cryogenic electron microscopy (CryoEM), combined with machine learning algorithms, provides a way to reveal the dynamics within the protein system from noisy micrographs. Here, we introduce an improved computational method that uses Gaussian mixture models for protein structure representation and deep neural networks for conformation space embedding. By integrating information from molecular models into the heterogeneity analysis, we can analyze continuous protein conformational changes using structural information at the frequency of 1/3 Å⁻¹, and present the results in a more interpretable form.     

3DSDSCAR—a three dimensional structural database for sialic acid-containing carbohydrates through molecular dynamics simulation

The inherent flexibility and lack of strong intramolecular interactions of oligosaccharides demand the use of theoretical methods for their structural elucidation. In spite of the developments of theoretical methods, not much research on glycoinformatics is done so far when compared to bioinformatics research on proteins and nucleic acids. We have developed three dimensional structural database for a sialic acid-containing carbohydrates (3DSDSCAR). This is an open-access database that provides 3D structural models of a given sialic acid-containing carbohydrate. At present, 3DSDSCAR contains 60 conformational models, belonging to 14 different sialic acid-containing carbohydrates, deduced through 10 ns molecular dynamics (MD) simulations. The database is available at the URL: http://www.3dsdscar.org.     

Proximity to forest edge does not affect crop production despite pollen limitation

A decline in pollination function has been linked to agriculture expansion and intensification. In northwest Argentina, pollinator visits to grapefruit, a self-compatible but pollinator-dependent crop, decline by approximately 50% at 1km from forest edges. We evaluated whether this decrease in visitation also reduces the pollination service in this crop. We analysed the quantity and quality of pollen deposited on stigmas, and associated limitation of fruit production at increasing distances (edge: 10, 100, 500 and 1000m) from the remnants of Yungas forest. We also examined the quantitative and qualitative efficiency of honeybees as pollen vectors. Pollen receipt and pollen tubes in styles decreased with increasing distance from forest edge; however, this decline did not affect fruit production. Supplementation of natural pollen with self- and cross-pollen revealed that both pollen quantity and quality limited fruit production. Despite pollen limitation, honeybees cannot raise fruit production because they often do not deposit sufficient high-quality pollen per visit to elicit fruit development. However, declines in visitation frequency well below seven visits during a flower's lifespan could decrease production beyond current yields. In this context, the preservation of forest remnants, which act as pollinator sources, could contribute to resilience in crop production. Like wild plants, pollen limitation of the yield among animal-pollinated crops may be common and indicative not only of pollinator scarcity, but also of poor pollination quality, whereby pollinator efficiency, rather than just abundance, can play a broader role than previously appreciated.     

Analysis of the evolution of the thrombin-inhibiting DNA aptamers using a genetic algorithm

We previously identified a thrombin-inhibiting DNA aptamer that was presumed to form a G-quartet structure with a duplex. To investigate the importance of the sequences in the duplex region and to obtain aptamers with higher inhibitory activities, we randomized the sequences of the duplex region of this aptamer and carried out selection based on inhibitory activity using a genetic algorithm. This method consisted of selection via an inhibition assay, crossover, and mutation in silico. After two cycles, we obtained ligands with greater inhibitory activities than that of the original aptamer. In addition, the duplex sequences were found to contribute to the inhibitory activities of aptamers.     

大石鸡兰州亚种的mtDNA种群遗传结构、单倍型分布和遗传多样性

大石鸡(Alectorismagna)是中国西北部的特有种。我们测定了大石鸡兰州亚种(A.m.lanzhouensis)8个地理种群106个样本的线粒体DNA控制区5′端458bp序列,研究其种群遗传结构和遗传多样性。27个变异位点共确定25种单倍型,其中单倍型M2广泛分布,而许多单倍型为一些地方种群特有。单倍型分布沿着南北方向变化,存在明显的地理结构。8个种群中核苷酸多样性最高的是定西种群,0.0069,最低的是海原种群,0.0028;单倍型多样性最高的是武山种群,0.86,最低的是北道种群,0.52。北方种群比南方种群具有更高的遗传多样性。系统发生树和单倍型分布表明,大石鸡兰州亚种存在两个明显的分支。溯祖理论、更新世冰期和花粉支持兰州亚种起源于兰州盆地,这个盆地是其遗传多样性的中心。     

嘉陵江四川段藻类植物群落结构及水质评价

为了揭示嘉陵江四川段藻类植物的群落结构特征和水质现状,分别于枯水期(1月)和丰水期(9月)沿江段至上而下分析了12个样点藻类群落的种类组成、Shannon多样性指数（H′）、Pielou均匀度指数（E）和Margalef丰富度指数（d).结果表明: 嘉陵江四川段共采集到藻类植物8门42科95属171种(包括变种),其中硅藻、绿藻和蓝藻为各样点的优势类群.整个江段枯水期藻类植物的平均细胞密度为14.71×10⁴ ind·L^-1,金溪和红岩子样点的密度最高,分别为28.33×10⁴和25.40×10⁴ ind·L^-1;群落中以硅藻的物种数量最为丰富.丰水期藻类植物的平均细胞密度为10.78×10⁴ ind·L^-1,以青居样点的密度最低,仅3.31×10⁴ind·L^-1,绿藻和蓝藻物种数量有所增加.整个江段12个样点枯水期和丰水期的平均d、平均H′和平均E分别为2.35、1.60、0.31和2.57、2.09和0.39.嘉陵江四川段的藻类植物群落结构、细胞密度、多样性指数和均匀度指数的时空分布格局差异显著.水质整体为中污染型,其中金溪和沙溪样点为寡污型或β中污型,水质较好;苍溪、红岩子、新政和青居样点水质较差,属α中-污型.     

分化抑制蛋白N端保守域结构预测及其基因突变体的构建

目的：对分化抑制蛋白（Id）家族的N端序列进行保守性结构分析,并构建其基因突变体。方法：用ClustalX（1.81）软件对Id蛋白家族中的3个成员（Id1～Id3）的N端序列进行同源性分析,用Swiss-PdbViewer3.7（SP5）软件模拟高同源区域中关键性氨基酸突变前后的三维结构模型;用PCR方法将突变点引入Id序列,再通过重叠PCR方法扩增出全长编码序列,酶切与测序确证突变序列的准确性。结果：Id1～Id3蛋白的N端存在一个由11个氨基酸残基形成的高度保守的环-螺旋（Loop-Helix）结构,将其中最保守的丝氨酸与亮氨酸分别突变为甘氨酸与缬氨酸,将突变后的Id基因序列重组到pGEX原核表达载体中。结论：在Id1～Id3蛋白N端识别了一个保守的Loop-Helix结构,为深入研究其协同的功能特征提供了结构依据;突变其中的丝氨酸为研究Id蛋白潜在的磷酸化修饰及相应功能特征的改变奠定了基础。     

森林生态系统年净初级生产力和生境复杂度对小型兽类物种多样性影响

本研究主要探讨黄龙自然保护区森林生态系统年净初级生产力水平和栖息地复杂程度对小型兽类物种多样性的影响。将调查区按海拔高度分为4 个调查点,每点的年净初级生产力水平各不相同,分别为: 24.9 MJ / (m²·a) ; 21.5 MJ / (m²·a) ; 17.5 MJ / (m²·a) 和14.1 MJ / (m²·a) 。在选择调查点时,同时考虑栖息地复杂程度,在生产力水平较高的调查点选择栖息地复杂程度较低的地点,而在生产力较低的调查点选择栖息地复杂程度较高的地点调查,以便分析森林生态系统年净初级生产力水平与栖息地复杂程度对小型兽类物种多样性的影响。采用鼠铗捕获小型兽类。结果表明,小型兽类物种多样性与森林生态系统年净初级生产力水平有密切关系,随着海拔升高,森林生态系统年净初级生产力的降低,所捕获的小型兽类生物量随之降低,其物种多样性也随之下降。小型兽类物种多样性也与栖息地复杂程度有关,森林生态系统年净初级生产力水平在一定范围内,大于17.5 MJ / (m²·a) ,栖息地复杂度的增加可以降低年净初级生产力水平对小型兽类物种多样性的影响。然而,森林生态系统年净初级生产力水平降低到一定程度时,小于14.1 MJ / (m²·a) ,生产力水平则为影响小型兽类物种多样性的主要因子。此外,小型兽类的生物量与森林生态系统年净初级生产力和栖息地复杂程度也有类似的关系。     

mRNA翻译起始区二级结构优化提高(R)-羰基还原酶的表达及催化效率

为了提高近平滑假丝酵母(Candida parapsilosis CCTCC M203011)的(R)-羰基还原酶在大肠杆菌中的表达水平及催化效率,对酶编码基因mRNA翻译起始区中+1～+78区进行二级结构的优化,并构建了相应的突变体。优化后mRNA翻译起始区的发夹结构明显减少,自由能显著下降(由原始的?9.5kcal/mol降至?5.0kcal/mol),使酶蛋白的表达水平及粗酶比活力分别比优化前提高了4～5倍和61.9%。在高底物浓度(5.0g/L2-羟基苯乙酮)下,优化突变株不对称转化效率较高,产物(R)-苯基乙二醇的光学纯度和产率分别为93.1%e.e.和81.8%,比优化前提高了27.5%和40.5%。研究结果表明:优化mRNA翻译起始区的二级结构,克服蛋白翻译启动的空间位阻,不仅能促进翻译的顺利进行,使目标蛋白得到高效表达,而且有利于蛋白空间结构的正确折叠,有效提高酶蛋白活力及生物催化功能。