Learning Biomarkers of Pluripotent Stem Cells in Mouse

Pluripotent stem cells are able to self-renew, and to differentiate into all adult cell types. Many studies report data describing these cells, and characterize them in molecular terms. Machine learning yields classifiers that can accurately identify pluripotent stem cells, but there is a lack of studies yielding minimal sets of best biomarkers (genes/features). We assembled gene expression data of pluripotent stem cells and non-pluripotent cells from the mouse. After normalization and filtering, we applied machine learning, classifying samples into pluripotent and non-pluripotent with high cross-validated accuracy. Furthermore, to identify minimal sets of best biomarkers, we used three methods: information gain, random forests and a wrapper of genetic algorithm and support vector machine (GA/SVM). We demonstrate that the GA/SVM biomarkers work best in combination with each other; pathway and enrichment analyses show that they cover the widest variety of processes implicated in pluripotency. The GA/SVM wrapper yields best biomarkers, no matter which classification method is used. The consensus best biomarker based on the three methods is Tet1, implicated in pluripotency just recently. The best biomarker based on the GA/SVM wrapper approach alone is Fam134b, possibly a missing link between pluripotency and some standard surface markers of unknown function processed by the Golgi apparatus.     

Gap formation and regeneration of tropical mangrove forests in Ranong,Thailand

Tropical mangrove forests are characterized by clear zonation along a tidal gradient, and it has been supposed that the zonation is primarily controlled by soil factors. However, effects of disturbance on mangrove forests are still not well understood and may play an important role on the vegetation patterns and forest dynamics in some forest formations. In this study, the pattern of disturbance regime and its effects on regeneration of tropical mangrove forests along a tidal gradient were investigated in Ranong, Thailand. We established one or two 0.5 ha plots in four vegetation zones, i.e. Sonneratia alba–Avicennia alba zone, Rhizophora apiculata zone, Ra – Bruguiera gymnorrhiza zone, Ceriops tagal–Xylocarpus spp. zone. Gap size (percentage gap area to total study area and individual gap size) was the largest in Sa–Aa zone which is located on the most seaward fringe, and it declined from seaward to inland. Canopy trees of S. alba and A. alba had stunted trunks and showed low tree density. On the contrary, canopy dominants in the other three inland zones, e.g. R. apiculata, B. gymnorrhiza, and Xylocarpus spp., had slender trunks and showed high tree density. Accordingly, differences in disturbance regime among the four zones were resulted from the forest structural features of each zone. Disturbance regime matched with regeneration strategies of canopy dominants. Seedlings and saplings of S. alba and A. alba, which need sunny condition for their growth, were abundant in gaps than in understorey. By contrast, R. apiculata, B. gymnorrhiza, and Xylocarpus spp., which can tolerate less light than S. alba and A. alba, had greater seedling and sapling density under closed canopy than gaps. Many large gaps may enhance the abundance of S. alba and A. alba in Sa–Aa zone, and a few small gaps may prevent the light demanding species to establish and grow in the other inland zones. Correspondence of disturbance regime and regeneration strategies (e.g. light requirement) of canopy dominants may contribute to the maintenance of the present species composition in each of the vegetation zones.     

峨眉髭蟾精子形态结构及分类学意义

应用透射电镜、扫描电镜和光学显微镜对峨眉髭蟾(Vibrissaphoraboringii)精子的形态和超微结构研究的结果表明:峨眉髭蟾的精子具角蟾科物种精子基本的形态和结构特征,即精子头部呈螺旋状,尾部呈弯曲状;精子具锥形的顶体、纤维束构成的穿孔器、平行排列的中心粒和双轴丝;线粒体位于尾部;精子核窝不明显、无轴纤维和波动膜等特征。此外,对已有报道的角蟾科和无尾类物种精子的特征进行分析比较表明:(1)角蟾科精子细胞核呈螺旋状,中心粒平行排列,尾部具双轴丝等结构不同于无尾类其他科精子的结构,具有明显的科间差别;(2)角蟾科精子各部的量度,尾部线粒体的分布和数量,以及轴丝的排列等特征在属间和种间表现出明显的差异;(3)峨眉髭蟾和东南亚拟髭蟾指名亚种精子的形态和超微结构存在明显的差异。     

人粒细胞-巨噬细胞集落刺激因子研究进展

hGM-CSF是一种重要的具有免疫调节功能的糖蛋白,在造血调控和免疫调节方面发挥重要作用,具有重要的临床应用价值。总结近些年来各国对hGM-CSF的研究情况,首先对hGM-CSF的基因结构、蛋白分子结构、生物学活性等方面做了详细的介绍;接下来,又从基因转录水平和转录后水平两个方面对hGM-CSF的表达调控做了介绍;最后,对比了利用基因工程技术将hGM-CSF基因在不同生物中的表达情况,详细讲解了优缺点。     

3D-QSAR studies of triazolopyrimidine derivatives of <Emphasis Type="Italic">Plasmodium falciparum</Emphasis> dihydroorotate dehydrogenase inhibitors using a combination of molecular dynamics,docking, and genetic algorithm-based methods

A series of 35 triazolopyrimidine analogues reported as Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors were optimized using quantum mechanics methods, and their binding conformations were studied by docking and 3D quantitative structure–activity relationship studies. Genetic algorithm-based criteria was adopted for selection of training and test sets while maintaining structural diversity of training and test sets, which is also very crucial for model development and validation. Both the comparative molecular field analyses ( q_\textLOO² = 0.841 q_{\text{LOO}}^2 = 0.{841} , r_\textncv² = 0.99 r_{\text{ncv}}^2 = 0.{99} ) and comparative molecular similarity indices analyses ( q_\textLOO² = 0.757 q_{\text{LOO}}^2 = 0.{757} , r_\textncv² = 0.943 r_{\text{ncv}}^2 = 0.{943} ) show excellent correlation and high predictive power. Furthermore, molecular dynamics simulations were performed to explore the binding mode of the two of the most active compounds of the series, 10 and 14. Harmonization in the two simulation results validate the analysis and therefore applicability of docking parameters based on crystallographic conformation of compound 14 bound to receptor molecule. This work provides useful information about the inhibition mechanism of this class of molecules and will assist in the design of more potent inhibitors of PfDHODH.     

A new discriminant NMF algorithm and its application to the extraction of subtle emotional differences in speech

In this study we propose a new feature extraction algorithm, dNMF (discriminant non-negative matrix factorization), to learn subtle class-related differences while maintaining an accurate generative capability. In addition to the minimum representation error for the standard NMF (non-negative matrix factorization) algorithm, the dNMF algorithm also results in higher between-class variance for discriminant power. The multiplicative NMF learning algorithm has been modified to cope with this additional constraint. The cost function was carefully designed so that the extraction of feature coefficients from a single testing pattern with pre-trained feature vectors resulted in a quadratic convex optimization problem in non-negative space for uniqueness. It also resolves issues related to the previous discriminant NMF algorithms. The developed dNMF algorithm has been applied to the emotion recognition task for speech, where it needs to emphasize the emotional differences while de-emphasizing the dominant phonetic components. The dNMF algorithm successfully extracted subtle emotional differences, demonstrated much better recognition performance and showed a smaller representation error from an emotional speech database.     

广东莲花山白盆珠省级自然保护区鸟类资源调查

于2008年1月～2010年12月对广东莲花山白盆珠省级自然保护区鸟类进行了调查,共记录到鸟类151种,隶属于45科16目。其中非雀形目鸟类74种(占49.01%),雀形目77种(50.99%);94种属东洋界种类(62.25%),42种属古北界种类(27.81%),15种属广布种(9.93%);留鸟88种(58.28%)、冬候鸟44种(29.14%)、夏候鸟15种(9.93%)、旅鸟和迷鸟4种(2.65%);国家Ⅱ级重点保护鸟类22种(14.57%)。该保护区鸟类特色是中华秋沙鸭种群数量较大,猛禽资源和水鸟资源较丰富。     

Structure and function of the tentpole in the reproductive process of Ginkgo biloba L.

The tentpole is a unique structure of the female gametophyte in Ginkgo biloba; however, its exact functions in the reproductive process are unclear. In the present study, we used semi-thin sectioning and electron microscopy to study the structure and function of the tentpole during fertilization in G. biloba. The tentpole was always initiated between two or more deeply immersed archegonia. Before fertilization, the tentpole had developed into a column-like structure, protruding toward the archegonial chamber; cells at the periphery of tentpole were loosely ranged, and abundant lipid droplets and starch grains were accumulated in the tentpole cells. After fertilization, the tentpole degenerated, and some membranous debris was overlaid on its surface. In addition, there were significant decreases in the lipids and starch grains. These results suggested that the tentpole led to the degeneration of the megaspore membrane and then supported the pliable apex of the nucellar tissues. Importantly, the tentpole also contributed to supplying nutrition for fertilization and embryo development.     

肌切蛋白的结构与功能多样性

肌切蛋白（scinderin）是一种重要的肌动蛋白结合蛋白,在哺乳动物和脊椎动物中广泛表达.肌切蛋白作为凝溶胶蛋白超家族的成员之一,通过肌动蛋白丝切割、肌动蛋白聚集等方式来控制肌动蛋白的结构.肌切蛋白生物活性具有多样性,除影响肌动蛋白丝重组外,肌切蛋白还参与细胞胞吐作用、调节细胞运动、细胞分化等细胞活动.此外,肌切蛋白在慢性炎症、凝血过程、免疫性疾病和肿瘤发生发展中也发挥了重要作用.本文对肌切蛋白的结构特点、参与调节细胞的功能和机制进行概述.     

A型激酶锚定蛋白及其复合物结构与功能

A型激酶锚定蛋白(A-kinase anchoring proteins,AKAPs)是一类结构不同而功能相关的蛋白家族,其主要功能是将cAMP依赖性蛋白激酶A（PKA）锚定于特定的亚细胞结构.PKA是第二信使cAMP的主要效应器,而AKAPs在靶向定位和调节PKA介导的磷酸化事件方面扮演重要角色. AKAPs更为重要的功能是与多种信号分子形成信号复合物,从时间和空间上整合cAMP-PKA和其他信号途径.本文将对AKAPs及其信号复合物的结构特点和参与细胞信号转导的功能机制及其研究现状进行概述.