PFRES: protein fold classification by using evolutionary information and predicted secondary structure

MOTIVATION: The number of protein families has been estimated to be as small as 1000. Recent study shows that the growth in discovery of novel structures that are deposited into PDB and the related rate of increase of SCOP categories are slowing down. This indicates that the protein structure space will be soon covered and thus we may be able to derive most of remaining structures by using the known folding patterns. Present tertiary structure prediction methods behave well when a homologous structure is predicted, but give poorer results when no homologous templates are available. At the same time, some proteins that share twilight-zone sequence identity can form similar folds. Therefore, determination of structural similarity without sequence similarity would be beneficial for prediction of tertiary structures. RESULTS: The proposed PFRES method for automated protein fold classification from low identity (<35%) sequences obtains 66.4% and 68.4% accuracy for two test sets, respectively. PFRES obtains 6.3-12.4% higher accuracy than the existing methods. The prediction accuracy of PFRES is shown to be statistically significantly better than the accuracy of competing methods. Our method adopts a carefully designed, ensemble-based classifier, and a novel, compact and custom-designed feature representation that includes nearly 90% less features than the representation of the most accurate competing method (36 versus 283). The proposed representation combines evolutionary information by using the PSI-BLAST profile-based composition vector and information extracted from the secondary structure predicted with PSI-PRED. AVAILABILITY: The method is freely available from the authors upon request.     

藤三七的组织培养与快速繁殖

1植物名称藤三七(Boussingaultia gracilis var. pseudobaselloides Bailey),别名藤子三七、山豆厨菜、野山葵、野落葵、落葵薯、洋葵薯。     

浮毛茛的组织培养与植株再生

1植物名称浮毛茛(Ranunculus natans C.A.Mey.),又称水毛。2材料类别基生茎。3培养条件愈伤组织诱导培养基:(1)MS 6-BA 1mg·L~(-1)(单位下同);(2)MS 6-BA 1 IBA 0.6:(3)MS 6-BA 1 IAA 0.6:(4)MS 6-BA 1 2,4-D 0.6;(5)MS 6-BA 1 NAA 0.6。愈伤组织分化培养基:(6)1/2MS 6-BA 0.2 NAA 0.1;(7)1/2MS 6-     

昼间亚高温下番茄叶中糖含量与蔗糖代谢相关酶的活性日变化

研究番茄品种‘辽园多丽’幼苗在昼间35℃亚高温条件下叶中糖含量及蔗糖代谢相关酶活性日变化的结果表明,昼间亚高温处理后的幼苗叶中果糖、葡萄糖和淀粉含量下降,蔗糖含量升高。与蔗糖代谢相关的酶活性有明显的昼夜节律性变化,转化酶、蔗糖合成酶呈现昼间活性低、夜间活性高的节律性,而蔗糖磷酸合成酶活性在进入夜间时立刻升高。35℃昼间亚高温处理后的幼苗叶中,转化酶活性下降,蔗糖合成酶活性明显升高,蔗糖磷酸合成酶活性则略有升高。     

土壤重金属向节肢动物的传递及影响

土壤中重金属可通过食物链传递至节肢动物,并在其体内累积。文章介绍影响重金属传递和积累的主要因子,及重金属对植食性、捕食性、寄生性、腐食性节肢动物种群及群落的影响情况。建议对影响传递与累积的机制开展深入研究,并重点从节肢动物群落生态学、行为学、生理学等角度开展更多工作。     

Pim-2抑制肿瘤细胞凋亡机制的研究

随着肿瘤发病学研究的深入,丝／苏氨酸激酶Pim-2抑制肿瘤细胞凋亡的机制越来越受到关注。通过比较Pim-2与其他癌基因作用机制的异同发现,Pim-2可与Myc协同作用,在多个位点磷酸化Bad,通过NF-κB发挥抗凋亡活性,是与Akt不同的抗凋亡通路。Pim-2强大而广泛的抗凋亡作用是多种肿瘤发生发展的重要机制之一。对Pim-2作用机制的深入研究将有助于阐明其在肿瘤发病中的作用,并有望将其作为肿瘤基因治疗的新靶点。     

粳稻SRAP分子标记遗传群的构建与分析

用超级稻品种‘沈农606’和普通粳稻‘丽江新团黑谷’为亲本杂交获得的102份F_2代单株,通过SRAP分子标记遗传分析,构建了包含14个连锁群,由129个多态性位点组成的水稻连锁图谱,此图谱覆盖基因组长度1671.5 cM,平均图距13.0 cM。连锁群上有17.2%的多态性位点表现偏分离,偏分离标记在连锁群上存在热点区域。     

Prediction of protein secondary structure content for the twilight zone sequences

Secondary protein structure carries information about local structural arrangements, which include three major conformations: alpha-helices, beta-strands, and coils. Significant majority of successful methods for prediction of the secondary structure is based on multiple sequence alignment. However, multiple alignment fails to provide accurate results when a sequence comes from the twilight zone, that is, it is characterized by low (<30%) homology. To this end, we propose a novel method for prediction of secondary structure content through comprehensive sequence representation, called PSSC-core. The method uses a multiple linear regression model and introduces a comprehensive feature-based sequence representation to predict amount of helices and strands for sequences from the twilight zone. The PSSC-core method was tested and compared with two other state-of-the-art prediction methods on a set of 2187 twilight zone sequences. The results indicate that our method provides better predictions for both helix and strand content. The PSSC-core is shown to provide statistically significantly better results when compared with the competing methods, reducing the prediction error by 5-7% for helix and 7-9% for strand content predictions. The proposed feature-based sequence representation uses a comprehensive set of physicochemical properties that are custom-designed for each of the helix and strand content predictions. It includes composition and composition moment vectors, frequency of tetra-peptides associated with helical and strand conformations, various property-based groups like exchange groups, chemical groups of the side chains and hydrophobic group, auto-correlations based on hydrophobicity, side-chain masses, hydropathy, and conformational patterns for beta-sheets. The PSSC-core method provides an alternative for predicting the secondary structure content that can be used to validate and constrain results of other structure prediction methods. At the same time, it also provides useful insight into design of successful protein sequence representations that can be used in developing new methods related to prediction of different aspects of the secondary protein structure.