Predicting protein function with hierarchical phylogenetic profiles: the Gene3D Phylo-Tuner method applied to eukaryotic genomes

“Phylogenetic profiling” is based on the hypothesis that during evolution functionally or physically interacting genes are likely to be inherited or eliminated in a codependent manner. Creating presence–absence profiles of orthologous genes is now a common and powerful way of identifying functionally associated genes. In this approach, correctly determining orthology, as a means of identifying functional equivalence between two genes, is a critical and nontrivial step and largely explains why previous work in this area has mainly focused on using presence–absence profiles in prokaryotic species. Here, we demonstrate that eukaryotic genomes have a high proportion of multigene families whose phylogenetic profile distributions are poor in presence–absence information content. This feature makes them prone to orthology mis-assignment and unsuited to standard profile-based prediction methods. Using CATH structural domain assignments from the Gene3D database for 13 complete eukaryotic genomes, we have developed a novel modification of the phylogenetic profiling method that uses genome copy number of each domain superfamily to predict functional relationships. In our approach, superfamilies are subclustered at ten levels of sequence identity—from 30% to 100%—and phylogenetic profiles built at each level. All the profiles are compared using normalised Euclidean distances to identify those with correlated changes in their domain copy number. We demonstrate that two protein families will “auto-tune” with strong co-evolutionary signals when their profiles are compared at the similarity levels that capture their functional relationship. Our method finds functional relationships that are not detectable by the conventional presence–absence profile comparisons, and it does not require a priori any fixed criteria to define orthologous genes.     

3D-QSAR studies on fluoropyrrolidine amides as dipeptidyl peptidase IV inhibitors by CoMFA and CoMSIA

Three-dimensional quantitative structure-activity relationship (3D-QSAR) analyses using CoMFA and CoMSIA methods were conducted on a series of fluoropyrrolidine amides as dipeptidyl peptidase IV (DP-IV) inhibitors. The selected ligands were docked into the binding site of the 3D model of DP-IV using the GOLD software, and the possible interaction models between DP-IV and the inhibitors were obtained. Based on the binding conformations of these fluoropyrrolidine amides and their alignment inside the binding pocket of DP-IV, predictive 3D-QSAR models were established by CoMFA and CoMSIA analyses, which had conventional r ² and cross-validated coefficient values () up to 0.982 and 0.555 for CoMFA and 0.953 and 0.613 for CoMSIA, respectively. The predictive ability of these models was validated by six compounds that were in the testing set. Structure-based investigations and the final 3D-QSAR results provide the guide for designing new potent inhibitors.     

Engineering the stem cell microenvironment

Multipotent stem cells in the body facilitate tissue regeneration, growth, and wound healing throughout life. The microenvironment in which they reside provides signals that direct these progenitors to proliferate, differentiate, or remain dormant; these factors include soluble molecules, the extracellular matrix, neighboring cells, and physical stimuli. Recent advances in the culture of embryonic stem cells and adult progenitors necessitate an increased understanding of these phenomena. Here, we summarize the interactions between stem cells and their local environment, drawing on in vivo observations and tissue culture studies. In addition, we describe novel methods of characterizing the effects of various environmental factors and review new techniques that enable scientists and engineers to more effectively direct stem cell fate.     

Changes in native and introduced host–parasite networks

Biological Invasions - Introduced species can alter the dynamics and structure of a native community. Network analysis provides a tool to study host–parasite interactions that can help to...     

GST pull-down筛选冠突曲霉MAT的互作蛋白*

目的: 冠突曲霉(Aspergillus cristatus)是一种同宗结合菌,它的产孢受渗透压调控,与构巢曲霉的光调控产孢机制存在较大差异。冠突曲霉的有性生殖主要受MAT1-1-1和MAT1-2-1调控,但MAT基因对该菌有性生殖的调控机制仍不清楚。期望筛选得到冠突曲霉MAT的互作蛋白,为深入研究冠突曲霉有性产孢机制奠定基础。方法: 利用GST pull-down联合液相色谱-串联质谱(LC-MS/MS)技术筛选可能与冠突曲霉MAT1-1-1和MAT1-2-1互作的蛋白,结合ProteinPilot和冠突曲霉基因组注释结果进行互作蛋白的注释及GO分析,其中互作蛋白SI65_00917和SI65_03348利用RT-qPCR探索它们与有性发育的联系,并利用酵母双杂交技术初步验证它们与MAT蛋白的互作关系。结果: 成功构建了GST-MAT1-1-1、GST-MAT1-2-1表达载体,诱导表达纯化出目的诱饵蛋白,分别利用诱饵蛋白捕获冠突曲霉总蛋白中的互作蛋白,经分析、筛选共鉴定出与MAT1-1-1互作的蛋白56个,与MAT1-2-1互作的蛋白413个。GO分析表明,这些蛋白参与翻译调控、代谢过程、蛋白质转运及蛋白结合等生物学过程,具有核苷酸结合活性、催化活性、蛋白结合活性;RT-qPCR结果表明互作蛋白SI65_00917可能与有性发育相关。酵母双杂交结果表明,SI65_00917蛋白具有自激活作用,可能是转录因子;SI65_03348蛋白与MAT1-1-1、MAT1-2-1在酵母中均有互作。结论: MAT通过与其他蛋白直接或间接的相互作用调控其有性发育过程。     

TTC染色鉴定葡萄抗寒性方法的优化与应用北大核心CSCD

以‘左山1号’、101-14、3309C、SO4、140R和‘黑比诺’等葡萄砧木和品种直径为0.5~0.7 cm的一年生枝条为材料,经低温梯度(0℃、-14℃、-19℃、-24℃、-29℃和-34℃)处理后,对TTC染色的温度和时间进行优化并观察统计葡萄枝条不同组织的存活情况,测定枝条的相对电导率,以及韧皮部和木质部的可溶性蛋白、游离脯氨酸、可溶性糖、淀粉含量和束缚水自由水比例(束自比)5个生理指标,分别用枝条纵切面染色面积、相对电导率拟合Logistic方程计算枝条的半致死温度(LT_(50))来评价枝条的抗寒性,同时通过隶属函数法综合评价枝条韧皮部和木质部抗寒性,并将3种方法的评价结果进行比较,以建立一种直观高效鉴定葡萄品种抗寒性的方法。结果表明:(1)依据低温胁迫下各品种葡萄砧木扦插枝条的萌芽率和生根率表现,其抗寒性由强到弱依次为‘左山1号’、101-14、3309C、SO4、140R和‘黑比诺’。(2)葡萄枝条TTC活力染色的最佳条件为pH=7.0,0.5%TTC-0.1 mol/L磷酸缓冲液在35℃下避光染色36 h。随着胁迫温度的降低,各品种枝条纵切面染色面积均逐渐降低,根据优化TTC法获得‘左山1号’、101-14、3309C、SO4、140R和‘黑比诺’枝条的LT_(50)分别为-31.38℃、-26.51℃、-26.10℃、-23.60℃、-23.33℃和-19.26℃。(3)随着胁迫温度的降低,各品种枝条的相对电导率逐渐增加,且‘黑比诺’的相对电导率基本保持最高、增幅最大(51.93%),而‘左山1号’的相对电导率始终最低、增幅最小(44.07%);根据相对电导率获得‘左山1号’、101-14、3309C、SO4、140R和‘黑比诺’枝条的LT_(50)分别为-30.02℃、-26.40℃、-25.75℃、-23.16℃、-21.13℃和-17.72℃。(4)通过5种生理指标进行枝条抗寒性隶属函数综合性评价结果显示,同一品种中韧皮部抗寒性强于木质部,同一部位不同品种的抗寒性表现为:‘左山1号’>101-14>3309C>SO4>140R>‘黑比诺’。研究发现,TTC染色法与电导法和综合隶属函数法获得的葡萄枝条抗寒力评价结果一致,也与枝条生长恢复鉴定结果一致;但与其他两种方法相比,TTC染色法能更加直观和有效地预测评估葡萄枝条的抗寒性。     

中国水韭属两个四倍体新种

水韭属(Isoëtes)是起源最为古老的水生维管植物,全属物种均被列为国家一级重点保护植物。通过对全国水韭属植物的调查和研究发现,不同产地的四倍体植株在形态上存在显著差异。基于形态学、孢粉学和细胞学证据,将分布于中国湖南省长沙地区和怀化地区的四倍体居群分别命名为隆平水韭(Isoëtes longpingii)和湘妃水韭(I. xiangfei),并详细描述了其形态特征。隆平水韭形态上与中华水韭(I. sinensis)相似,不同之处在于其大孢子具小的瘤状或冠状纹饰,叶细长而柔弱,长达60 cm; 该种也与六倍体东方水韭(I. orientalis)相似,不同之处在于其染色体44条,大孢子具瘤状或冠状纹饰。湘妃水韭的大孢子纹饰虽与二倍体云贵水韭(I. yunguiensis)相似,但在小孢子纹饰、孢子囊形状和染色体数目方面却不同。隆平水韭仅少数植株生长于湖南省宁乡市一处池塘,完全沉水生长,而湘妃水韭则分布于怀化市通道县和会同县的湿地。由于这两个新种的分布区狭窄,野生居群数量和个体数较少,栖息地环境受到人为干扰,因此根据IUCN红色名录评估标准,将隆平水韭评为极危(CR)等级,湘妃水韭评为易危(VU)等级。所编制的中国已知水韭属物种的分种检索表,为本属物种的鉴定和保护工作提供了重要参考。