入侵植物印加孔雀草在不同生境的种群构件生物量及其分配特征

印加孔雀草是中国西藏新近入侵种,其危害已初见端倪,但我国鲜有对其入侵机理的研究.为探究印加孔雀草在异质环境下的种群构件生物量及其分配特征,进一步深入了解其生存策略和易入侵生境.该研究在菜园、果园、路边、荒地和河滩等五种典型入侵生境内对其花果期的种群构件生物量进行了测定和分析,计算了表型可塑性指标值.结果表明:(1)印加...     

“七步法”课堂设计与实践：构建研究导向型微生物学“金课”课堂

研究导向型教学是以学生成长和发展为中心的创新性教育模式,其核心目标与“金课”的建设目标一致,强调培养学生的研究技能,使其具有创新性和高阶性。在微生物学一流课程建设过程中,将研究导向型教学理念与BOPPPS课堂[导入(bridge-in)、目标(objective)、前测(pre-assessment)、参与式学习(participatory-learning)、后测(post-assessment)和总结(summary)]组织形式相结合,并创新性引入“提升”模块,以问题为驱动,聚焦科学前沿,融入思政材料,形成导入—目标—前测—参与式学习—后测—提升—总结(七步法)的新型模块化闭环教学模式。该模式的实施能够有效提升课堂教学的逻辑性和组织性,提高教学效率,提升学生分析问题和解决问题的高阶性,为学生将来开展科研工作奠定良好的基础,并为打造以学生为中心的“金课”课堂实践提供借鉴参考。     

Essential role of a family-32 carbohydrate-binding module in substrate recognition by Clostridium thermocellum mannanase CtMan5A

The family-5 glycoside hydrolase domain (GH5) and the family-32 carbohydrate-binding module (CBM32) of Clostridium thermocellum mannanase CtMan5A, along with their genetically inactivated derivatives, were collectively or separately expressed. Their catalytic and substrate-binding abilities were measured to investigate importance of CBM32 in substrate recognition by CtMan5A. Characterization of the truncated derivatives of CtMan5A and isothermal calorimetry analysis of the interaction between the inactivated proteins and mannooligosaccharides suggested that GH5 and CBM32 collectively formed a substrate-binding site capable of accommodating a mannotetraose unit in CtMan5A. This suggested that CBM32 directly participated in the substrate recognition required for catalytic action.     

New Insights into an Old Organelle: Meeting Report on Biology of Cilia and Flagella

The rising interest of the scientific community in cilia biology was evident from the fact that registration for the third FASEB conference on ‘The Biology of Cilia and Flagella’ closed out before the early bird deadline. Cilia and flagella are organelles of profound medical importance; defects in their structure or function result in a plethora of human diseases called ciliopathies. 240 clinicians and basic scientists from around the world gathered from 23 June 2013 to 28 June 2013 at Sheraton at the Falls, Niagara Falls, NY to present and discuss their research on this intensely studied subcellular structure. The meeting was organized by Gregory Pazour (University of Massachusetts Medical School), Bradley Yoder (University of Alabama‐Birmingham), and Maureen Barr (Rutgers University) and was sponsored by the Federation of American Societies for Experimental Biology (FASEB). Here, we report highlights, points of discussion, and emerging themes from this exciting meeting.     

Bioinformatic analysis of ciliary transition zone proteins reveals insights into the evolution of ciliopathy networks

Background

Cilia are critical for diverse functions, from motility to signal transduction, and ciliary dysfunction causes inherited diseases termed ciliopathies. Several ciliopathy proteins influence developmental signalling and aberrant signalling explains many ciliopathy phenotypes. Ciliary compartmentalisation is essential for function, and the transition zone (TZ), found at the proximal end of the cilium, has recently emerged as a key player in regulating this process. Ciliary compartmentalisation is linked to two protein complexes, the MKS and NPHP complexes, at the TZ that consist largely of ciliopathy proteins, leading to the hypothesis that ciliopathy proteins affect signalling by regulating ciliary content. However, there is no consensus on complex composition, formation, or the contribution of each component.

Results

Using bioinformatics, we examined the evolutionary patterns of TZ complex proteins across the extant eukaryotic supergroups, in both ciliated and non-ciliated organisms. We show that TZ complex proteins are restricted to the proteomes of ciliated organisms and identify a core conserved group (TMEM67, CC2D2A, B9D1, B9D2, AHI1 and a single TCTN, plus perhaps MKS1) which are present in >50% of all ciliate/flagellate organisms analysed in each supergroup. The smaller NPHP complex apparently evolved later than the larger MKS complex; this result may explain why RPGRIP1L, which forms the linker between the two complexes, is not one of the core conserved proteins. We also uncovered a striking correlation between lack of TZ proteins in non-seed land plants and loss of TZ-specific ciliary Y-links that link microtubule doublets to the membrane, consistent with the interpretation that these proteins are structural components of Y-links, or regulators of their formation.

Conclusions

This bioinformatic analysis represents the first systematic analysis of the cohort of TZ complex proteins across eukaryotic evolution. Given the near-ubiquity of only 6 proteins across ciliated eukaryotes, we propose that the MKS complex represents a dynamic complex built around these 6 proteins and implicated in Y-link formation and ciliary permeability.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-531) contains supplementary material, which is available to authorized users.     

MAE-FMD: Multi-agent evolutionary method for functional module detection in protein-protein interaction networks

Background

Studies of functional modules in a Protein-Protein Interaction (PPI) network contribute greatly to the understanding of biological mechanisms. With the development of computing science, computational approaches have played an important role in detecting functional modules.

Results

We present a new approach using multi-agent evolution for detection of functional modules in PPI networks. The proposed approach consists of two stages: the solution construction for agents in a population and the evolutionary process of computational agents in a lattice environment, where each agent corresponds to a candidate solution to the detection problem of functional modules in a PPI network. First, the approach utilizes a connection-based encoding scheme to model an agent, and employs a random-walk behavior merged topological characteristics with functional information to construct a solution. Next, it applies several evolutionary operators, i.e., competition, crossover, and mutation, to realize information exchange among agents as well as solution evolution. Systematic experiments have been conducted on three benchmark testing sets of yeast networks. Experimental results show that the approach is more effective compared to several other existing algorithms.

Conclusions

The algorithm has the characteristics of outstanding recall, F-measure, sensitivity and accuracy while keeping other competitive performances, so it can be applied to the biological study which requires high accuracy.     

The N-terminal family 22 carbohydrate-binding module of xylanase 10B of Clostridium themocellum is not a thermostabilizing domain

Xylanase Xyn10B from Clostridium thermocellum is a modular enzyme that contains two family 22 carbohydrate binding modules N- (CBM22-1) and C- (CBM22-2) terminal of the family 10 glycoside hydrolase catalytic domain (GH10). In a previous study, we showed that removal of CBM22-1 reduces the resistance to thermoinactivation of the enzyme suggesting that this module is a thermostabilizing domain. Here, we show that it is the module border on the N-terminal side of GH10 that confers resistance to thermoinactivation and to proteolysis. Therefore, CBM22-1 does not function as a thermostabilizing domain and the role for this apparently non-functional CBM remains elusive.     

Insect group II chitinase OfChtII promotes chitin degradation during larva–pupa molting

The insect group II chitinase (ChtII, also known as Cht10) is a unique chitinase with multiple catalytic and chitin-binding domains. It has been proven genetically to be an essential chitinase for molting. However, ChtII's role in chitin degradation during insect development remains poorly understood. Obtaining this knowledge is the key to fully understanding the chitin degradation system in insects. Here, we investigated the role of OfChtII during the molting of Ostrinia furnacalis, a model lepidopteran pest insect. OfChtII was expressed earlier than OfChtI (OfCht5) and OfChi-h, at both the gene and protein levels during larva–pupa molting as evidenced by quantitative polymerase chain reaction and western blot analyses. A truncated OfChtII, OfChtII-B4C1, was recombinantly expressed in Pichia pastoris cells and purified to homogeneity. The recombinant OfChtII-B4C1 loosened compacted chitin particles and produced holes in the cuticle surface as evidenced by scanning electron microscopy. It synergized with OfChtI and OfChi-h when hydrolyzing insoluble α-chitin. These findings suggested an important role for ChtII during insect molting and also provided a strategy for the coordinated degradation of cuticular chitin during insect molting by ChtII, ChtI and Chi-h.     

食物网稳定性机制研究进展:一个基于等级系统的框架

食物网理论沟通了群落生态学和生态系统生态学,将生物多样性和生态系统功能的研究统一起来,是理解生态系统运作机制的关键。自从1973年Robert May的经典研究引发著名的"复杂性-稳定性"论辩之后,人们认识到食物网的稳定性是其结构维持、功能发挥和动态演化的一个重要前提,并开始了对食物网稳定性机制的探索。早期研究主要关注只包含拓扑关系的定性食物网,但后来人们逐渐认识到相互作用强度的重要性,并提出了诸如自限性、弱相互作用、适应性捕食等一系列机制。本文系统梳理了过往研究中模块层面的各类稳定性机制和全网层面对各模块的整合机制,从而清晰地展示了"模块-全网"双层框架的全貌。通过在其基础上的扩展,进而提出了一个基于等级系统的食物网稳定性框架,并从动力学和能量学角度,对各层级内部的稳定性机制以及层级之间的关系进行了探讨,以期为建立普适的食物网稳定性理论提供一些思路。未来的研究方向包括：①将稳定性机制的研究从食物网扩展到更一般的生态网络;②综合考虑生物物理要素、动力学稳定性、系统对能流功率的追求、环境的平稳程度、演化历史等影响因素,从而得到关于食物网结构和动态的更为深刻的认识。