环境中生物膜的菌群结构与污染物降解特性

生物膜是细菌最常见的生长方式。结构有序、功能分化的生物膜群落为内部细菌提供在不利环境中生存的庇护,其环境功效也日益受到关注。本文综述了多种环境中微生物与不同材料表面相互作用、进而发展为生物膜的机制;介绍了环境工程领域中生物膜的先锋菌种和菌群结构动态变化;介绍了生物膜在污染环境中的抗逆与降解特性。     

糜蛋白酶提高膜蛋白质谱分析序列覆盖率的胶内消化方法

近年来,质谱技术在膜蛋白结构与功能研究中被广泛应用。由于膜蛋白的跨膜结构域含有大量疏水性氨基酸,常常导致液质串联质谱检测的序列覆盖率较低,从而限制了质谱技术在膜蛋白结构与功能研究中的应用。文中利用人的整合膜蛋白维生素K环氧化物还原酶为模型,优化胶内消化条件,建立了一种稳定提高膜蛋白质谱序列覆盖率的糜蛋白酶胶内消化方法。通过探索钙离子浓度、pH值和缓冲体系对序列覆盖率、检测特异肽段的总数和类型以及特异肽段大小的影响,发现在5–10 mmol/L钙离子浓度、pH 8.0–8.5的Tris-HCl缓冲液中,可以兼顾序列覆盖率和肽段的多样性。该方法可以使膜蛋白的质谱覆盖率达到80%以上,将在膜蛋白结构与功能、膜蛋白相互作用位点的鉴定以及膜蛋白与小分子药物结合位点的鉴定等研究中具有广泛的应用价值。     

培养的内皮细胞和平滑肌细胞之间间隙连接形成及连接通讯的研究

本实验以离子电渗法将荧光黄注入细胞内,观察培养的EC 与SMC 同类及异类细胞间连接通讯现象,证实SMC 与EC 在培养中可形成同类或异类细胞GJ 结构,两种细胞间有接触介导的物质交流。EC-EC 之间的细胞通讯比SMC-SMC 和SMC-EC 之间为强。对SMC 有促增殖作用的LDL(100 μg LDL-蛋白质/ml)及胰岛素(15 mu/ml)对这种连接通讯有抑制作用,促癌剂TPA 几乎完全抑制此种连接通讯。结果提示高浓度LDL 及胰岛素等可能通过抑制SMC 与EC 之间的连接通讯而使SMC 脱离正常控制而大量增殖,促进AS发生、发展。故推论促进细胞连接通讯的因子,可能对AS 有防治作用,值得进一步研究。     

The ABC transporters in Candidatus Liberibacter asiaticus

Candidatus Liberibacter asiaticus (Ca. L. asiaticus) is a Gram‐negative bacterium and the pathogen of Citrus Greening disease (Huanglongbing, HLB). As a parasitic bacterium, Ca. L. asiaticus harbors ABC transporters that play important roles in exchanging chemical compounds between Ca. L. asiaticus and its host. Here, we analyzed all the ABC transporter‐related proteins in Ca. L. asiaticus. We identified 14 ABC transporter systems and predicted their structures and substrate specificities. In‐depth sequence and structure analysis including multiple sequence alignment, phylogenetic tree reconstruction, and structure comparison further support their function predictions. Our study shows that this bacterium could use these ABC transporters to import metabolites (amino acids and phosphates) and enzyme cofactors (choline, thiamine, iron, manganese, and zinc), resist to organic solvent, heavy metal, and lipid‐like drugs, maintain the composition of the outer membrane (OM), and secrete virulence factors. Although the features of most ABC systems could be deduced from the abundant experimental data on their orthologs, we reported several novel observations within ABC system proteins. Moreover, we identified seven nontransport ABC systems that are likely involved in virulence gene expression regulation, transposon excision regulation, and DNA repair. Our analysis reveals several candidates for further studies to understand and control the disease, including the type I virulence factor secretion system and its substrate that are likely related to Ca. L. asiaticus pathogenicity and the ABC transporter systems responsible for bacterial OM biosynthesis that are good drug targets. Proteins 2012. © 2012 Wiley Periodicals, Inc.     

Solution structure of the Mesorhizobium loti K1 channel cyclic nucleotide‐binding domain in complex with cAMP

Cyclic nucleotide‐sensitive ion channels, known as HCN and CNG channels, are crucial in neuronal excitability and signal transduction of sensory cells. HCN and CNG channels are activated by binding of cyclic nucleotides to their intracellular cyclic nucleotide‐binding domain (CNBD). However, the mechanism by which the binding of cyclic nucleotides opens these channels is not well understood. Here, we report the solution structure of the isolated CNBD of a cyclic nucleotide‐sensitive K⁺ channel from Mesorhizobium loti. The protein consists of a wide anti‐parallel β‐roll topped by a helical bundle comprising five α‐helices and a short 3₁₀‐helix. In contrast to the dimeric arrangement (‘dimer‐of‐dimers’) in the crystal structure, the solution structure clearly shows a monomeric fold. The monomeric structure of the CNBD supports the hypothesis that the CNBDs transmit the binding signal to the channel pore independently of each other.     

The more food webs change,the more they stay the same

Here, we synthesize a number of recent empirical and theoretical papers to argue that food-web dynamics are characterized by high amounts of spatial and temporal variability and that organisms respond predictably, via behaviour, to these changing conditions. Such behavioural responses on the landscape drive a highly adaptive food-web structure in space and time. Empirical evidence suggests that underlying attributes of food webs are potentially scale-invariant such that food webs are characterized by hump-shaped trophic structures with fast and slow pathways that repeat at different resolutions within the food web. We place these empirical patterns within the context of recent food-web theory to show that adaptable food-web structure confers stability to an assemblage of interacting organisms in a variable world. Finally, we show that recent food-web analyses agree with two of the major predictions of this theory. We argue that the next major frontier in food-web theory and applied food-web ecology must consider the influence of variability on food-web structure.     

Crystal structure of peptidoglycan recognition protein SA in Apis mellifera (Hymenoptera: Apidae)

Peptidoglycan recognition protein SA (PGRP‐SA) is a key pattern recognition receptor in the insect innate immune system. PGRP‐SA can bind to bacterial PGN and activate the Toll pathway, which triggers the expression and release of antimicrobial peptides to prevent bacterial infection. Here, we report the first structure of Apis mellifera PGRP‐SA from Hymenoptera at 1.86 Å resolution. The overall architecture of Am‐PGRP‐SA was similar to the Drosophila PGRP‐SA; however, the residues involved in PGN binding groove were not conserved, and the binding pocket was narrower. This structure gives insight into PGN binding characteristics in honeybees.     

SPIN2: Predicting sequence profiles from protein structures using deep neural networks

Designing protein sequences that can fold into a given structure is a well‐known inverse protein‐folding problem. One important characteristic to attain for a protein design program is the ability to recover wild‐type sequences given their native backbone structures. The highest average sequence identity accuracy achieved by current protein‐design programs in this problem is around 30%, achieved by our previous system, SPIN. SPIN is a program that predicts sequences compatible with a provided structure using a neural network with fragment‐based local and energy‐based nonlocal profiles. Our new model, SPIN2, uses a deep neural network and additional structural features to improve on SPIN. SPIN2 achieves over 34% in sequence recovery in 10‐fold cross‐validation and independent tests, a 4% improvement over the previous version. The sequence profiles generated from SPIN2 are expected to be useful for improving existing fold recognition and protein design techniques. SPIN2 is available at http://sparks-lab.org .     

中国生物多样性核心监测指标遥感产品体系构建与思考

生物多样性的稳定维持关乎人类生存发展与地球健康。生物多样性核心监测指标(Essential Biodiversity Variables, EBVs)旨在结合地面调查与遥感技术, 为大尺度、长时间序列的生物多样性监测提供新的解决方案。然而, 目前学界仍然缺乏一套国家尺度标准化EBVs遥感监测产品数据集, 以进行生物多样性评估。本研究旨在对中国生物多样性核心监测指标遥感产品进行体系构建与思考, 首先综述了目前EBVs的遥感研究概况, 并根据EBVs研究文献的数量进行调研分析; 同时, 本文在已有遥感生物多样性产品优先标准的基础上, 添加了“可重复性”的新标准, 并据此构建了中国EBVs遥感产品体系与监测数据集的指标清单, 最终对中国EBVs遥感研究存在的问题进行思考与讨论。本研究可为中国的生物多样性遥感监测提供科学依据, 有望为中国生物多样性政策的制定提供支撑。