基于微生物的可控生物制造

微生物种类丰富,尺寸涵盖纳米与微米级,是天然的可用于纳米、微米及多层次跨尺度加工的"基本单元"。目前的生物制造方法大多不适用于微生物活细胞,无法发挥其整体的生物学功能及优势。本研究探索并建立了微流控和磁控的可用于微生物活体的微纳米生物制造新方法,定位操纵和有序排列微生物活体。以微生物为微纳米机器人,诱发其特有的生物学功能,进行受控自组装等生物制造过程,由此有望设计和创制一系列新型特殊功能材料和器件。     

矿物电子能量协同微生物胞外电子传递与生长代谢

微生物的电子传递过程在生命进化和生物地球化学循环中发挥着关键作用。近年来,随着微生物电子传递研究的深入开展,微生物纳米导线、导电生物被膜及种间电子传递等多种新型的微生物胞外电子传递机制不断被发现,微生物电子传递的距离也从纳米级拓展至厘米级。这些微生物的长距离电子传递过程环环相扣、相互协同,从而构成长距离电子传递网络,并在物质循环和能量转化中共同发挥作用。微生物长距离电子传递网络的结构功能及其调控机制已成为多个学科共同关注的焦点。本文以电子传递的距离为主线,对不同尺度的微生物长距离电子传递过程及网络研究的新进展进行综述,包括纳米尺度的电子传递网络（周质空间和外膜表层）、微米至毫米尺度的电子传递网络（纳米导线、细胞间电子和导电生物被膜）、厘米尺度的电子传递网络（电缆细菌）等,并分析了该研究现存的主要问题和下一步的发展方向,以期为进一步推进微生物长距离电子传递网络理论和应用研究提供科学参考。     

生态系统结构与功能

生态系统包括多种生物群体,有植物、动物和微生物,植物利用光能及无机元素制造有机物,动物摄取植物,而动植物遗体及其排泄物,既是微生物的原料,又须依赖后者进行加工分解,方能再度被植物利用。植物——动物——微生物共同构成生态系统的基本结构。通过该结构完成系统中物质与能量的循环和转化过程,称     

单分子层次上相互作用自动检测

任何生命过程都与分子间相互作用有关。这些相互作用决定了生物分子间的＂交流＂方式,组成了生物过程的基本语言。Müller教授研究组发展了一种全自动＂机器人＂（一种全自动原子力显微镜）,可以通过检测细胞上的＂分子机器＂分析分子间相互作用。为了实现这样的目标,该仪器需要将不同的空间尺度联系起来：宏观尺度的悬臂利用其微观尺度的针尖与纳米尺度的蛋白质相接触,进而在亚纳米的尺度上定位与检测分子间相互作用。这项技术能够帮助人们以亚纳米尺度的分辨率定位细胞内分子机器的相互作用位置,并且观察分子间相互作用如何驱动这些分子机器行使功能。在药物筛选研究领域,该技术可以被用来检测配体以及抑制剂与蛋白质结合的位点和强度,还可以检测受体的不同功能状态。     

单分子装置：传感器、连接器、致动器

生物大分子之所以可以实现生物学功能是与其独特的力学性质息息相关的。作为纳米科技领域一个重要工具,原子力显微镜（AFM）可以对纳米尺度的生物大分子进行操纵并检测其力学性质。本文介绍了利用原子力显微镜对几类特殊蛋白以及DNA的力学性质的研究结果,发现这些生物分子具有很好的力学传感、连接和致动能力,将来有望作为单分子装置在纳米世界发挥更多功用。     

纳米技术与生物学实验的微型化

纳米技术是近年来发展迅速的新技术,有着几乎无限的潜力。一方面生物分子的尺度是纳米与亚纳米级的,纳米技术可以从生物科学学到许多生物分子作用的奥秘;另一方面,纳米技术为生物学的研究提供新材料、新方法,使生物学研究可以多快好省地进行。本文简单介绍几种利用纳米技术开展生物学研究的思路与方法。     

一株促甲烷氧化假单胞菌Pseudomonas putida P7的分离及电活性特征

微生物胞外呼吸是厌氧环境中控制性能量代谢方式,直接驱动着C、N、S、Fe等关键元素的生物地球化学循环。微生物纳米导线（Microbial nanowires）的发现,被认为是微生物胞外呼吸的里程碑事件,推动了电微生物学（Electromicrobiology）的形成与发展。微生物纳米导线是一类由微生物合成的,具有导电性的纤维状表面附属结构。通过细菌纳米导线,微生物胞内代谢产生的电子可以长距离输送到胞外受体或其他微生物,改变了电子传递链仅仅局限于细胞胞内的认识,从而大大拓展了微生物-胞外环境互作的范围。微生物纳米导线的良好导电性,赋予了其作为天然纳米材料的广阔应用前景。目前,微生物纳米导线的导电机制、生态功能及其在生物材料、生物能源、生物修复及人体健康多领域的应用,已经成为新兴电微生物学的前沿与热点。然而,微生物纳米导线的生物学、生态学功能尚不清楚,它的电子传递机制仍存在分歧。本文在系统性总结微生物纳米导线性质、功能的基础上,以Geobacter sulfurreducens和Shewanella oneidensis纳米导线为模型,详细阐述了纳米导线的组成与结构、表征与测量方法、导电理论（类金属导电学说与电子跃迁学说）及其潜在的应用,最后提出了未来微生物纳米导线研究的重点方向、挑战与机遇。     

悦目金蛛和棒络新妇卵袋丝物理化学结构表征及其力学性能研究

蜘蛛丝是一种具有优良机械性能的天然动物蛋白纤维,它特有的结构和性能与其生物学功能密切相关。作者采用氨基酸自动分析仪、傅立叶转换红外光谱仪、扫描电镜和电子单纤强力仪对悦目金蛛（Argiope amoena）和棒络新妇（Nephila clavata）的卵袋丝进行了物理化学结构表征与力学性能的研究,结果表明两种蜘蛛卵袋均由微米级柱状腺丝、大壶状腺丝、亚微米级或纳米级葡萄状腺丝构成。卵袋丝的表面形貌特征、极性氨基酸含量、大侧链与小侧链氨基酸的比值、无定型区、β-折叠结构与结晶结构的含量等氨基酸组成种类与蛋白质二级结构特征,均满足各自生物学功能对断裂强度、延展性、初始模量等力学性能的要求。     

原子力显微镜在生物医学上的应用

原子力显微镜(atomic force microscope,AFM)是扫描探针显微镜(SPM)的一种,其分辨率达到纳米级,能对从原子到分子尺度的结构进行三维成像和测量,能观察任何活的生命样品及动态过程。本文概述了AFM的基本工作原理及在生物医学上对DNA、蛋白质、细胞及生物过程等方面进行的研究。     

川东北二叠系-三叠系界线附近微生物岩微观表面特征观察研究

对采自四川通江平溪坝二叠系-三叠系界线(PTB)剖面发育的微生物岩样品,选用2.5%盐酸、10%盐酸、10%氢氧化钠溶液、20%双氧水、10%醋酸以及0.1M乙二胺四乙酸钠(EDTA)进行处理,根据微生物岩表面处理结果的异同,和在扫描电镜(SEM)图像上的表现,确定最适合于微生物岩表面结构观察的化学处理方法是使用2.5%盐酸处理样品表面。用该法处理,并通过SEM观察发现,通常被当作白云岩的PTB微生物岩,实际上只是含有白云岩微晶的泥晶灰岩,微生物岩中含有与硫酸盐还原菌有关的大量的纳米级微球粒与形似草莓状黄铁矿的颗粒。通过实验结果对比分析了不同层位的微生物岩与白云岩的SEM微米级的特征和区别,以及建造微生物岩的微生物群落对其层位上下地层的影响。     

Quantitative regularities of development of endogenous infection in irradiated organism (survey of literature)

Statistical analysis of data from the literature and the author's own experimental results was carried out in order to reveal functional dependence between the dose of irradiation and the development of endogenous infection in an irradiated organism. Direct linear dependence was established between the dose of irradiation and the severity of endogenous infection at doses causing death from the "bone-marrow" syndrome in acute radiation sickness. In the case of death from the "intestinal" syndrome, inverse linear dependence can be observed between the dose of irradiation and the culture yield of microbes from internal organs. In this case, the pathological effect on the organism is due to bacterial endotoxins formed during disintegration of microbial cells in the organism. Endogenous infection and endotoxinaemia essentially aggravate the course of acute radiation disease. The importance of endogenous infection in death of the organism is neutralized after irradiation in doses causing death "under the ray".     

Mini review: Biomimetic models and bioinspired surfaces for fouling control

Nature provides many examples of mechanisms to control fouling. These defences can be copied (biomimetic) or tailored (bioinspired) to solve problems of fouling on manmade structures. With increasing research in this area over the last two decades, it is timely to review this burgeoning subject, in particular as the biofouling field shifts focus towards novel, physical mechanisms to prevent and control fouling. This change is being promoted by advances in nano- and micro-scale patterning as well as in a variety of nano-biotechnologies, which are transforming the translation of natural surfaces into experimental materials. In this article, research on the defence of marine organisms against fouling and the technologies they are defining is reviewed.     

Hierarchical protein folding pathways: a computational study of protein fragments

We have previously presented a building block folding model. The model postulates that protein folding is a hierarchical top-down process. The basic unit from which a fold is constructed, referred to as a hydrophobic folding unit, is the outcome of combinatorial assembly of a set of "building blocks." Results obtained by the computational cutting procedure yield fragments that are in agreement with those obtained experimentally by limited proteolysis. Here we show that as expected, proteins from the same family give very similar building blocks. However, different proteins can also give building blocks that are similar in structure. In such cases the building blocks differ in sequence, stability, contacts with other building blocks, and in their 3D locations in the protein structure. This result, which we have repeatedly observed in many cases, leads us to conclude that while a building block is influenced by its environment, nevertheless, it can be viewed as a stand-alone unit. For small-sized building blocks existing in multiple conformations, interactions with sister building blocks in the protein will increase the population time of the native conformer. With this conclusion in hand, it is possible to develop an algorithm that predicts the building block assignment of a protein sequence whose structure is unknown. Toward this goal, we have created sequentially nonredundant databases of building block sequences. A protein sequence can be aligned against these, in order to be matched to a set of potential building blocks.     

Structure-based ligand design by dynamically assembling molecular building blocks at binding site.

A structure-based ligand design method is proposed and tested. The method is based on stochastic dynamics simulation of multiple copies of molecular building blocks in the presence of a receptor molecule. The molecular building blocks are assembled into candidate compounds "on the fly" at given intervals during the simulation. In the algorithm, a special effort is made to explore different possible combinations of building blocks and to select an optimum combination. By repeating the cycle of deconstruction and reconstruction in a single simulation, a set of candidate compounds that can be built from the building blocks evolves and is dynamically optimized. The method was tested by breaking two known flexible human immunodeficiency virus type 1 protease inhibitors into building blocks and reassembling them in the active site of the enzyme. For the inhibitor L700417, a set of conformations was generated by the calculation. Among these, the original compound was recovered with the lowest energy at the experimentally observed binding site and in the correct conformation. For pepstatin, the experimentally observed binding mode of the backbone of the inhibitor was reproduced by a calculation in which the building blocks corresponding to the side-chain groups were omitted. Proteins 1999;36:462-470.     

未培养微生物研究:方法、机遇与挑战

自然界中绝大部分的微生物仍是未培养的,称之为未培养微生物或微生物"暗物质"。对其进行研究不仅有助于认识微生物多样性及其代谢特征,加深对环境中微生物参与的生态学过程的理解,还有利于重构生命之树,揭示微生物的进化历程,具有重要的科学意义。同时未培养微生物是发现新基因资源和新活性物质的巨大宝库。随着现代分子生物学研究方法和培养技术的成熟和完善,从环境中直接破译未培养微生物的遗传信息,并实现培养逐渐成为可能。本文主要介绍了基于宏基因组技术和单细胞基因组技术或两者结合运用,研究环境中未培养微生物的主要方法和挑战,总结分析了目前已经解析的未培养微生物的主要类群,并对未来研究的机遇进行了展望。     

Mechanical property determination of bone through nano- and micro-indentation testing and finite element simulation

Measurement of the mechanical properties of bone is important for estimating the stresses and strains exerted at the cellular level due to loading experienced on a macro-scale. Nano- and micro-mechanical properties of bone are also of interest to the pharmaceutical industry when drug therapies have intentional or non-intentional effects on bone mineral content and strength. The interactions that can occur between nano- and micro-indentation creep test condition parameters were considered in this study, and average hardness and elastic modulus were obtained as a function of indentation testing conditions (maximum load, load/unload rate, load-holding time, and indenter shape). The results suggest that bone reveals different mechanical properties when loading increases from the nano- to the micro-scale range (microN to N), which were measured using low- and high-load indentation testing systems. A four-parameter visco-elastic/plastic constitutive model was then applied to simulate the indentation load vs. depth response over both load ranges. Good agreement between the experimental data and finite element model was obtained when simulating the visco-elastic/plastic response of bone. The results highlight the complexity of bone as a biological tissue and the need to understand the impact of testing conditions on the measured results.     

Understanding the dynamic behavior of genetic regulatory networks by functional decomposition

A number of mechanistic and predictive genetic regulatory networks (GRNs) comprising dozens of genes have already been characterized at the level of cis-regulatory interactions. Reconstructions of networks of 100's to 1000's of genes and their interactions are currently underway. Understanding the organizational and functional principles underlying these networks is probably the single greatest challenge facing genomics today. We review the current approaches to deciphering large-scale GRNs and discuss some of their limitations. We then propose a bottom-up approach in which large-scale GRNs are first organized in terms of functionally distinct GRN building blocks of one or a few genes. Biological processes may then be viewed as the outcome of functional interactions among these simple, well-characterized functional building blocks. We describe several putative GRN functional building blocks and show that they can be located within GRNs on the basis of their interaction topology and additional, simple and experimentally testable constraints.     

Some aspects of protein folding.

The mechanisms by which a polypeptide chain reaches the three dimensional structure which generates its functional properties are not yet totally understood. The great amount of data now available in the field of protein structure and the data already obtained on protein folding by in vitro experiments allow some schematic representation as, at least, a working hypothesis. In this respect the emphasis is put on the hierarchy in protein structure and the possibility of a folding by stages, some elements or "building blocks" being able to reach independently a native structure and to refine this structure by interacting with each other in the whole molecule.     

Biosynthesis of polyesters and polyamide building blocks using microbial fermentation and biotransformation

Biopolymers can be a green alternative to fossil-based polymers and can contribute to environmental protection because they are produced using renewable raw materials. Biopolymers are composed of various small subunits (building blocks) that are the intermediates or end products of major metabolic pathways. Most building blocks are secreted directly outside of cells, making downstream processes easier and more economic. These molecules can be extracted from fermentation broth and polymerized to produce a variety of biopolymers, e.g., polybutylene terephthalate, polyethylene terephthalate, polytrimethylene terephthalate, nylon-5,4 and nylon-4,6, with applications in medicine, pharmaceuticals, and textiles. Microbes are unable to naturally produce these types of polymers; thus, the production of building blocks and their polymerization is a fascinating approach for the production of these polymers. In comparison to naturally occurring biopolymers, synthesized polymers have improved and controlled structures and higher purity. The production of monomer units provides a new direction for polymer science because new classes of polymers with unique properties that were not previously possible can be prepared. Furthermore, the engineering of microbes for building-block production is an easy process compared to engineering an entire biopolymer synthesis pathway in a single microbe. Polyesters and polyamide polymers have become an important part of human life, and their demand is increasing daily. In this review, recent approaches and technology are discussed for the production of polyester/polyamide building blocks, i.e., 2-hydroxyisobutyric acid, 3-hydroxypropionic acid, mandelic acid, itaconic acid, adipic acid, terephthalic acid, succinic acid, 1,3-propanediol, 2,3-butanediol, 1,4-butanediol, 1,3-butanediol, cadaverine, and putrescine.