用碱洗脱法检测DNA-蛋白质交联和DNA链间交联

本方法以DNA单链断裂的检测为基础,在背景γ射线照射下进行DNA交联检测。所建方法与Kohn氏原法相比,洗脱时间大为缩短,实验所用主要材料都能立足国内。本文引入“交联度”这个参数,能同时相对定量地表示DNA总交联、DNA-蛋白质交联和DNA链间交联。此外还从DNA、蛋白质两方面确证了DNA-蛋白质交联的存在。     

化学交联在蛋白质结构研究中的应用

在交联剂分子两端各有一个相同或不同的活性基团,它们能与蛋白质侧链上的氨基、巯基、羟基等形成共价交联.利用交联反应,可以测定寡聚蛋白质的亚基数量、研究蛋白质的高级结构、测量氨基酸残基间的距离及研究蛋白质间的相互作用.     

剂量率等因素对聚乙烯辐照交联的影响

本文研究了聚乙烯塑料在＾６０Ｃｏ－γ射线辐照下,剂量率等因素对交联度的影响,实验结果表明：交联度随辐照强度提高而增加,当交联度相同时,不同的材料需不同的辐照剂量,在相同的辐照条件下,当制备样品的方法不同时,交联度也不同。     

代谢光反应交联技术在生物大分子相互作用研究中的应用

具备光反应交联活性的苯甲酮基团、叠氮苯基团以及双吖丙啶基团被广泛应用于对糖、氨基酸等代谢底物的修饰。利用生物自身的代谢机制,引入带有光反应交联基团的底物类似物,可以实现生物大分子间相互作用的原位、实时研究,从而获得更为准确的相互作用复合物的信息。本文将综述代谢光反应交联技术在聚糖-蛋白质、蛋白质-蛋白质相互作用研究中的应用进展。     

原子力显微镜观测紫外线诱导的K562肿瘤细胞DNA损伤

利用彗星电泳检测出UVB、UVC短时间照射会使肿瘤细胞的DNA发生断裂,而长时间照射之后彗星电泳无法检测到碎片,推测可能是由于DNA分子交联的原因[1],国内外尚无定论.为了更直观的研究这种现象,提取了UVB,UVA照射后K562细胞的DNA,并调节到合适的浓度在原子力显微镜下观测.实验结果表明UVB对K562肿瘤细胞DNA损伤的影响呈现时间/剂量效应,较短时间照射主要产生DNA的链断裂,较长时间辐射则主要产生DNA链的交联.UVC对K562肿瘤细胞DNA的损伤大于UVB.UVC短时照射即可引起DNA的断裂和交联,较长时间辐射主要产生交联和一些断裂;长时间照射不但产生大量交联,同时有大量断裂产生,并发生凝缩和缠绕等结构破坏.     

蛋白质结构与相互作用研究新方法——交联质谱技术

蛋白质的空间结构信息以及蛋白质间的相互作用信息对于研究蛋白质的功能有重要意义.研究蛋白质结构与相互作用的传统技术,如核磁共振技术、X射线晶体衍射技术等,对于蛋白质的纯度、结晶性和绝对量均有比较高的要求,限制了其广泛应用.交联质谱技术是近十多年来发展起来的新技术,它将质谱技术与交联技术相结合,在研究蛋白质结构与相互作用方面具有速度快、成本小、蛋白质各方面性状要求低等优势.本文就交联质谱技术各个环节的技术方法加以综述,包括交联质谱实验分离富集技术、常见交联剂特性、交联质谱数据库搜索算法、结果验证研究和交联质谱技术的应用等方面,并展望了该研究方向未来的发展.     

交联法在分子生物学研究中的应用

本文概要介绍了交联法用于阐明染色质、核小体、病毒粒子、核糖体结构、观察HS70基因-组蛋白等七种核酸-蛋白质复合物中大分子相互作用的实例;列举了它在DNA构象、RNA立体结构及mRNA、tRNA、snRNA、hnRNA、rRNA间相互作用等研宄中的应用。从文中可以看出,交联法的应用范围遍及遗传信息储存的高级结构、转录体系及调控、翻译系统及调控等分子生物学研究的几个主要侧面。     

戊二醛交联法制备固定化酶的改进研究

本文对以交联聚丙烯酰胺为载体的戊二醛交联法制备固定化酶进行了两点改进t (1)将戊二醛进行醛基保护,避免发生交联反应; (2)将载体的酰胺基经酰肼化反应,使其转化成较活泼的酰肼基。然后将含有活泼酰肼基的载体用保护了醛基的戌二醛进行载体,活化反应,再偶联脲酶、L－门冬酰胺酶,可缩短反应时间、提高偶联酶量及酶活性。     

交联酶聚集体--一种无载体酶固定化方法

对一种崭新的无载体酶固定化技术——交联酶聚集体(Cross-linked Enzyme Aggregates,CLEAs)技术进行了文献综述。CLEAs技术是一种将蛋白质先沉淀后交联形成不溶性的、稳定的固定化酶。研究结果显示其活性和稳定性可与交联酶晶体(Cross-linked Enzyme Crystals,CLECs)技术相媲美。由于其制备不需要复杂耗时的结晶、纯化步骤,一般实验室都能实行,因而更有利于研究和应用的普及。该文就CLEAs的制备、在水溶液中的活性和稳定性在有机溶剂中的活性和作用机理及研究进行了介绍讨论。     

枯草芽孢杆菌FM208849产果胶酶的固定化及酶学性质研究

为了提高游离果胶酶的稳定性,对罗布麻脱胶具有特异性的枯草芽孢杆菌(FM208849)进行产果胶酶发酵时,采用交联酶聚集体(CLEAs)技术制备固定化果胶酶,并对交联果胶酶聚集体的制备条件、酶学性质进行研究。结果表明,游离果胶酶经80%饱和硫酸铵沉淀后,在30℃,经4%的戊二醛溶液交联135 min,所形成的交联果胶酶聚集体的活回收率为61.5%,其最适反应温度45℃和最适pH10,在对交联果胶酶聚集体的热稳定性和有机溶剂稳定性分析中,均显示了比游离酶更高的稳定性。     

Pulse coupled oscillators and the phase resetting curve

Limit cycle oscillators that are coupled in a pulsatile manner are referred to as pulse coupled oscillators. In these oscillators, the interactions take the form of brief pulses such that the effect of one input dies out before the next is received. A phase resetting curve (PRC) keeps track of how much an input advances or delays the next spike in an oscillatory neuron depending upon where in the cycle the input is applied. PRCs can be used to predict phase locking in networks of pulse coupled oscillators. In some studies of pulse coupled oscillators, a specific form is assumed for the interactions between oscillators, but a more general approach is to formulate the problem assuming a PRC that is generated using a perturbation that approximates the input received in the real biological network. In general, this approach requires that circuit architecture and a specific firing pattern be assumed. This allows the construction of discrete maps from one event to the next. The fixed points of these maps correspond to periodic firing modes and are easier to locate and analyze for stability compared to locating and analyzing periodic modes in the original network directly. Alternatively, maps based on the PRC have been constructed that do not presuppose a firing order. Specific circuits that have been analyzed under the assumption of pulsatile coupling include one to one lockings in a periodically forced oscillator or an oscillator forced at a fixed delay after a threshold event, two bidirectionally coupled oscillators with and without delays, a unidirectional N-ring of oscillators, and N all-to-all networks.     

Interaction of coupled nonlinear oscillators having different intrinsic resting levels

The interaction among coupled oscillators is governed by oscillator properties (intrinsic frequency and amplitude) and coupling mechanisms. This study considers another oscillator property, the intrinsic resting level, and evaluates its role in governing oscillator interactions. The results of computer experiments on a chain of either three or five bidirectionally coupled nonlinear oscillators, suggest that an intrinsic resting level gradient, if present, is one of the factors governing the interaction between coupled oscillators. If there is no intrinsic frequency gradient, then an intrinsic resting level gradient is sufficient to produce many features of interaction among coupled oscillators. If both intrinsic frequency and intrinsic resting level gradients are present, then both of them determine the manner in which the coupled oscillators interact with each other.     

Estimation of the transmission time of stimulus-locked responses: modelling and stochastic phase resetting analysis

A model of two coupled phase oscillators is studied, where both oscillators are subject to random forces but only one oscillator is repetitively stimulated with a pulsatile stimulus. A pulse causes a reset, which is transmitted to the other oscillator via the coupling. The transmission time of the cross-trial (CT) averaged responses, i.e. the difference in time between the maxima of the CT averaged responses of both oscillators differs from the time difference between the maxima of the oscillators' resets. In fact, the transmission time of the CT averaged responses directly corresponds to the phase difference in the stable synchronized state with integer multiples of the oscillators' mean period added to it. With CT averaged responses it is impossible to reliably estimate the time elapsing, owing to the stimulus' action being transmitted between the two oscillators.     

Coupled oscillators and the design of central pattern generators

Much can be deduced about the behavior of chains of oscillators under minimal assumptions about the nature of the oscillators or the coupling. This paper reviews work on such chains, and provides a framework within which implications may be drawn about the neural networks that govern undulatory locomotion in lower vertebrates.     

Phase Resetting Curves Allow for Simple and Accurate Prediction of Robust N:1 Phase Locking for Strongly Coupled Neural Oscillators

Existence and stability criteria for harmonic locking modes were derived for two reciprocally pulse coupled oscillators based on their first and second order phase resetting curves. Our theoretical methods are general in the sense that no assumptions about the strength of coupling, type of synaptic coupling, and model are made. These methods were then tested using two reciprocally inhibitory Wang and Buzsáki model neurons. The existence of bands of 2:1, 3:1, 4:1, and 5:1 phase locking in the relative frequency parameter space was predicted correctly, as was the phase of the slow neuron's spike within the cycle of the fast neuron in which it occurred. For weak coupling the bands are very narrow, but strong coupling broadens the bands. The predictions of the pulse coupled method agreed with weak coupling methods in the weak coupling regime, but extended predictability into the strong coupling regime. We show that our prediction method generalizes to pairs of neural oscillators coupled through excitatory synapses, and to networks of multiple oscillatory neurons. The main limitation of the method is the central assumption that the effect of each input dies out before the next input is received.     

Transitory behaviors in diffusively coupled nonlinear oscillators

We study collective behaviors of diffusively coupled oscillators which exhibit out-of-phase synchrony for the case of weakly interacting two oscillators. In large populations of such oscillators interacting via one-dimensionally nearest neighbor couplings, there appear various collective behaviors depending on the coupling strength, regardless of the number of oscillators. Among others, we focus on an intermittent behavior consisting of the all-synchronized state, a weakly chaotic state and some sorts of metachronal waves. Here, a metachronal wave means a wave with orderly phase shifts of oscillations. Such phase shifts are produced by the dephasing interaction which produces the out-of-phase synchronized states in two coupled oscillators. We also show that the abovementioned intermittent behavior can be interpreted as in-out intermittency where two saddles on an invariant subspace, the all-synchronized state and one of the metachronal waves play an important role.     

Simple models for excitable and oscillatory neural networks

 Chains of coupled oscillators of simple “rotator” type have been used to model the central pattern generator (CPG) for locomotion in lamprey, among numerous applications in biology and elsewhere. In this paper, motivated by experiments on lamprey CPG with brainstem attached, we investigate a simple oscillator model with internal structure which captures both excitable and bursting dynamics. This model, and that for the coupling functions, is inspired by the Hodgkin–Huxley equations and two-variable simplifications thereof. We analyse pairs of coupled oscillators with both excitatory and inhibitory coupling. We also study traveling wave patterns arising from chains of oscillators, including simulations of “body shapes” generated by a double chain of oscillators providing input to a kinematic musculature model of lamprey.. Received: 25 November 1996 / Revised version: 9 December 1997     

Typical trajectories of coupled degrade-and-fire oscillators: from dispersed populations to massive clustering

We consider the dynamics of a piecewise affine system of degrade-and-fire oscillators with global repressive interaction, inspired by experiments on synchronization in colonies of bacteria-embedded genetic circuits. Due to global coupling, if any two oscillators happen to be in the same state at some time, they remain in sync at all subsequent times; thus clusters of synchronized oscillators cannot shrink as a result of the dynamics. Assuming that the system is initiated from random initial configurations of fully dispersed populations (no clusters), we estimate asymptotic cluster sizes as a function of the coupling strength. A sharp transition is proved to exist that separates a weak coupling regime of unclustered populations from a strong coupling phase where clusters of extensive size are formed. Each phenomena occurs with full probability in the thermodynamics limit. Moreover, the maximum number of asymptotic clusters is known to diverge linearly in this limit. In contrast, we show that with positive probability, the number of asymptotic clusters remains bounded, provided that the coupling strength is sufficiently large.     

Spatially Organized Dynamical States in Chemical Oscillator Networks: Synchronization,Dynamical Differentiation,and Chimera Patterns

Dynamical processes in many engineered and living systems take place on complex networks of discrete dynamical units. We present laboratory experiments with a networked chemical system of nickel electrodissolution in which synchronization patterns are recorded in systems with smooth periodic, relaxation periodic, and chaotic oscillators organized in networks composed of up to twenty dynamical units and 140 connections. The reaction system formed domains of synchronization patterns that are strongly affected by the architecture of the network. Spatially organized partial synchronization could be observed either due to densely connected network nodes or through the ‘chimera’ symmetry breaking mechanism. Relaxation periodic and chaotic oscillators formed structures by dynamical differentiation. We have identified effects of network structure on pattern selection (through permutation symmetry and coupling directness) and on formation of hierarchical and ‘fuzzy’ clusters. With chaotic oscillators we provide experimental evidence that critical coupling strengths at which transition to identical synchronization occurs can be interpreted by experiments with a pair of oscillators and analysis of the eigenvalues of the Laplacian connectivity matrix. The experiments thus provide an insight into the extent of the impact of the architecture of a network on self-organized synchronization patterns.