Analysis of complex protein-polypeptide systems for proteomic studies

Two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), followed by protein extraction and characterization with chemical sequencing or mass spectrometry (MS), is the most commonly used method to analyze complex protein systems such as cells and organelles. However, it is claimed that 2-D PAGE is a slow and labor-intensive technique and also needs subsequent efforts for one-by-one identification of proteins. Recently, the combined methods of Fourier transform ion cyclotron resonance (FTICR) mass spectrometry, with preceding separation techniques such as capillary isoelectric focusing (CIEF) or liquid chromatography, have been demonstrated as high-throughput techniques suitable for proteomic analysis of protein systems. The studies which employ FTICR MS, aimed at the analysis of complex protein systems, have been reviewed, comparing their performance with that of 2-D PAGE. Also, the possibilities of combining 2-D PAGE and the FTICR MS method to analyze and reconstruct the structures and functions of complex systems are discussed.     

Spatial synchrony in red grouse population dynamics

Red grouse Lagopus lagopus scoticus populations exhibit unstable dynamics that are often characterised by regular periodic fluctuations in abundance. Time-series' of grouse harvesting records collected from 287 management units (moors) across Scotland, England and Wales were analysed to investigate the broad scale patterns of synchrony in these fluctuations. Estimation of the spatial autocorrelation of grouse population dynamics across moors indicates relatively high levels of synchrony between populations on adjacent moors, but that this synchrony declines sharply with increasing inter-moor distance. At distances of greater than 100  km, grouse population time-series exhibit only weakly positive cross-correlation coefficients. Twenty-eight geographical, environmental and other candidate variables were examined to construct a general linear model to explain variation in local synchrony. Grouse moor productivity (average size of shooting bag), distance from the Atlantic coast moving in a north-easterly direction, April and June temperatures, and June rainfall significantly increased the explanatory power of this model. An understanding of the processes underlying synchrony in red grouse population dynamics is a prerequisite to anticipating the effects of large-scale environmental change on regional patterns of grouse distribution and abundance.     

Quantification of the spatial aspect of chaotic dynamics in biological and chemical systems

The need to study spatio-temporal chaos in a spatially extended dynamical system which exhibits not only irregular, initial-value sensitive temporal behavior but also the formation of irregular spatial patterns, has increasingly been recognized in biological science. While the temporal aspect of chaotic dynamics is usually characterized by the dominant Lyapunov exponent, the spatial aspect can be quantified by the correlation length. In this paper, using the diffusion-reaction model of population dynamics and considering the conditions of the system stability with respect to small heterogeneous perturbations, we derive an analytical formula for an ‘intrinsic length’ which appears to be in a very good agreement with the value of the correlation length of the system. Using this formula and numerical simulations, we analyze the dependence of the correlation length on the system parameters. We show that our findings may lead to a new understanding of some well-known experimental and field data as well as affect the choice of an adequate model of chaotic dynamics in biological and chemical systems.     

不同干扰下荒漠啮齿动物种群动态的空间同步性

荒漠啮齿动物是动物生态学研究中的重要类群,对于丰富种群和群落生态学理论具有重要意义.国外关于荒漠啮齿动物的研究较多,尤以北美的研究较为深入,涉及群落组成(Brown,1973)、生态位(Harris, 1984;Kenagy and Bartholomew, 1985)、物种共存(Brown and Munger,1985)、资源分享及微生境选择(Brown and Lieberman,1973;Price,1978)等方面;而国内关于荒漠啮齿动物研究相对较少.     

Molecular dynamics studies of the full-length integrase-DNA complex

We have carried out a molecular dynamics (MD) simulation of full-length HIV-1 integrase (IN) dimer complexed with viral DNA with the aim of gaining information about the enzyme motion and investigating the movement of the catalytic flexible loop (residues 140-149) thought to be essential in the catalytic mechanism of IN. During the simulation, we observed quite a different behavior of this region in the presence or absence of the viral DNA. In particular, the MD results underline the crucial role of the residue Tyr143 in the mechanism of integration of viral DNA into the host chromosome. The present findings confirm the experimental data (e.g., site-directed mutagenesis experiments) showing that the loop is involved in the integration reactions and its mobility is correlated with the catalytic activity of HIV-1 integrase.     

复杂天然产物合成人工生物系统的设计与构建

天然产物是人类疾病预防和治疗药物的最重要来源。合成生物学技术的蓬勃发展为天然产物的开发注入了全新的活力。文中重点介绍了如何利用合成生物技术进行复杂天然产物合成人工生物系统的设计与构建,包括与此相关的生物元件理性设计、生物元件挖掘、途径装配与集成,模块的组装与系统的适配等内容。     

Molecular dynamics simulation studies of lipid bilayer systems

The main structural element of biological membranes is a liquid-crystalline lipid bilayer. Other constituents, i.e. proteins, sterols and peptides, either intercalate into or loosely attach to the bilayer. We applied a molecular dynamics simulation method to study membrane systems at various levels of compositional complexity. The studies were started from simple lipid bilayers containing a single type phosphatidylcholine (PC) and water molecules (PC bilayers). As a next step, cholesterol (Chol) molecules were introduced to the PC bilayers (PC-Chol bilayers). These studies provided detailed information about the structure and dynamics of the membrane/water interface and the hydrocarbon chain region in bilayers built of various types of PCs and Chol. This enabled studies of membrane systems of higher complexity. They included the investigation of an integral membrane protein in its natural environment of a PC bilayer, and the antibacterial activity of magainin-2. The latter study required the construction of a model bacterial membrane which consisted of two types of phospholipids and counter ions. Whenever published experimental data were available, the results of the simulations were compared with them.     

Single-molecule studies of complex systems: the replisome

A complete, system-level understanding of biological processes requires comprehensive information on the kinetics and thermodynamics of the underlying biochemical reactions. A wide variety of structural, biochemical, and molecular biological techniques have led to a quantitative understanding of the molecular properties and mechanisms essential to the processes of life. Yet, the ensemble averaging inherent to these techniques limits us in understanding the dynamic behavior of the molecular participants. Recent advances in imaging and molecular manipulation techniques have made it possible to observe the activity of individual enzymes and record "molecular movies" that provide insight into their dynamics and reaction mechanisms. An important future goal is extending the applicability of single-molecule techniques to the study of larger, more complex multi-protein systems. In this review, the DNA replication machinery will be used as an example to illustrate recent progress in the development of various single-molecule techniques and its contribution to our understanding of the orchestration of multiple enzymatic processes in large biomolecular systems.     

Effects of light dynamics on coral spawning synchrony

Synchrony of spawning in many hermatypic corals, typically a few nights after the full moon, is putatively dependent on solar and lunar light cycles in conjunction with other possible cues such as tides and temperature. We analyze here the contributions of separate components of light dynamics, because the effects of twilight and lunar skylight on coral spawning synchrony have previously been conflated and the alternative hypothesis that these components have differential contributions as proximate cues has not been tested. Moonlight-dependent changes in spectra during twilight, rates of decreasing twilight intensities, and changes in lunar photoperiod were experimentally decoupled using programmed light-emitting diodes and compared for their separate effects on spawning synchrony in Acropora humilis. Effects on synchrony under the control of synthetic lunar cues were greatest in response to changes in lunar photoperiod; changes in light intensities and spectra had lesser influence. No significant differences among treatment responses were found at the circa-diel time scale. We conclude that spawning synchrony on a particular lunar night and specific time of night is a threshold response to differential periods of darkness after twilight that is primarily influenced by lunar photoperiod and secondarily by discrete optical components of early nocturnal illumination.     

Modern X-ray scattering studies of complex biological systems

1. Download : Download high-res image (166KB)
2. Download : Download full-size image

Highlights► We review modern advances to characterize biological nano-complexes using X-ray scattering. ► X-ray scattering is used to study both the structures and macro-molecular interactions. ► Contemporary techniques include integration of complementary techniques together with X-ray scattering. ► Novel computational and technological advances, including coherent scattering technique, will be discussed.     

Unravelling mechanisms of short-term vegetation dynamics in complex coppice forest systems

The silvicultural management of coppicing has been very common in deciduous forests in many European countries. After decades of decline of this practice, socio-economic changes might induce a revival valuing the biomass as a resource. New insights in the ecological processes that regulate plant diversity are relevant for a sustainable forest management. While studies on long-term changes are available, the short-term dynamics of the coppice forest understorey has not yet been explored. In this context, it is interesting to evaluate the species compositional changes, including the processes of species turnover and species impoverishment (nestedness) and to investigate the role of plant functional traits. For this purpose, we resampled a chronosequence of complex coppice beech forests of the Central Apennines (Italy) monitoring the short-time species dynamics of five years (i.e. from 2006 to 2011) in three age classes, i.e. post-logged, recovering and old coppice stands (0–16, 17–31 and > 32 years, respectively). In contrast to our expectation, declining species richness appeared only in the recovering stands, while the landscape scale (between-stand) heterogeneity, except for post-logged and recovering stands in 2011, did not change over five years. Significant temporal nestedness was found in each stage of succession. However, the rate of species turnover and species impoverishment do not significantly differ among the three age classes, indicating their constant importance along the forest regeneration after disturbance. Only in the early stage of forest regeneration after coppicing, species compositional changes are reflected by functional changes with surviving understorey species having clonal regeneration traits. Our results suggest an overall landscape-scale stability (and sustainability) of this coppice forest system. We conclude with management indications, highlighting the importance of maintaining the traditional local approach (coppicing with standards in small 0.5–1.0 ha sized management units with a ca 30-year rotation cycle) where active coppice parcels are interspersed by abandoned stands.     

Analysis of metabolic systems with complex slow and fast dynamics

We briefly review the results of other authors concerning the analysis of systems with time hierarchy, especially the Tikhonov theorem. A theorem, recently proved by the authors, making possible rigorous analysis of systems with complex fast dynamics is stated and discussed. A model example of a simple enzymatic reaction with product activation and slow (genetically driven) enzyme turnover is rigorously studied. It is shown that even in such a simple model there exist certain regions of parameters for which fast variables oscillate. Thus the classical Tikhonov theorem is not applicable here and we are forced to use another method-for example the author's presented theorem—or a purely numerical solution. These two methods are compared.     

Molecular modeling and molecular dynamics simulation studies of Delta-Notch complex

Notch is a single-pass transmembrane receptor protein which is composed of a short extracellular region, a single-pass transmembrane domain and a small intracellular region. Notch ligand like Delta, member of the DSL protein family, is also single-pass transmembrane protein. It has been demonstrated that of the 36 EGF repeats of Notch, 11th and 12th are sufficient to mediate interactions with Delta. Crystal structure of mammalian Notch extracellular ligand binding domain contains 11 and 12 EGF-like repeats. Here a portion of the Delta protein of Drosophila, known to interact with Notch extracellular domain (ECD) has been modeled using homology modeling. The structure of the Delta-Notch complex was subsequently modeled by protein docking method using GRAMM. MD simulations of the modeled structures were performed. The structure for Delta-Notch complex has been proposed based on interaction energy parameter and planarity studies.     

SC-CNNs for chaotic signal applications in secure communication systems

In this paper a CNNs based circuit for the generation of hyperchaotic signals is proposed. The circuit has been developed for applications in secure communication systems. An Saito oscillator has been designed by using a suitable configuration of a four-cells State-Controlled CNNs. A cryptography system based on the Saito oscillator has been implemented by using inverse system synchronization. The proposed circuit implementation and experimental results are given.