Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation

The chemokine receptor CCR5 is the receptor for several chemokines and major coreceptor for R5 human immunodeficiency virus type-1 strains entry into cell. Three-dimensional models of CCR5 were built by using homology modeling approach and 1 ns molecular dynamics (MD) simulation, because studies of site-directed mutagenesis and chimeric receptors have indicated that the N-terminus (Nt) and extracellular loops (ECLs) of CCR5 are important for ligands binding and viral fusion and entry, special attention was focused on disulfide bond function, conformational flexibility, hydrogen bonding, electrostatic interactions, and solvent-accessible surface area of Nt and ECLs of this protein part. We found that the extracellular segments of CCR5 formed a well-packet globular domain with complex interactions occurred between them in a majority of time of MID simulation, but Nt region could protrude from this domain sometimes. The disulfide bond Cys20-Cys269 is essential in controlling specific orientation of Nt region and maintaining conformational integrity of extracellular domain. RMS comparison analysis between conformers revealed the ECL1 of CCR5 stays relative rigid, whereas the ECL2 and Nt are rather flexible. Solvent-accessible surface area calculations indicated that the charged residues within Nt and ECL2 are often exposed to solvent. Integrating these results with available experimental data, a two-step gp120-CCR5 binding mechanism was proposed. The dynamic interaction of CCR5 extracellular domain with gp120 was emphasized. (C) 2004 Elsevier B.V. All rights reserved.

Holographic offset launch for dynamic optimization and characterization of multimode fiber bandwidth

Optimization of the bandwidth of a 2 km 50 μm multimode fiber at 850 nm is investigated theoretically and experimentally by steering a single spot, or two in antiphase spots across the core of the fiber in two dimensions using a ferroelectric liquid-crystal-based spatial light modulator. This method not only allows an optimal offset launch position to be chosen in situ but can also characterize the geometry and position of the core, identify defects, and measure the maximum differential mode delay. Its ability to selectively excite specific mode groups is also of relevance to mode-group division multiplexing. © 2012 IEEE.

Entrepreneurial innovation problems associated with the dynamic growth of university spin-outs in China: A capabilities perspective

This research aims to develop a capabilities-based conceptual framework in order to study the stage-specific innovation problems associated with the dynamic growth process of university spin-outs (hereafter referred to as USOs) in China. Based on the existing literature, pilot cases and five critical cases, this study attempts to explore the interconnections between the entrepreneurial innovation problems and the configuration of innovative capabilities (that acquire, mobilise and re-configure the key resources) throughout the lifecycle of a firm in four growth phases. This paper aims to contribute to the literature in a holistic manner by providing a theoretical discussion of USOs' development through adding evidence from a rapid growth emerging economy. To date, studies that have investigated the development of USOs in China recognised the heterogeneity of USOs in terms of capabilities still remain sparse. Addressing this research gap will be of great interest to entrepreneurs, policy makers and venture investors. © Copyright 2010 Inderscience Enterprises Ltd.

A structured modelling approach to simulating dynamic behaviours in complex organisations

This article reports a case study application of a systematic approach to modelling complex organisations, centred on simulation modelling (SM). The approach leads to populated instances of complementary model types, in ways that systematically capture, validate and facilitate various uses of organisational understandings, knowledge and data normally distributed amongst multiple knowledge holders. The model-driven approach to decision making enables improved manufacturing responsiveness. Literature on modelling technologies relevant to manufacturing systems organisation design and change is presented, as is literature on production planning and control. This provides a rationale for the development of a new modelling methodology which combines the use of enterprise, causal loop and SM. Subsequently, this article describes how in the case of a specific manufacturing enterprise the combined modelling techniques have informed the choice of alternative production planning and control policies. An example enterprise model of a capacitor manufacturing company is illustrated as derivative causal-loop models that structure and enable the design and use of a general purpose simulation model.

Influence of specific HSP70 domains on fibril formation of the yeast prion protein Ure2.

Ure2p is the protein determinant of the Saccharomyces cerevisiae prion state [URE3]. Constitutive overexpression of the HSP70 family member SSA1 cures cells of [URE3]. Here, we show that Ssa1p increases the lag time of Ure2p fibril formation in vitro in the presence or absence of nucleotide. The presence of the HSP40 co-chaperone Ydj1p has an additive effect on the inhibition of Ure2p fibril formation, whereas the Ydj1p H34Q mutant shows reduced inhibition alone and in combination with Ssa1p. In order to investigate the structural basis of these effects, we constructed and tested an Ssa1p mutant lacking the ATPase domain, as well as a series of C-terminal truncation mutants. The results indicate that Ssa1p can bind to Ure2p and delay fibril formation even in the absence of the ATPase domain, but interaction of Ure2p with the substrate-binding domain is strongly influenced by the C-terminal lid region. Dynamic light scattering, quartz crystal microbalance assays, pull-down assays and kinetic analysis indicate that Ssa1p interacts with both native Ure2p and fibril seeds, and reduces the rate of Ure2p fibril elongation in a concentration-dependent manner. These results provide new insights into the structural and mechanistic basis for inhibition of Ure2p fibril formation by Ssa1p and Ydj1p.

Influence of specific HSP70 domains on fibril formation of the yeast prion protein Ure2.

Ure2p is the protein determinant of the Saccharomyces cerevisiae prion state [URE3]. Constitutive overexpression of the HSP70 family member SSA1 cures cells of [URE3]. Here, we show that Ssa1p increases the lag time of Ure2p fibril formation in vitro in the presence or absence of nucleotide. The presence of the HSP40 co-chaperone Ydj1p has an additive effect on the inhibition of Ure2p fibril formation, whereas the Ydj1p H34Q mutant shows reduced inhibition alone and in combination with Ssa1p. In order to investigate the structural basis of these effects, we constructed and tested an Ssa1p mutant lacking the ATPase domain, as well as a series of C-terminal truncation mutants. The results indicate that Ssa1p can bind to Ure2p and delay fibril formation even in the absence of the ATPase domain, but interaction of Ure2p with the substrate-binding domain is strongly influenced by the C-terminal lid region. Dynamic light scattering, quartz crystal microbalance assays, pull-down assays and kinetic analysis indicate that Ssa1p interacts with both native Ure2p and fibril seeds, and reduces the rate of Ure2p fibril elongation in a concentration-dependent manner. These results provide new insights into the structural and mechanistic basis for inhibition of Ure2p fibril formation by Ssa1p and Ydj1p.

Evolutionary Conservation of Dazl Genomic Organization and its Continuous and Dynamic Distribution Throughout Germline Development in Gynogenetic Gibel Carp

To investigate germline development and germ cell specification, we identified a Dazl homolog (CagDazl) from gynogenetic gibel carp (Carassius auratus gibelio). Its cDNA sequence and BAC clone sequence analyses revealed the genomic organization conservation and conserved synteny of the Dazl family members and their neighborhood genes among vertebrates, especially in fish. Moreover, a polyclonal antibody specific to CagDazl was produced and used to examine its expression and distribution throughout germline development at protein level. Firstly, ovary-specific expression pattern of CagDazl was confirmed in adult tissues by RT-PCR and Western blot. In addition, in situ hybridization and immunofluorescence localization demonstrated its specific expression in germ cells, and both its transcript and protein were localized to germ plasm. Then, co-localization of CagDazl and mitochondrial cloud was found, confirming that CagDazl transcript and its protein are germ plasm component and move via METRO pathway during oogenesis. Furthermore, the CagDazl is abundant and continuous throughout germline development and germ cell specification including primordial germ cell (PGC) formation, oogonium differentiation, oocyte development, and embryogenesis, and the dynamic distribution occurs at different development stages. The data suggest that maternal CagDazl might play an important role in gibel carp PGC formation. Therefore, CagDazl is a useful and specific marker for tracing germ plasm and germ cell development in the gynogenetic gibel carp. In addition, in comparison with previous studies in sexual reproduction species, the continuous and dynamic distribution of CagDazl protein in the germ plasm throughout the life cycle seems to have significant implication in sex evolution of vertebrates. J. Exp. Zool. (Mol. Deu. Euol.) 312B:855-871, 2009. (C) 2009 Wiley-Liss, Inc.

Identification of a putative oocyte-specific small nuclear ribonucleoprotein polypeptide C in gibel carp

Previous studies have demonstrated that germinal vesicle of amphibian oocyte contains small nuclear ribonucleoprotein polypeptide C (SNRPC). In this study, a putative member of SNRPC was identified from Carassius auratus gibelio oocyte cDNA library. Its full-length cDNA has an open reading frame of 201 nt for encoding a peptide of 66 an, a short 5'-UTR of 19 nt and a long 3'-UTR of 347 nt including a polyadenylation signal and poly- (A) tail, and the deduced amino acid sequence has 47% identity with the C-terminal of the zebrafish small nuclear ribonucleoprotein polypeptide C. Western blot analysis revealed its oocyte-specific expression. Immunofluorescence localization indicated that its gene product localized to numerous nucleoli within the oocytes and showed dynamic changes with the nucleoli during oocyte maturation. RT-PCR and Western blot analysis further revealed its constant presence in the oocytes and in the embryos until hatching. The data suggested that the newly identified CagOSNRPC might be a nucleolar protein. (c) 2006 Elsevier Inc. All rights reserved.

Specific Adsorption of Trace Amounts of Calcium and Strontium by Hydrous Oxides of Iron and Aluminum1

Freshly prepared Fe and Al hydrous oxide gels and the amorphous product of heating gibbsite selectively adsorbed traces of Ca and Sr from solutions containing a large excess (∼1M) of NaNO3. The fraction of the added Ca (Sr) adsorbed depended principally on the suspension pH, the amount of solid present, and to a lesser extent on the NaNO3 concentration. Significant Ca and Sr adsorption occurred on the Fe and Al gels, and heated gibbsite, at pH values below the points of zero charge (8.1, 9.4, and 8.3±0.1, respectively), indicating specific adsorption. The pH (± 0.10) at which 50% of the Ca was adsorbed (pH50) occurred at pH 7.15 for the Fe gel (0.093M Fe), 8.35 for the Al gel (0.093M Al), and 6.70 for the heated gibbsite (0.181M Al); for Sr, the pH50 values were 7.10, 9.00, and 6.45, respectively. For the Fe gel and heated gibbsite, an empirical model based on the law of mass action described the pH dependence of adsorption reasonably well and suggested that for each Ca or Sr fraction adsorbed, approximately one proton was released. Failure of the Al gel to fit this model may have resulted from its rapid aging.

An electrochemical DNA sensor based on electrodepositing aluminum ion films on stearic acid-modified carbon paste electrode and its application for the detection of specific sequences related to bar gene and CP4 Epsps gene

An electrochemical DNA biosensor was fabricated by immobilizing DNA probe on aluminum ion films that were electrodeposited on the surface of the stearic acid-modified carbon paste electrode (CPE). DNA immobilization and hybridization were characterized with cyclic voltammetry (CV) by using methylene blue (MB) as indicator. MB has a couple of well-defined voltammetric redox peaks at the CPE. The currents of redox peaks of MB decreased after depositing aluminum ion films on the CPE (Al(III)/CPE) and increased dramatically after immobilizing DNA probe (ssDNA/Al(III)/CPE). Hybridization of DNA probe led to a marked decrease of the peak currents of MB, which can be used to detect the target single-stranded DNA. The conditions for the preparation of Al(III)/CPE, and DNA immobilization and hybridization were optimized. The specific sequences related to bar transgene in the transgenic corn and the PCR amplification of CP4 epsps gene from the sample of transgenic roundup ready soybean were detected by differential pulse voltammetry (DPV) with this new electrochemical DNA biosensor. The difference between the peak currents of MB at ssDNA/Al(III)/CPE and that at hybridization DNA modified electrode (dsDNA/Al(III)/CPE) was applied to determine the Specific sequence related to the target bar gene with the dynamic range comprised between 1.0 X 10(-7) mol/L to 1.0 x 10(-4) mol/L. A detection limit of 2.25 x.10(-8) mol/L. of oligonucleotides can be estimated.

White spot syndrome virus (WSSV) infects specific hemocytes of the shrimp Penaeus merguiensis

White spot syndrome virus (WSSV) was specifically detected by PCR in Penaeus merguiensis hemocytes, hemolymph and plasma. This suggested a close association between the shrimp hemolymph and the virus. Three types of hemocyte from shrimp were isolated using flow cytometry. Dynamic changes of the hemocyte subpopulations in P. merguiensis at different times after infection were observed, indicating that the WSSV infection selectively affected specific subpopulations. Immunofluorescence assay (IFA) and a Wright-Giemsa double staining study of hemocyte types further confirmed the cellular localization of the virus in the infected hemocytes. Electron microscopy revealed virus particles in both vacuoles and the nucleus of the semigranular cells (SGC), as well as in the vacuoles of the granular cells (GC). However, no virus could be detected in the hyaline cells (HC). Our results suggest that the virus infects 2 types of shrimp hemocytes-GCs and SGCs. The SGC type contains higher virus loads and exhibits faster infection rates, and is apparently more susceptible to WSSV infection.

降雨条件下碎石土滑坡稳定性研究

Debris Landslide is one of the types of landslides with the widest distribution, largest quantity, and the closest relationship with engineering construction. It is also one of the most important types of landslides that can cause disaster. This kind of landslide often occurs in the loose slopes which are made up of loose congeries formed by earth filling, residual soil, slope wash, dilapidation, landslide or full weathered material of hard rock. Rainfall is always the chief inducing factor of debris Landslide. Therefore, to research stability of debris Landslide during rainfall not only has important theoretical significance for understanding developing law and deformation and failure mechanism of debris landslide, but also has important practical significance for investigating, appraising, forecasting, preventing and controlling debris landslides. This thesis systematically summarized the relationships between rainfall and landslide, the method to survey water table in the landslides, the deformation and failure mechanism of debris landslide, and the progress in the stability analysis of landslides based on the analyses of data collected widely at home and abroad. The problems in the study of the stability of debris landslide during rainfall was reviewed and discussed. Due to the complicated geological conditions and the random rainfall conditions, the research on the landslides' stability must be based on engineering geological qualitative analysis. Through the collection of the data about the Panxi region and the Three Gorges Reservoir region, the author systematically summarized the engineering geological conditions, hydro-geological condition, distribution characteristics of stress field in the slope, physical and mechanical properties and hydro-mechanical properties of debris. In the viewpoint of dynamics of soil water and hydromechanics, physical process of rainfall to supply groundwater of debris landslides can be divided into two phases, i.e. non-saturated steady infiltrating phase and saturated unsteady supplying phase. The former can be described by mathematical model of surface water infiltration while the latter can be described by equivalent continuous medium model of groundwater seepage. With regard to specific hydrological geology system, we can obtain the dynamic variation law of water content, water table, landslide stability of rock and soil mass, along with quantity and duration of rainfall after the boundary condition on hydrological geology has been ascertained. This is a new way to study the response law of groundwater in the landslides during rainfall. After wet face of rock and soil mass connects with ground water table, the raising of water table will occur due to the supply of rainfall. Then interaction between ground water and rock and soil mass will occur, such as the action of physics, water, chemistry and mechanics, which caused the decrease of shearing strength of sliding zone. According to the action of groundwater on rock and soil mass, a concise mechanical model of debris landslide’s deformation was established during rainfall. The static equilibrium condition of landslide mass system was achieved according to the concise mechanical model, and then the typical deformation and failure process and failure mode of debris landslide during rainfall were discussed. In this thesis, the former limiting equilibrium slice method was modified and improved based on shearing strength theory of , a stability analysis program of debris landslide was established and developed taking account of the saturated-unsaturated seepage, by introducing the shearing strength theory of unsaturated soil mass made by (1978). The program has reasonable data storage and simple interface and is easy to operate, and can be perfectly used to carry out sensitivity analysis of influencing factors of landslides' stability, integrated with the program of Office Excel. The design of drainage engineering are always bases on empirical methods and is short of effective quantitative analysis and appraise, therefore, the conception of critical water table of debris landslide was put forward. For debris landslides with different kinds of slide face in the engineering practice, a program to search the critical water table of debris landslide was developed based on native groundwater table. And groundwater table in the slope should be declined below the critical water table in the drainage works, so the program can be directly used to guide drainage works in the debris landslide. Taking the slope deformation body in the back of former factory building of Muli Shawan hydroelectric power station as an example, a systematic and detailed research on debris landslides' stability during rainfall was researched systematically, the relationship among quantity of rainfall, water table and stability of slope was established, the debris landslides' stability in process of rainfall from dynamic viewpoint was analyzed and researched.

Supporting Dynamic Languages on the Java Virtual Machine

In this note, I propose two extensions to the Java virtual machine (or VM) to allow dynamic languages such as Dylan, Scheme and Smalltalk to be efficiently implemented on the VM. These extensions do not affect the performance of pure Java programs on the machine. The first extension allows for efficient encoding of dynamic data; the second allows for efficient encoding of language-specific computational elements.

Reflections on the development of a dynamic learning, teaching and assessment strategy.

Developing learning, teaching and assessment strategies that foster ongoing engagement and provide inspiration to academic staff is a particular challenge. This paper demonstrates how an institutional learning, teaching and assessment strategy was developed and a ‘dynamic’ strategy created in order to achieve the ongoing enhancement of the quality of the student learning experience. The authors use the discussion of the evolution, development and launch of the Strategy and underpinning Resource Bank to reflect on the hopes and intentions behind the approach; firstly the paper will discuss the collaborative and iterative approach taken to the development of an institutional learning, teaching and assessment strategy; and secondly, the development of open access educational resources to underpin the strategy. The paper then outlines staff engagement with the resource bank and positive outcomes which have been identified to date, identifies the next steps in achieving the ambition behind the strategy and outlines the action research and fuller evaluation which will be used to monitor progress and ensure responsive learning at institutional level.

Evolution feature oriented model driven product line engineering approach for synergistic and dynamic service evolution in Clouds: four kinds of schema.

The proposed research will focus on developing a novel approach to solve Software Service Evolution problems in Computing Clouds. The approach will support dynamic evolution of the software service in clouds via a set of discovered evolution patterns. An initial survey informed us that such an approach does not exist yet and is in urgent need. Evolution Requirement can be classified into evolution features; researchers can describe the whole requirement by using evolution feature typology, the typology will define the relation and dependency between each features. After the evolution feature typology has been constructed, evolution model will be created to make the evolution more specific. Aspect oriented approach can be used for enhance evolution feature-model modularity. Aspect template code generation technique will be used for model transformation in the end. Product Line Engineering contains all the essential components for driving the whole evolution process.