Finite-time Lyapunov exponents and metabolic control coefficients for threshold detection of stimulus–response curves

In biochemical networks transient dynamics plays a fundamental role, since the activation of signalling pathways is determined by thresholds encountered during the transition from an initial state (e.g. an initial concentration of a certain protein) to a steady-state. These thresholds can be defined in terms of the inflection points of the stimulus–response curves associated to the activation processes in the biochemical network. In the present work, we present a rigorous discussion as to the suitability of finite-time Lyapunov exponents and metabolic control coefficients for the detection of inflection points of stimulus–response curves with sigmoidal shape.     

Effect of external stresses on protein conformation: a computer modelling study

The increasing use of digital technologies such as mobile phones has led to major health concerns about the effects of non-ionizing pulsed radiation exposure. We believe that the health implications of exposure to radiation cannot be fully understood without establishing the molecular mechanisms of biological effects of pulsed microwaves. We aim to establish methods for studying the molecular mechanisms of protein structural and energetic changes occurring due to external stresses related to non-ionizing radiation by using a combination of experimental and theoretical approaches. In this paper, we present the results from our fully atomistic simulation study of chemical and thermal stress response of a prototype protein, insulin. We performed a series of molecular dynamics simulations of insulin in solution under equilibrium conditions, under chemical stress (imitated by reducing the disulfide bonds in the protein molecule), and under short-lived thermal stress (imitated by increasing simulation temperature for up to 2 ns). The resultant protein conformational behaviour was analysed for various properties with the aim of establishing analysis routines for classification of protein unfolding pathways and associated molecular mechanisms.Submitted as a record of the 2002 Australian Biophysical Society meeting     

水溶性有机物对水田土壤中水溶性氮磷含量及其利用率的影响

采用田间微区试验,研究了施用有机物料对土壤氮磷的变化动态及活性的影响.结果表明,水稻生长过程中土壤溶液中水溶性氮（铵态氮、硝态氮）及磷的含量都随着时间的延长而下降,且氮、磷含量的变化与施入的化学肥料量以及溶液中DOC含量有关;有机物料施用增加了水稻的生物量和对氮、磷的吸收利用;15N示踪显示,与对照的化肥处理相比,施用有机物料处理的微区氮肥利用率及土壤残留率明显增加,同时减少了土壤氮磷的损失.     

两种品系油菜植株成分与蚜虫种群消长及成蚜翅型的关系

本文研究两种品系油菜植株成分与桃蚜(Myzus persicae(Sulzer))、萝卜蚜(Lipaphis erysimi(Kaltenbach))的种群消长及成蚜翅型的关系.经分析得出如下结果:1.桃蚜种群消长与苏氨酸、赖氨酸、组氨酸、丙氨酸、硬脂酸等含量有关;桃蚜成蚜无翅率与精氨酸、谷氨酸、酪氨酸、异亮氨酸等含量有关.2.萝卜蚜种群消长与苏氨酸、蛋氨酸、异亮氨酸、苯丙氨酸、酪氨酸、含水量有关;萝卜蚜成蚜无翅率与含水量.亚麻酸.苏氨酸、油酸,天门冬氨酸、丝氯酸、亚油酸等含量有关.     

Determination of the structural ensemble of the molten globule state of a protein by computer simulations

We have used computer simulations to investigate the structural nature of the molten globule (MG) state of canine milk lysozyme. To sample the conformational space efficiently, we performed replica-exchange umbrella sampling simulations with the radius of gyration as a reaction coordinate. We applied the Weighted Histogram Analysis Method to the trajectory of the simulations to obtain the potential of mean force, from which we identified representative structures corresponding to local minima in the free energy surface. The representative structures obtained in this way are in accord with the characteristics of the MG state reported previously by experimental studies. We conjecture that the MG state comprises a series of partially structured states undergoing relatively fast conformational interchange.     

High Conformational Variability in the GluK2 Kainate Receptor Ligand-Binding Domain

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In silico epitope-based vaccine design against influenza a neuraminidase protein: Computational analysis established on B- and T-cell epitope predictions

ObjectiveInfluenza A virus belongs to the most studied virus and its mutant initiates epidemic and pandemics outbreaks. Inoculation is the significant foundation to diminish the risk of infection. To prevent an incidence of influenza from the transmission, various practical approaches require more advancement and progress. More efforts and research must take in front to enhance vaccine efficacy.MethodsThe present research emphasizes the development and expansion of a universal vaccine for the influenza virus. Research focuses on vaccine design with high efficacy. In this study, numerous computational approaches were used, covering a wide range of elements and ideas in bioinformatics methodology. Various B and T-cell epitopic peptides derived from the Neuraminidase protein N1 are recognized by these approaches. With the implementation of numerous obtained databases and bioinformatics tools, the different immune framework methods of the conserved sequences of N1 neuraminidase were analyzed. NCBI databases were employed to retrieve amino acid sequences. The antigenic nature of the neuraminidase sequence was achieved by the VaxiJen server and Kolaskar and Tongaonkar method. After screening of various B and T cell epitopes, one efficient peptide each from B cell epitope and T cell epitopes was assessed for their antigenic determinant vaccine efficacy. Identical two B cell epitopes were recognized from the N1 protein when analyzed using B-cell epitope prediction servers. The detailed examination of amino acid sequences for interpretation of B and T cell epitopes was achieved with the help of the ABCPred and Immune Epitope Database.ResultsComputational immunology via immunoinformatic study exhibited RPNDKTG as having its high conservancy efficiency and demonstrated as a good antigenic, accessible surface hydrophilic B-cell epitope. Among T cell epitope analysis, YVNISNTNF was selected for being a conserved epitope. T cell epitope was also analyzed for its allergenicity and cytotoxicity evaluation. YVNISNTNF epitope was found to be a non-allergen and not toxic for cells as well. This T-cell epitope with maximum world populace coverages was scrutinized for its association with the HLA-DRB1*0401 molecule. Results from docking simulation analyses showed YVNISNTNF having lower binding energy, the radius of gyration (Rg), RMSD values, and RMSE values which make the protein structure more stable and increase its ability to become an epitopic peptide for influenza virus vaccination.ConclusionsWe propose that this epitope analysis may be successfully used as a measurement tool for the robustness of an antigen–antibody reaction between mutant strains in the annual design of the influenza vaccine.     

Integrated computational approaches to screen gene expression data to determine key genes and therapeutic targets for type-2 diabetes mellitus

There is a rapid rise in cases of Type-2-diabetes mellitus (T2DM) globally, irrespective of the geography, ethnicity or any other variable factors. The molecular mechanisms that could cause the condition of T2DM need to be more thoroughly analysed to understand the clinical manifestations and to derive better therapeutic regimes. Tools in bioinformatics are used to trace out key gene elements and to identify the key causative gene elements and their possible therapeutic agents. Microarray datasets were retrieved from the Gene expression omnibus database and studied using R to derive different expressed gene (DEG) elements. With the comparison of the expressed genes with disease specific genes in DisGeNET, the final annotated genes were taken for analysis. Gene Ontology studies, Protein–protein interaction (PPI), Co-expression analysis, Gene-drug interactions were performed to scale down the hub genes and to identify the novelty across the genes analysed so far. In vivo and invitro analysis of key genes and the trace of interaction pathway is crucial to better understand the unique outcomes from the novel genes, forming the basis to understand the pathway that ends up causing T2DM. Afterwards, docking was executed enabling recognition of interacting residues involved in inhibition. The complex CCL5-265 and CD8A-40585 thus docked showed best results as is evident from its PCA analysis and MMGBSA calculation. There is now scope for deriving candidate drugs that could possibly detect personalized therapies for T2DM.     

用转基因棉籽作平菇培养料时平菇主要害虫的发生动态

为了评估转基因棉籽对平菇害虫发生的影响,利用转Bt基因棉籽及其亲本对照棉籽配制平菇培养的菌棒,在菇棚中自然感虫,观察了平菇厉眼菌蚊、粪蚊、蚤蝇和螨类的发生情况。结果表明,含对照棉籽菌棒中平菇厉眼菌蚊和螨类发生量高于含转基因棉籽菌棒, 随着棉籽浓度的增加,对照棉和转Bt基因棉对平菇厉眼菌蚊均表现出抑制作用。对照棉籽对粪蚊的抑制作用比转Bt基因棉籽强,但随着棉籽浓度的增加,含对照棉籽菌棒中粪蚊发生量呈递增趋势。随着棉籽浓度的增加,含对照棉籽菌棒中蚤蝇发生量呈递增趋势,含转Bt基因棉籽菌棒中蚤蝇发生量递减;低含量时对照棉籽对蚤蝇的抑制作用强,而高含量时转Bt基因棉籽对蚤蝇的抑制作用强。