Differential Regulation of beta-1,3-Glucanase Messenger RNAs in Response to Pathogen Infection

The acidic, extracellular, glucan endo-1,3-β-glucosidases (EC 3.2.1.39; β-1,3-glucanases), pathogenesis-related proteins-2, -N, and -O (i.e. PR-2, PR-N, and PR-O) were purified from Nicotiana tabacum (tobacco) and their partial amino acid sequences determined. Based on these data, complementary DNA (cDNA) clones encoding the proteins were isolated. Additional cDNAs were isolated that encoded proteins approximately 90% identical with PR-2, PR-N, and PR-O. Although the proteins encoded by these cDNAs have not been identified, their deduced amino acid sequences have slightly basic or neutral calculated isoelectric points, as well as carboxy-terminal extensions. These physical characteristics are shared by the vacuolar form of β-1,3-glucanase and other vacuolar localized analogs of PR proteins, suggesting that the unidentified proteins may be similarly localized. A preliminary evolutionary model that separates the β-1,3-glucanase gene family from tobacco into at least five distinct subfamilies is proposed. The expression of β-1,3-glucanase messenger RNAs (mRNAs) in response to infection by tobacco mosaic virus was examined. Messages for the acidic glucanases were induced similarly to the mRNAs for other PR proteins. However, the basic glucanase showed a different response, suggesting that different isoforms are differentially regulated by tobacco mosaic virus infection at the mRNA level.     

Non-monotonic Response to Monotonic Stimulus: Regulation of Glyoxylate Shunt Gene-Expression Dynamics in Mycobacterium tuberculosis

Understanding how dynamical responses of biological networks are constrained by underlying network topology is one of the fundamental goals of systems biology. Here we employ monotone systems theory to formulate a theorem stating necessary conditions for non-monotonic time-response of a biochemical network to a monotonic stimulus. We apply this theorem to analyze the non-monotonic dynamics of the σ^B-regulated glyoxylate shunt gene expression in Mycobacterium tuberculosis cells exposed to hypoxia. We first demonstrate that the known network structure is inconsistent with observed dynamics. To resolve this inconsistency we employ the formulated theorem, modeling simulations and optimization along with follow-up dynamic experimental measurements. We show a requirement for post-translational modulation of σ^B activity in order to reconcile the network dynamics with its topology. The results of this analysis make testable experimental predictions and demonstrate wider applicability of the developed methodology to a wide class of biological systems.     

Frequency Response of a Protein to Local Conformational Perturbations

Signals created by local perturbations are known to propagate long distances through proteins via backbone connectivity and nonbonded interactions. In the current study, signal propagation from the flexible ligand binding loop to the rest of Protein Tyrosine Phosphatase 1B (PTP1B) was investigated using frequency response techniques. Using restrained Targeted Molecular Dynamics (TMD) potential on WPD and R loops, PTP1B was driven between its crystal structure conformations at different frequencies. Propagation of the local perturbation signal was manifested via peaks at the fundamental frequency and upper harmonics of 1/f distributed spectral density of atomic variables, such as C_α atoms, dihedral angles, or polar interaction distances. Frequency of perturbation was adjusted high enough (simulation length >∼10×period of a perturbation cycle) not to be clouded by random diffusional fluctuations, and low enough (<∼0.8 ns⁻¹) not to attenuate the propagating signal and enhance the contribution of the side-chains to the dissipation of the signals. Employing Discrete Fourier Transform (DFT) to TMD simulation trajectories of 16 cycles of conformational transitions at periods of 1.2 to 5 ns yielded C_α displacements consistent with those obtained from crystal structures. Identification of the perturbed atomic variables by statistical t-tests on log-log scale spectral densities revealed the extent of signal propagation in PTP1B, while phase angles of the filtered trajectories at the fundamental frequency were used to cluster collectively fluctuating elements. Hydrophobic interactions were found to have a higher contribution to signal transduction between side-chains compared to the role of polar interactions. Most of in-phase fluctuating residues on the signaling pathway were found to have high identity among PTP domains, and located over a wide region of PTP1B including the allosteric site. Due to its simplicity and efficiency, the suggested technique may find wide applications in identification of signaling pathways of different proteins.     

基于脉冲扰动作用下的一个捕食者-食饵模型的动力学性质

基于害虫的生物控制和化学控制策略,考虑到化学杀虫剂对天敌的影响,利用脉冲微分方程建立了在不同的固定时刻分别喷洒杀虫剂和释放天敌的具有依氏(Ivlev)功能性反应的捕食者-食饵脉冲动力系统．证明了当脉冲周期小于某个临界值时,系统存在一个渐近稳定的害虫根除周期解,否则系统是持续生存的．通过分析表明如果采取有效的化学控制策略,那么这种综害虫合控制策略更有效．     

Dynamics to Equilibrium in Network Games: Individual Behavior and Global Response

Various social contexts can be depicted as games of strategic interactions on networks, where an individual’s welfare depends on both her and her partners’ actions. Whereas much attention has been devoted to Bayes-Nash equilibria in such games, here we look at strategic interactions from an evolutionary perspective. To this end, we present the results of a numerical simulations program for these games, which allows us to find out whether Nash equilibria are accessible by adaptation of player strategies, and in general to identify the attractors of the evolution. Simulations allow us to go beyond a global characterization of the cooperativeness at equilibrium and probe into individual behavior. We find that when players imitate each other, evolution does not reach Nash equilibria and, worse, leads to very unfavorable states in terms of welfare. On the contrary, when players update their behavior rationally, they self-organize into a rich variety of Nash equilibria, where individual behavior and payoffs are shaped by the nature of the game, the social network’s structure and the players’ position within the network. Our results allow to assess the validity of mean-field approaches we use to describe the dynamics of these games. Interestingly, our dynamically-found equilibria generally do not coincide with (but show qualitatively the same features of) those resulting from theoretical predictions in the context of one-shot games under incomplete information.     

番茄响应生物胁迫相关miRNA的研究进展

mi RNA(micro RNA)是一类长约22 nt的非编码小RNA分子,参与植物生长发育和胁迫响应等过程。近年来,通过生物学实验和生物信息学预测两种方法,陆续发现了一些响应病毒、真菌和共生真菌胁迫的番茄mi RNA。这些mi RNA的研究以及ami RNA(artificial mi RNA)技术的应用,将为番茄乃至其他植物病害的防治提供新的契机。     

Regulation of heterochromatin by histone methylation and small RNAs

Heterochromatin mediates various nuclear processes including centromere function, gene silencing and nuclear organization. Although it was discovered nearly 75 years ago, the pathways involved in heterochromatin establishment, assembly and epigenetic maintenance have been elusive. Recent reports have demonstrated that distinct and novel chromatin-associated factors, including DNA, RNA and histone modifications, are involved in each of these events. These new findings define a novel conserved mechanism of heterochromatin formation that is likely to have an impact on all eukaryotic silencing pathways.     

Metabolic Regulation of Brain Response to Food Cues

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Dynamics of the Microbiota in Response to Host Infection

Longitudinal studies of the microbiota are important for discovering changes in microbial communities that affect the host. The complexity of these ecosystems requires rigorous integrated experimental and computational methods to identify temporal signatures that promote physiologic or pathophysiologic responses in vivo. Employing a murine model of infectious colitis with the pathogen Citrobacter rodentium, we generated a 2-month time-series of 16S rDNA gene profiles, and quantitatively cultured commensals, from multiple intestinal sites in infected and uninfected mice. We developed a computational framework to discover time-varying signatures for individual taxa, and to automatically group signatures to identify microbial sub-communities within the larger gut ecosystem that demonstrate common behaviors. Application of this model to the 16S rDNA dataset revealed dynamic alterations in the microbiota at multiple levels of resolution, from effects on systems-level metrics to changes across anatomic sites for individual taxa and species. These analyses revealed unique, time-dependent microbial signatures associated with host responses at different stages of colitis. Signatures included a Mucispirillum OTU associated with early disruption of the colonic surface mucus layer, prior to the onset of symptomatic colitis, and members of the Clostridiales and Lactobacillales that increased with successful resolution of inflammation, after clearance of the pathogen. Quantitative culture data validated findings for predominant species, further refining and strengthening model predictions. These findings provide new insights into the complex behaviors found within host ecosystems, and define several time-dependent microbial signatures that may be leveraged in studies of other infectious or inflammatory conditions.     

Effect of Hawk-Dove Game on the Dynamics of Two Competing Species

Outcomes of interspecific competition, and especially the possibility of coexistence, have been extensively studied in theoretical ecology because of their implications in community assemblages. During the last decades, the influence of different time scales through the local/regional dynamics of animal communities has received an increasing attention. Nevertheless, different time scales involved in interspecific competition can result form other processes than spatial dynamics. Here, we envision and analyze a new theoretical framework that couples a game theory approach for competition with a demographic model. We take advantage of these two time scales to derive a reduced model governing the total densities of the two populations and we study how these two time scales interfere and influence outcomes of species competition. We find that a competition process occurring on a faster time scale than demography yields a “priority effect” where the first species introduced outcompetes the other one. We then confirm previous findings stipulating that species coexistence is favored by large difference in time scales because the extinction/recolonization process. Our results then highlight that an integration of demographic and competition time scales at both local and regional levels is mandatory to explain communities assemblages and should become a research priority.     

Regulation of gene expression by trans-encoded antisense RNAs

Members of a class of antisense RNAs are encoded by genes that are located at loci other than those of their target genes. Three examples of antisense RNA genes are discussed here. micF is found in Escherichia coli and other bacteria and functions to control outer membrane protein F levels in response to environmental stimuli. dicF is also found in E. coli and is involved in the regulation of cell division, lin-4 is found in the nematode Caenorhabditis elegans and functions during larval development. Nucleotide sequences of at least two of these genes appear to be phylogenetically conserved. The trans-encoded antisense RNAs are small RNAs which display only partial complementarity to their target RNAs. Models for RNA/RNA interactions have been proposed. It is possible that currently known unlinked antisense RNA genes are part of a larger class of heretofore undiscovered regulatory RNA genes. Possible ways of detecting other unlinked antisense RNA genes are discussed.