Shaping dots and lines: adding modularity into protein interaction networks using structural information

Determining protein interaction networks and generating models to simulate network changes in time and space are crucial for understanding a biological system and for predicting the effect of mutants found in diseases. In this review we discuss the great potential of using structural information together with computational tools towards reaching this goal: the prediction of new protein interactions, the estimation of affinities and kinetic rate constants between protein complexes, and finally the determination of which interactions are compatible with each other and which interactions are exclusive. The latter one will be important to reorganize large scale networks into functional modular networks.     

激活FXR抑制结肠癌细胞浸润转移及MMP-7的表达

目的:探讨法尼酯X受体(FXR)特异性激动剂GW4064抑制结肠癌细胞浸润转移的机制。方法:在体外培养人结肠癌细胞HT-29,应用GW4064作用于结肠癌细胞,以四唑氮蓝还原法(MTT)检测细胞活性的变化。用transwell小室研究结肠癌细胞的迁移及浸润。用RT-PCR检测FXRm RNA及MMP-7mRNA表达的变化,用western blot检测FXR及MMP-7蛋白表达的变化。结果:MTT结果显示GW4064作用于人结直肠HT-29细胞的生长抑制率呈浓度依赖性;transwell小室结果显示GW4064抑制结肠癌细胞的浸润转移,与对照组相比,差异具有统计学意义(P0.05),RT-PCR及Western blot显示GW4064促进FXR m RNA及蛋白表达,抑制MMP-7mRNA及蛋白的表达,与对照组相比差异有统计学意义(P0.05)。结论:GW4064抑制结肠癌细胞的生长及转移,上调HT-29细胞FXR m RNA及蛋白的表达,下调HT-29细胞MMP-7 m RNA及蛋白的表达。FXR被激活后抑制结肠癌细胞转移,MMP-7可能是其作用通路之一。     

Induction of adhesion-dependent signals using low-intensity ultrasound

In multicellular organisms, cell behavior is dictated by interactions with the extracellular matrix. Consequences of matrix-engagement range from regulation of cell migration and proliferation, to secretion and even differentiation. The signals underlying each of these complex processes arise from the molecular interactions of extracellular matrix receptors on the surface of the cell. Integrins are the prototypic receptors and provide a mechanical link between extracellular matrix and the cytoskeleton, as well as initiating some of the adhesion-dependent signaling cascades. However, it is becoming increasingly apparent that additional transmembrane receptors function alongside the integrins to regulate both the integrin itself and signals downstream. The most elegant of these examples is the transmembrane proteoglycan, syndecan-4, which cooperates with α(5)β(1)-integrin during adhesion to fibronectin. In vivo models demonstrate the importance of syndecan-4 signaling, as syndecan-4-knockout mice exhibit healing retardation due to inefficient fibroblast migration. In wild-type animals, migration of fibroblasts toward a wound is triggered by the appearance of fibronectin that leaks from damaged capillaries and is deposited by macrophages in injured tissue. Therefore there is great interest in discovering strategies that enhance fibronectin-dependent signaling and could accelerate repair processes. The integrin-mediated and syndecan-4-mediated components of fibronectin-dependent signaling can be separated by stimulating cells with recombinant fibronectin fragments. Although integrin engagement is essential for cell adhesion, certain fibronectin-dependent signals are regulated by syndecan-4. Syndecan-4 activates the Rac1 protrusive signal, causes integrin redistribution, triggers recruitment of cytoskeletal molecules, such as vinculin, to focal adhesions, and thereby induces directional migration. We have looked for alternative strategies for activating such signals and found that low-intensity pulsed ultrasound (LIPUS) can mimic the effects of syndecan-4 engagement. In this protocol we describe the method by which 30 mW/cm(2), 1.5 MHz ultrasound, pulsed at 1 kHz (Fig. 1) can be applied to fibroblasts in culture (Fig. 2) to induce Rac1 activation and focal adhesion formation. Ultrasound stimulation is applied for a maximum of 20 minutes, as this combination of parameters has been found to be most efficacious for acceleration of clinical fracture repair. The method uses recombinant fibronectin fragments to engage α(5)β(1)-integrin, without engagement of syndecan-4, and requires inhibition of protein synthesis by cycloheximide to block deposition of additional matrix by the fibroblasts. The positive effect of ultrasound on repair mechanisms is well documented, and by understanding the molecular effect of ultrasound in culture we should be able to refine the therapeutic technique to improve clinical outcomes.     

Probabilistic methods for addressing uncertainty and variability in biological models: application to a toxicokinetic model

Population variability and uncertainty are important features of biological systems that must be considered when developing mathematical models for these systems. In this paper we present probability-based parameter estimation methods that account for such variability and uncertainty. Theoretical results that establish well-posedness and stability for these methods are discussed. A probabilistic parameter estimation technique is then applied to a toxicokinetic model for trichloroethylene using several types of simulated data. Comparison with results obtained using a standard, deterministic parameter estimation method suggests that the probabilistic methods are better able to capture population variability and uncertainty in model parameters.     

Increased number of Arginine-based salt bridges contributes to the thermotolerance of thermotolerant acetic acid bacteria, Acetobacter tropicalis SKU1100

Thermotolerant acetic acid bacteria (AAB), Acetobacter tropicalis SKU1100, can grow above 40 °C. To investigate the basis of its thermotolerance, we compared the genome of A. tropicalis SKU1100 with that of mesophilic AAB strain Acetobacter pasteurianus IFO3283-01. The comparative genomic study showed that amino acid substitutions from large to small residue and Lys to Arg occur in many orthologous genes. Furthermore, comparative modeling study was carried out with the orthologous proteins between SKU1100 and IFO3283-01 strains, indicating that the number of Arg-based salt bridges increased in protein models. Since it has been reported that Arg-based salt bridges are important factor for thermo-stability of protein structure, our results strongly suggest that the increased number of Arg-based salt bridges may contributes to the thermotolerance of A. tropicalis SKU1100 (the thermo-stability of proteins in A. tropicalis SKU1100).     

Predicting impacts of climate change on habitat connectivity of Kalopanax septemlobus in South Korea

Understanding the drivers of habitat distribution patterns and assessing habitat connectivity are crucial for conservation in the face of climate change. In this study, we examined a sparsely distributed tree species, Kalopanax septemlobus (Araliaceae), which has been heavily disturbed by human use in temperate forests of South Korea. We used maximum entropy distribution modeling (MaxEnt) to identify the climatic and topographic factors driving the distribution of the species. Then, we constructed habitat models under current and projected climate conditions for the year 2050 and evaluated changes in the extent and connectivity of the K. septemlobus habitat. Annual mean temperature and terrain slope were the two most important predictors of species distribution. Our models predicted the range shift of K. septemlobus toward higher elevations under medium-low and high emissions scenarios for 2050, with dramatic reductions in suitable habitat (51% and 85%, respectively). In addition, connectivity analysis indicated that climate change is expected to reduce future levels of habitat connectivity. Even under the Representative Construction Pathway (RCP) 4.5 medium-low warming scenario, the projected climate conditions will decrease habitat connectivity by 78%. Overall, suitable habitats for K. septemlobus populations will likely become more isolated depending on the severity of global warming. The approach presented here can be used to efficiently assess species and habitat vulnerability to climate change.