Copying nodes versus editing links: the source of the difference between genetic regulatory networks and the WWW. (41/499)

We study two kinds of networks: genetic regulatory networks and the World Wide Web. We systematically test microscopic mechanisms to find the set of such mechanisms that optimally explain each networks' specific properties. In the first case we formulate a model including mainly random unbiased gene duplications and mutations. In the second case, the basic moves are website generation and rapid surf-induced link creation (/destruction). The different types of mechanisms reproduce the appropriate observed network properties. We use those to show that different kinds of networks have strongly system-dependent macroscopic experimental features. The diverging properties result from dissimilar node and link basic dynamics. The main non-uniform properties include the clustering coefficient, small-scale motifs frequency, time correlations, centrality and the connectivity of outgoing links. Some other features are generic such as the large-scale connectivity distribution of incoming links (scale-free) and the network diameter (small-worlds). The common properties are just the general hallmark of autocatalysis (self-enhancing processes), while the specific properties hinge on the specific elementary mechanisms. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.  (+info)

Expeditious syntheses of conjugated allenyl esters and oxazoles through a cascade reaction of alpha-alkynyl malonates under alkaline conditions. (42/499)

Diethyl alpha-alkynyl-alpha-methoxymalonates (2a--e) were smoothly hydrolyzed and then decarboxylated under alkaline conditions employing 1 N KOH in EtOH to give conjugated allenyl esters (6a--e) in high yields, and similar alkaline treatment of diethyl alpha-alkynyl-alpha-acetylaminomalonates (5a, b, d, e) furnished unexpectedly the oxazoles (7a, b, d, e) having three substituent groups in excellent yields.  (+info)

Phospholipid vesicle fusion on micropatterned polymeric bilayer substrates. (43/499)

As an approach to create versatile model systems of the biological membrane we have recently developed a novel micropatterning strategy of substrate-supported planar lipid bilayers (SPBs) based on photolithographic polymerization of a diacetylene phospholipid, 1,2-bis(10,12-tricosadiynoyl)-sn-glycero-3-phosphocholine. The micropatterned SPBs are composed of a polymeric bilayer matrix and embedded fluid lipid bilayers. In this study, we investigated the incorporation of fluid bilayers into micropatterned polymeric bilayer matrices through the adsorption and reorganization of phospholipid vesicles (vesicle fusion). Total internal reflection fluorescence microscopy observation showed that vesicle fusion started at the boundary of polymeric bilayers and propagated into the central part of lipid-free regions. On the other hand, quartz crystal microbalance with dissipation monitoring revealed that the transformation from adsorbed vesicles into SPBs was significantly accelerated for substrates with micropatterned polymeric bilayers. These results indicate that the edges of polymeric bilayers catalyze the formation of SPBs by destabilizing adsorbed vesicles and also support the premise that polymeric bilayers and embedded fluid bilayers are forming a continuous hybrid bilayer membrane, sealing energetically unfavorable bilayer edges.  (+info)

Biomimetics: its practice and theory. (44/499)

Biomimetics, a name coined by Otto Schmitt in the 1950s for the transfer of ideas and analogues from biology to technology, has produced some significant and successful devices and concepts in the past 50 years, but is still empirical. We show that TRIZ, the Russian system of problem solving, can be adapted to illuminate and manipulate this process of transfer. Analysis using TRIZ shows that there is only 12% similarity between biology and technology in the principles which solutions to problems illustrate, and while technology solves problems largely by manipulating usage of energy, biology uses information and structure, two factors largely ignored by technology.  (+info)

Hydrophobic alpha-helices 1 and 2 of herpes simplex virus gH interact with lipids, and their mimetic peptides enhance virus infection and fusion. (45/499)

Entry of herpes simplex virus into cells occurs by fusion and requires four glycoproteins. gD serves as the receptor binding glycoprotein. Of the remaining glycoproteins, gH carries structural and functional elements typical of class 1 fusion glycoproteins, in particular alpha-helix 1 (alpha-H1), with properties of a candidate fusion peptide, and two heptad repeats. Here, we characterized alpha-H2 and compared it to alpha-H1. alpha-H2 (amino acids 513 to 531) is of lower hydrophobicity than alpha-H1. Its deletion or mutation decreased virus infection and cell fusion. Its replacement with heterologous fusion peptides did not rescue infection and cell fusion beyond the levels exhibited by the alpha-H2-deleted gH. This contrasts with alpha-H1, which cannot be deleted and can be functionally replaced with heterologous fusion peptides (T. Gianni et al., J. Virol. 79:2931-2940, 2005). Synthetic peptides mimicking alpha-H1 and alpha-H2 induced fusion of nude lipid vesicles. Importantly, they increased infection of herpes simplex virus, pseudorabies virus, bovine herpesvirus 1, and vesicular stomatitis virus. The alpha-H1 mimetic peptide was more effective than the alpha-H2 peptide. Consistent with the findings that gH carries membrane-interacting segments, a soluble form of gH, but not of gD or gB, partitioned with lipid vesicles. Current findings highlight that alpha-H2 is an important albeit nonessential region for virus entry and fusion. alpha-H1 and alpha-H2 share the ability to target the membrane lipids; they contribute to virus entry and fusion, possibly by destabilizing the membranes. However, alpha-H2 differs from alpha-H1 in that it is of lower hydrophobicity and cannot be replaced with heterologous fusion peptides.  (+info)

Towards synthesis of a minimal cell. (46/499)

Construction of a chemical system capable of replication and evolution, fed only by small molecule nutrients, is now conceivable. This could be achieved by stepwise integration of decades of work on the reconstitution of DNA, RNA and protein syntheses from pure components. Such a minimal cell project would initially define the components sufficient for each subsystem, allow detailed kinetic analyses and lead to improved in vitro methods for synthesis of biopolymers, therapeutics and biosensors. Completion would yield a functionally and structurally understood self-replicating biosystem. Safety concerns for synthetic life will be alleviated by extreme dependence on elaborate laboratory reagents and conditions for viability. Our proposed minimal genome is 113 kbp long and contains 151 genes. We detail building blocks already in place and major hurdles to overcome for completion.  (+info)

Melanin and Glycera jaws: emerging dark side of a robust biocomposite structure. (47/499)

Defining the design principles guiding the fabrication of superior biocomposite structures from an assemblage of ordinary molecules is a key goal of biomimetics. Considering their low degree of mineralization, Glycera jaws have been shown to be extraordinarily resistant to abrasion based on the metric hardness3/Young's modulus2. The jaws also exhibit an impressive chemical inertness withstanding boiling concentrated hydrochloric acid as well as boiling concentrated sodium hydroxide. A major organic component largely responsible for the chemical inertness of the jaws has been characterized using a spectrophotometric assay for melanin content, 13C solid state nuclear magnetic resonance, IR spectroscopy, and laser desorption ionization-time of flight mass spectrometry and is identified here as a melanin-like network. Although melanin is widely distributed as a pigment in tissues and other structural biomaterials, to our knowledge, Glycera jaws represent the first known integument to exploit melanin as a cohesive load- and shape-bearing material.  (+info)

Mapping information flow in sensorimotor networks. (48/499)

Biological organisms continuously select and sample information used by their neural structures for perception and action, and for creating coherent cognitive states guiding their autonomous behavior. Information processing, however, is not solely an internal function of the nervous system. Here we show, instead, how sensorimotor interaction and body morphology can induce statistical regularities and information structure in sensory inputs and within the neural control architecture, and how the flow of information between sensors, neural units, and effectors is actively shaped by the interaction with the environment. We analyze sensory and motor data collected from real and simulated robots and reveal the presence of information structure and directed information flow induced by dynamically coupled sensorimotor activity, including effects of motor outputs on sensory inputs. We find that information structure and information flow in sensorimotor networks (a) is spatially and temporally specific; (b) can be affected by learning, and (c) can be affected by changes in body morphology. Our results suggest a fundamental link between physical embeddedness and information, highlighting the effects of embodied interactions on internal (neural) information processing, and illuminating the role of various system components on the generation of behavior.  (+info)