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At least 73 records · Page 4Linked to original sources
PubMed2005

Three-dimensional fiber-deposited PEOT/PBT copolymer scaffolds for tissue engineering: influence of porosity, molecular network mesh size, and swelling in aqueous media on dynamic mechanical properties.

Among novel scaffold fabrication techniques, 3D fiber deposition (3DF) has recently emerged as a means to fabricate well-defined and custom-made scaffolds for tissue regeneration, with 100% interconnected pores. The mechanical behavior of these constructs is dependent not only on different three-dimensional architectural and geometric features, but also on the intrinsic chemical properties of the material used. These affect the mechanics of the solid material and eventually of 3D porous constructs derived from them. For instance, poly(ethylene oxide terephthalate)-poly(butylene terephthalate) (PEOT/PBT) block copolymers are known to have mechanical properties, depending on the PEOT/PBT weight ratio in block form and on the molecular weight of the initial poly(ethylene glycol) (PEG) blocks. These differences are enhanced even more by their different swelling properties in aqueous media. Therefore, this article examines the influence of copolymer compositions in terms of their swelling on dynamic mechanical properties of solid material and porous 3DF scaffolds. The molecular weight of the starting PEG blocks used in the copolymer synthesis varied from 300 to 1000 g/mol. The PEOT/PBT weight ratio in the blocks used varied from 55/45 to 80/20. This corresponded to an increase of the swelling ratio Q from 1.06 to 2.46, and of the mesh size xi from approximately 9 Angstrom to approximately 47 Angstrom. With increased swelling, dynamic mechanical analysis (DMA) revealed a decrease in elastic response and an increase of viscoelasticity. Thus, by coupling structural and chemical characteristics, the viscoelastic properties of PEOT/PBT 3DF scaffolds may be fine tuned to achieve mechanical requirements for a variety of engineered tissues. Ultimately, the combination of 3DF and DMA may be useful to validate the hypothesis that mimicking the biomechanical behavior of a specific tissue for its optimal replacement is an important issue for at least some tissue-engineering applications.

Animals↗
PubMed2006

Two-dimensional porous molecular networks of dehydrobenzo[12]annulene derivatives via alkyl chain interdigitation.

The self-assembly of a series of hexadehydrotribenzo[12]annulene (DBA) derivatives has been scrutinized by scanning tunneling microscopy (STM) at the liquid-solid interface. First, the influence of core symmetry on the network structure was investigated by comparing the two-dimensional (2D) ordering of rhombic bisDBA 1a and triangular DBA 2a (Figure 1). BisDBA 1a forms a Kagomé network upon physisorption from 1,2,4-trichlorobenzene (TCB) onto highly oriented pyrolytic graphite (HOPG). Under similar experimental conditions, DBA 2a shows the formation of a honeycomb network. The core symmetry and location of alkyl substituents determine the network structure. The most remarkable feature of the DBA networks is the interdigitation of the nonpolar alkyl chains: they connect the pi-conjugated cores and direct their orientation. As a result, 2D open networks with voids are formed. Second, the effect of alkyl chain length on the structure of DBA patterns was investigated. Upon increasing the length of the alkyl chains (DBAs 3c-e) a transition from honeycomb networks to linear networks was observed in TCB, an observation attributed to stronger molecule-substrate interactions. Third, the effect of solvent on the structure of the nonpolar DBA networks was investigated in four different solvents: TCB as a polar aromatic solvent, 1-phenyloctane as a solvent having both aromatic and aliphatic moieties, n-tetradecane as an aliphatic solvent, and octanoic acid as a polar alkylated solvent. The solvent dramatically changes the structure of the DBA networks. The solvent effects are discussed in terms of factors that influence the mobility of molecules at the liquid-solid interface such as solvation.

Alkylation↗
PubMed2003

Molecular network and functional implications of macromolecular tRNA synthetase complex.

Understanding the complex network and multi-functionality of proteins is one of the main objectives of post-genome research. Aminoacyl-tRNA synthetases (ARSs) are the family of enzymes that are essential for cellular protein synthesis and viability that catalyze the attachment of specific amino acids to their cognate tRNAs. However, a lot of evidence has shown that these enzymes are multi-functional proteins that are involved in diverse cellular processes, such as tRNA processing, RNA splicing and trafficking, rRNA synthesis, apoptosis, angiogenesis, and inflammation. In addition, mammalian ARSs form a macromolecular complex with three auxiliary factors or with the elongation factor complex. Although the functional meaning and physiological significance of these complexes are poorly understood, recent data on the molecular interactions among the components for the multi-ARS complex are beginning to provide insights into the structural organization and cellular functions. In this review, the molecular mechanism for the assembly and functional implications of the multi-ARS complex will be discussed.

Amino Acyl-tRNA Synthetases↗
PubMed2006

Bifurcation and singularity analysis of a molecular network for the induction of long-term memory.

Withdrawal reflexes of the mollusk Aplysia exhibit sensitization, a simple form of long-term memory (LTM). Sensitization is due, in part, to long-term facilitation (LTF) of sensorimotor neuron synapses. LTF is induced by the modulatory actions of serotonin (5-HT). Pettigrew et al. developed a computational model of the nonlinear intracellular signaling and gene network that underlies the induction of 5-HT-induced LTF. The model simulated empirical observations that repeated applications of 5-HT induce persistent activation of protein kinase A (PKA) and that this persistent activation requires a suprathreshold exposure of 5-HT. This study extends the analysis of the Pettigrew model by applying bifurcation analysis, singularity theory, and numerical simulation. Using singularity theory, classification diagrams of parameter space were constructed, identifying regions with qualitatively different steady-state behaviors. The graphical representation of these regions illustrates the robustness of these regions to changes in model parameters. Because persistent protein kinase A (PKA) activity correlates with Aplysia LTM, the analysis focuses on a positive feedback loop in the model that tends to maintain PKA activity. In this loop, PKA phosphorylates a transcription factor (TF-1), thereby increasing the expression of an ubiquitin hydrolase (Ap-Uch). Ap-Uch then acts to increase PKA activity, closing the loop. This positive feedback loop manifests multiple, coexisting steady states, or multiplicity, which provides a mechanism for a bistable switch in PKA activity. After the removal of 5-HT, the PKA activity either returns to its basal level (reversible switch) or remains at a high level (irreversible switch). Such an irreversible switch might be a mechanism that contributes to the persistence of LTM. The classification diagrams also identify parameters and processes that might be manipulated, perhaps pharmacologically, to enhance the induction of memory. Rational drug design, to affect complex processes such as memory formation, can benefit from this type of analysis.

Algorithms↗
PubMed2003

Molecular networks controlling epithelial cell polarity in development.

During embryonic development, polarized epithelial cells are either formed during cleavage or formed from mesenchymal cells. Because the formation of epithelia during embryogenesis has to occur with high fidelity to ensure proper development, embryos allow a functional approach to study epithelial cell polarization in vivo. In particular, genetic model organisms have greatly advanced our understanding of the generation and maintenance of epithelial cell polarity. Many novel and important polarity genes have been identified and characterized in invertebrate systems, like Drosophila melanogaster and Caenorhabditis elegans. With the rapid identification of mammalian homologues of these invertebrate polarity genes, it has become clear that many important protein domains, single proteins and even entire protein complexes are evolutionarily conserved. It is to be expected that the field of epithelial cell polarity is just experiencing the 'top of the iceberg' of a large protein network that is fundamental for the specific adhesive, cell signalling and transport functions of epithelial cells.

Adherens Junctions↗
PubMed2001

The dynamics of molecular networks: applications to therapeutic discovery.

Recent advances in biomedical research, genomics and bioinformatics have given the pharmaceutical and biotechnology industries new promises and expectations: providing effective cures for complex diseases, discovering and prioritizing drug targets more efficiently, eliminating toxic and ineffective compounds earlier and delivering the right drug therapy to the appropriate patients. Ultimately, the biomedical information generated today must be transformed into integrated predictive models that can be consulted for decision-making in drug discovery, efficacy and toxicity screening and individualized therapy. Here we describe how models that capture different aspects of network dynamics can be generated and applied in disease pathway identification, drug screening, diagnostics and individualized therapy.

Journal Article↗
PubMed2005

Submaximal interpenetration and bicontinuous three-dimensional channels in porous molecular networks.

Crystallization of tetrakis(3,5-dihydroxyphenyl)silane (1) from various solvents produces structures built from interpenetrated hydrogen-bonded diamondoid networks. Crystals grown from hexane/methyl propiolate show 5-fold interpenetration, with no volume remaining for the inclusion of guests. In contrast, crystals grown from mixtures of hexane with ethyl acrylate, ethyl acetate, THF, or dioxolane all exhibit submaximal 3-fold interpenetration. Approximately 50% of the volumes are accessible to guests, which occupy regions of diamondoid topology that replace missing networks of tetraresorcinol 1. Of particular interest are crystals containing THF or dioxolane, in which guests occupy two independent systems of interpenetrating diamondoid channels. The submaximally interpenetrated structures of tetraresorcinol 1 provide detailed models of complex topologies adopted by block copolymers and amphiphilic assemblies to optimize interfacial contact.

Journal Article↗
PubMed2002

Second sphere supramolecular chirality: racemic hybrid H-bonded 2-D molecular networks.

Neutral hybrid 2-D networks have been generated using a bis-amidinium capable of chelating M(CN)6(3-) anions via hydrogen bonds: the packing of the achiral 2-D networks leads to channels which are occupied by water molecules forming polymeric H-bonded chains; furthermore, owing to the dihapto mode of H-bonding, the presence of supramolecular chirality of the delta' and lambda' types taking place within the second coordination sphere of the metallic centre has been demonstrated.

Journal Article↗
PubMed2004

Molecular tectonics: design of luminescent H-bonded molecular networks.

Using bis-amidinium dications as tetra H-bond donor tectons and Au(CN)(2)(-) anion, neutral 1-D networks based on a bis monohapto mode of H-bonding are obtained. Owing to the short metal-metal distance within the network, luminescent crystals are obtained. The emission phenomena may be tuned by the nature of the spacer connecting the two cyclic amidinium groups.

Journal Article↗
PubMed1998

A molecular network that produces spontaneous oscillations in excitable cells of Dictyostelium.

A network of interacting proteins has been found that can account for the spontaneous oscillations in adenylyl cyclase activity that are observed in homogenous populations of Dictyostelium cells 4 h after the initiation of development. Previous biochemical assays have shown that when extracellular adenosine 3',5'-cyclic monophosphate (cAMP) binds to the surface receptor CAR1, adenylyl cyclase and the MAP kinase ERK2 are transiently activated. A rise in the internal concentration of cAMP activates protein kinase A such that it inhibits ERK2 and leads to a loss-of-ligand binding by CAR1. ERK2 phosphorylates the cAMP phosphodiesterase REG A that reduces the internal concentration of cAMP. A secreted phosphodiesterase reduces external cAMP concentrations between pulses. Numerical solutions to a series of nonlinear differential equations describing these activities faithfully account for the observed periodic changes in cAMP. The activity of each of the components is necessary for the network to generate oscillatory behavior; however, the model is robust in that 25-fold changes in the kinetic constants linking the activities have only minor effects on the predicted frequency. Moreover, constant high levels of external cAMP lead to attenuation, whereas a brief pulse of cAMP can advance or delay the phase such that interacting cells become entrained.

3',5'-Cyclic-AMP Phosphodiesterases↗
PubMed2003

Pathway studio--the analysis and navigation of molecular networks.

SUMMARY: PathwayAssist is a software application developed for navigation and analysis of biological pathways, gene regulation networks and protein interaction maps. It comes with the built-in natural language processing module MedScan and the comprehensive database describing more than 100 000 events of regulation, interaction and modification between proteins, cell processes and small molecules. AVAILABILITY: PathwayAssist is available for commercial licensing from Ariadne Genomics, Inc. The light version with limited functionality will be available for free for academic users at www.ariadnegenomics.com/downloads/.

Database Management Systems↗
PubMed2004

Control of yeast filamentous-form growth by modules in an integrated molecular network.

On solid growth media with limiting nitrogen source, diploid budding-yeast cells differentiate from the yeast form to a filamentous, adhesive, and invasive form. Genomic profiles of mRNA levels in Saccharomyces cerevisiae yeast-form and filamentous-form cells were compared. Disparate data types, including genes implicated by expression change, filamentation genes known previously through a phenotype, protein-protein interaction data, and protein-metabolite interaction data were integrated as the nodes and edges of a filamentation-network graph. Application of a network-clustering method revealed 47 clusters in the data. The correspondence of the clusters to modules is supported by significant coordinated expression change among cluster co-member genes, and the quantitative identification of collective functions controlling cell properties. The modular abstraction of the filamentation network enables the association of filamentous-form cell properties with the activation or repression of specific biological processes, and suggests hypotheses. A module-derived hypothesis was tested. It was found that the 26S proteasome regulates filamentous-form growth.

Cell Cycle↗
PubMed2001

Maternal VegT is the initiator of a molecular network specifying endoderm in Xenopus laevis.

During cleavage stages, maternal VegT mRNA and protein are localized to the Xenopus embryo's vegetal region from which the endoderm will arise and where several zygotic gene transcripts will be localized. Previous loss-of-function experiments on this T-box transcription factor suggested a role for VegT in Xenopus endoderm formation. Here, we test whether VegT is required to initiate endoderm formation using a loss of function approach. We find that the endodermal genes, Bix1, Bix3, Bix4, Milk (Bix2), Mix.1, Mix.2, Mixer, Xsox17 alpha, Gata4, Gata5, Gata6 and endodermin, as well as the anterior endodermal genes Xhex and cerberus, and the organizer specific gene, Xlim1, are downstream of maternal VegT. We also find that the TGF beta s, Xnr1, Xnr2, Xnr4 and derrière rescue expression of these genes, supporting the idea that cell interactions are critical for proper endoderm formation. Additionally, inhibitory forms of Xnr2 and Derrière blocked the ability of VegT mRNA injection to rescue VegT-depleted embryos. Furthermore, a subset of endodermal genes was rescued in VegT-depleted vegetal masses by induction from an uninjected vegetal mass. Finally, we begin to establish a gene hierarchy downstream of VegT by testing the ability of Mixer and Gata5 to rescue the expression of other endodermal genes. These results identify VegT as the maternal regulator of endoderm initiation and illustrate the complexity of zygotic pathways activated by VegT in the embryo's vegetal region.

Animals↗