Finite element simulation of skeletal muscular structures obtained from images of histological serial sections

In this study, we present a method for the three-dimensional reconstruction of objects obtained from histological serial sections (exemplified by those of a pennate striated skeletal muscle) and its application to the finite element method. A hyperelastic material model is used for modeling biological soft tissue. The reconstruction process relies on the direct construction of a volumetric mesh using an octree approach which leads to a stable finite element method. Stability can be expressed in the spectral matrix condition number. To visualize stress patterns within the underlying anatomy the simulation results are projected onto images of the histological scenario.     

Half-sib mating structures

All ways in which all matings in a population can be between half-sibs under a generalization of regular systems of inbreeding are characterized for both finite and infinite populations. A model of random half-sib mating is developed and analyzed, and the asymptotic configuration of populations subject to it is described. The classical model of half-sib mating which ensues from the standard definition of regular systems of inbreeding is only one of many ways a population can propagate by half-sib mating, and a wide range of genetic identity is possible dependent on which half-sib mating structure governs a population.     

Pseudomorphic microbial structures

According to the recent data, carbonaceous chondrites occasionally have pseudomorphoses after microbes. The meteorite ages suggest that life had developed earlier than the Earth was formed.     

Potassium channel structures

The molecular basis of K+ channel function is universally conserved. K+ channels allow K+ flux and are essential for the generation of electric current across excitable membranes. K+ channels are also the targets of various intracellular control mechanisms, such that the suboptimal regulation of channel function might be related to pathological conditions. Because of the fundamental role of K+ channels in controlling membrane excitability, a structural understanding of their function and regulation will provide a useful framework for understanding neuronal physiology. Many recent physiological and crystallographic studies have led to new insights into the workings of K+ channels.     

GPCR structures in drug design,emerging opportunities with new structures

In recent years, GPCR targets from diverse regions of phylogenetic space have been determined. This effort has culminated this year in the determination of representatives of all major classes of GPCRs (A, B, C, and F). Although much of the now well established knowledge on GPCR structures has been known for some years, the new high-resolution structures allow structural insight into the causes of ligand efficacy, biased signaling, and allosteric modulation. In this digest the structural basis for GPCR signaling in the light of the new structures is reviewed and the use of the new non-class A GPCRs for drug design is discussed.     

Intrapopulational differences of genome structures in two structures of salmon-like fishes

The natural populations of salmon-like catadromous fishes usually include several percents of residual (dwarf) forms, which are 10-15 times smaller than normal forms. A comparative investigation of normal and residual forms in two species: Oncorhynchus nerka and Salvelinus malma (Salmoniformes order) was made by means of DNA molecular hybridization technique. The essential differences in reassociation kinetics was detected in DNA from normal and residual forms of both species. The genome sizes (kinetic complexity) of normal and residual forms are approximately the same. But some families of repetitive nucleotide sequences are represented by considerably different amount of copies. Intrapopulational differences of genome structures of normal and residual forms in both species seem to be more rough in respect to reassociation kinetic than corresponding interspecies differences between malma and nerka. Comparative analyses and reassociation kinetics for long and shrt DNA fragments imply "xenopus type" of nucleotide sequence organization in both species which is common for the majority of animal and plant genomes investigated.     

Finite populations choose an optimal language

This paper studies the evolution of a proto-language in a finite population under the frequency-dependent Moran process. A proto-language can be seen as a collection of concept-to-sign mappings. An efficient proto-language is a bijective mapping from objects of communication to used signs and vice versa. Based on the comparison of fixation probabilities, a method for deriving conditions of evolutionary stability in a finite population [Nowak et al., 2004. Emergence of cooperation and evolutionary stability in finite populations. Nature 428, 246-650], it is shown that efficient proto-languages are the only strategies that are protected by selection, which means that no mutant strategy can have a fixation probability that is greater than the inverse population size. In passing, the paper provides interesting results about the comparison of fixation probabilities as well as Maynard Smith's notion of evolutionary stability for finite populations [Maynard Smith, 1988. Can a mixed strategy be stable in a finite population? J. Theor. Biol. 130, 247-251] that are generally true for games with a symmetric payoff function.     

Finite element analysis of covered microstents

Currently available neuroendovascular devices are inadequate for effective treatment of many wide-necked or fusiform intracranial aneurysms and intracranial carotid-cavernous fistulae (CCF). Placing a covered microstent across the intracranial aneurysm neck and CCF rent could restore normal vessel morphology by preventing blood flow into the aneurysm lumen or CCF rent. To fabricate covered microstents, our research group has developed highly flexible ultra thin (approximately 150 microm) silicone coverings and elastomerically captured them onto commercially available metal stents without stitching. Preliminary in vivo studies were conducted by placing these covered microstents in the common carotid artery of rabbits. The feasibility of using covered stents was demonstrated. However, the cover affected the deployment pressure and the stents failed occasionally during deployment due to tearing of the cover. Appropriate modeling of covered stents will assist in designing suitable coverings, and help to reduce the failure rate of covered microstents. The purpose of this study is to use the finite element method to determine the mechanical properties of the covered microstent and investigate the effects of the covering on the mechanical behavior of the covered microstent. Variations in the mechanical properties of the covered microstent such as deployment pressure, elastic recoil and longitudinal shortening due to change in thickness and material properties of the cover have been investigated. This work is also important for custom design of covered microstents such as adding cutout holes to save adjacent perforating arteries.     

Pseudopeptides and beta folding: x-ray structures compared with structures in solution

In order to restrain the flexibility of the peptide molecules and reduce their biodegradation, modifications of the main chain are now introduced in pseudopeptide analogues. Surprisingly, there is very little data on the conformational properties of these derivatives. We have examined pseudopeptide analogues of RCO-X-Y-NHR' model dipeptides in the depsi, N-methylated, reduced, retro, alpha, beta-dehydro, beta-amino acid, and hydrazino series, in the solid state by x-ray diffraction, and in solution by ir and 1H-nmr spectroscopy. This study provides us with accurate dimensions of the peptide surrogates, and gives some information on the conformational tendencies induced by these substitutions, with reference to those of the related dipeptide sequences.     

Supramolecular structures in mycoplasmas

Mycoplasma pneumoniae cells treated with Triton X-100 showed a detergent-resistant cytoskeleton. This cytoskeleton consists of microfilaments which seem related to eukaryotic actin filaments, both morphologically and in some chemical properties, including specific staining by anti-actin antibodies and rhodamine-labeled phalloidin. The degree of homology, however, is still unclear. In motile cells the filaments form an irregular network in the cytoplasm of the cell body and a bundle in the frontal projection corresponding to the leading edge of the gliding cells. This particular arrangement may reflect different functions. The microfilaments could be isolated by differential centrifugation. Analysis of the microfilament fraction by SDS gel electrophoresis revealed five major polypeptide bands. One of these proteins, with a molecular weight of 42.5 kd, co-migrated with rabbit muscle actin. No filaments could be found in a nonmotile mutant, M-22.     

Experimentally determined lipocalin structures

Twelve structures of distinct members of the lipocalin protein family have been solved experimentally. These structures have revolutionised our understanding of the properties of the lipocalins. Many more members of the family have been crystallised and now await structure solution. The number of solved lipocalin structures is steadily increasing, and with it increases our knowledge of this enigmatic and challenging protein family.     

Well-defined secondary structures.

Molecules and assemblies of molecules with well-defined secondary structures have been designed and characterized by controlling noncovalent interactions. By specifying intermolecular interactions, a class of information-storing molecular duplexes have been successfully developed. These H-bonded molecular duplexes demonstrate programmable, sequence-specificity and predictable, tunable stabilities. Based on these highly specific molecular zippers (or glues), a systematic approach to designing self-assembled structures is now feasible. Duplex-directed formation of beta-sheets, block copolymers and templated organic reactions have been realized. By specifying intramolecular noncovalent interactions, a backbone-rigidification strategy has been established, leading to unnatural molecular strands that adopt well-defined, crescent or helical conformations. The generality of this backbone-rigidification strategy has been demonstrated in three different classes of unnatural oligomers: oligoaramides, oligoureas and oligo(phenylene ethynylenes). Large nanosized cavities have been created based on the folding of these helical foldamers. Tuning the size of the nanocavities has been achieved without changing the underlying helical topology. These helical foldamers can serve as novel platforms for the systematic design of nanostructures.     

Realization of dependency structures

In this paper we show how to construct block diagram realizations of a given dependency structure and investigate some elementary properties.