The fin musculature of cuttlefish and squid (Mollusca, Cephalopoda): morphology and mechanics

The lateral fins of cuttlefish and squid consist of a tightly packed three-dimensional array of musculature that lacks bony skeletal support or fluid-filled cavities for hydrostatic skeletal support. During swimming and manoeuvring, the fins are bent upward and downward in undulatory waves. The fin musculature is arranged in three mutually perpendicular planes. Transverse muscle bundles extend parallel to the fin surface from the base of the fin to the fin margin. Dorso-ventral muscle bundles extend from dorsal and ventral connective tissue fasciae to a median connective tissue fascia. A layer of longitudinal muscle bundles is situated adjacent to both the dorsal and ventral surface of the median fascia. The muscle fibres are obliquely striated and include a core of mitochondria. A zone of muscle fibres with a more extensive core of mitochondria is present in both the dorsal and the ventral transverse muscle bundles. It is hypothesized that these muscle masses include two fibre types with different aerobic capacity. A network of connective tissue fibres is present in the transverse and dorso-ventral muscle masses. These fibres, probably collagen, are oriented at 45 to the long axes of the transverse and dorsoventral muscle fibres in transverse planes.
A biomechanicayl analysis of the morphology suggests that support for fin movements is provided by simultaneous contractile activity of muscles of specific orientations in a manner similar to that proposed for other 'muscular-hydrostats'. The musculature therefore provides both the force and support for movement. Connective tissue fibres may aid in providing support and may also serve for elastic energy storage.     

Distributed sensory coding applied to simulations of iconic storage and metacontrast

If information is coded in the combination of activities of many neurons operating in parallel, then information present in a network can be defined by the correlation of present network activity with the activity which had been elicited by a stimulus in the past; a high correlation indicates the presence of the previously encoded stimulus. Information is distributed in the network because coding is dependent upon the activities of all cells. A model based on Hartline-Ratliff lateral inhibition with a time delay shows that lateral inhibition can distribute information across a parallel network, reduce output noise, and also briefly store information. With no changes in model parameters, and the use of a correlation measure for recognition, the model can stimulate psychophysical results in eleven variations of the metacontrast masking paradigm.     

Ultrastructural and cytochemical studies on the connective tissue of chaetognaths

The hydroskeleton plays a central role in the architecture of the trunk of the Chaetognath. Its fibrous part is composed by a ‘basement membrane’ which separates the epithelial and nervous level from the locomotory muscle and other tissues which surround the general cavity. This structure corresponds to a dense connective tissue sheath; together with the aqueous phase of the general cavity it constitutes the main part of the hydroskeleton. The axes of the lateral and caudal fins are extensions of this connective tissue; they are rich in ground substance and contain several kinds of fibrils and granules.The ‘basement membrane’ is made of a network of densely packed parallel layers of collagen fibrils which form helices which wrap around the trunk. The collagen fibrils of this connective stratum are sandwiched between two basal lamina; they are embedded in a reduced extracellular matrix whose components are closely related to the architecture of the collagen fibrils. In the core of the fin, the ground substance is very abundant and classical cross-striated collagen fibrils are not to be found. A compact fibrillar transition zone is to be noted between the dense connective stratum surrounding the body and the hyaline axis of the fins. In this zone, no crossbanded collagen fibrils are to be seen.The hydroskeleton and the fins show variations within the phylum. They could be related to speciation, and the ancestral pathway of the phylum. Furthermore these variations are related to the general problem of the evolution of the extracellular matrices and collagen molecule itself.     

Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles

An important open question in the field of NMR-based biomolecular structure determination is how best to characterize the precision of the resulting ensemble of structures. Typically, the RMSD, as minimized in superimposing the ensemble of structures, is the preferred measure of precision. However, the presence of poorly determined atomic coordinates and multiple "RMSD-stable domains"--locally well-defined regions that are not aligned in global superimpositions--complicate RMSD calculations. In this paper, we present a method, based on a novel, structurally defined order parameter, for identifying a set of core atoms to use in determining superimpositions for RMSD calculations. In addition we present a method for deciding whether to partition that core atom set into "RMSD-stable domains" and, if so, how to determine partitioning of the core atom set. We demonstrate our algorithm and its application in calculating statistically sound RMSD values by applying it to a set of NMR-derived structural ensembles, superimposing each RMSD-stable domain (or the entire core atom set, where appropriate) found in each protein structure under consideration. A parameter calculated by our algorithm using a novel, kurtosis-based criterion, the epsilon-value, is a measure of precision of the superimposition that complements the RMSD. In addition, we compare our algorithm with previously described algorithms for determining core atom sets. The methods presented in this paper for biomolecular structure superimposition are quite general, and have application in many areas of structural bioinformatics and structural biology.     

The vascularization of the vagina bulbi

The construction of the vagina bulbi was examined in injection preparations with the aid of microdissection methods, and its layers were defined. Inside the connective tissue leaves occur loop capillaries up to 14 mm in length. The course of the venae vorticosae through the vagina bulbi as well as the width of the episcleral vessel network were measured. Also the subconjunctival network and arteries and nerves perforating sclera were studied. The ascertained results are discussed with former and recent anatomical and clinical reports.     

Towards a mechanism for histone chaperones

Histone chaperones can be broadly defined as histone-binding proteins that influence chromatin dynamics in an ATP-independent manner. Their existence reflects the importance of chromatin homeostasis and the unique and unusual biochemistry of the histone proteins. Histone supply and demand at chromatin is regulated by a network of structurally and functionally diverse histone chaperones. At the core of this network is a mechanistic variability that is only beginning to be appreciated. In this review, we highlight the challenges in determining histone chaperone mechanism and discuss possible mechanisms in the context of nucleosome thermodynamics. We discuss how histone chaperones prevent promiscuous histone interactions, and consider if this activity represents the full extent of histone chaperone function in governing chromatin dynamics. This article is part of a Special Issue entitled: Histone chaperones and Chromatin assembly.     

Defining invasiveness and invasibility in ecological networks

The success of a biological invasion is context dependent, and yet two key concepts—the invasiveness of species and the invasibility of recipient ecosystems—are often defined and considered separately. We propose a framework that can elucidate the complex relationship between invasibility and invasiveness. It is based on trait-mediated interactions between species and depicts the response of an ecological network to the intrusion of an alien species, drawing on the concept of community saturation. Here, invasiveness of an introduced species with a particular trait is measured by its per capita population growth rate when the initial propagule pressure of the introduced species is very low. The invasibility of the recipient habitat or ecosystem is dependent on the structure of the resident ecological network and is defined as the total width of an opportunity niche in the trait space susceptible to invasion. Invasibility is thus a measure of network instability. We also correlate invasibility with the asymptotic stability of resident ecological network, measured by the leading eigenvalue of the interaction matrix that depicts trait-based interaction intensity multiplied by encounter rate (a pairwise product of propagule pressure of all members in a community). We further examine the relationship between invasibility and network architecture, including network connectance, nestedness and modularity. We exemplify this framework with a trait-based assembly model under perturbations in ways to emulate fluctuating resources and random trait composition in ecological networks. The maximum invasiveness of a potential invader (greatest intrinsic population growth rate) was found to be positively correlated with invasibility of the recipient ecological network. Additionally, ecosystems with high network modularity and high ecological stability tend to exhibit high invasibility. Where quantitative data are lacking we propose using a qualitative interaction matrix of the ecological network perceived by a potential invader so that the structural network stability and invasibility can be estimated from the literature or from expert opinion. This approach links network structure, invasiveness and invasibility in the context of trait-mediated interactions, such as the invasion of insects into mutualistic and antagonistic networks.     

Direct measurement of the rupture force of single pair of decorin interactions

Decorin is one important member of the family of small leucine-rich proteoglycans, which are widely distributed in connective tissues in the body such as tendon and ligament. Decorin may be responsible for collagen fibril connection in those tissues. A recent hypothesis suggests that decorin may bind to collagen with its core protein while binding to another decorin through the interaction with their glycosaminoglycan (GAG) chains. However, there is no direct evidence supporting this hypothesis to date. In this study, the interaction of decorin GAG chains was directly determined for the first time. The rupture force of single bonds between decorins (GAG chains interaction) was determined directly as 16.5+/-5.1 pN using a laser tweezers/interferometer single molecular nanomechanical testing system. This information can improve our understanding of the mechanical properties of connective tissues at the molecular level.     

Poisson's ratio of a crossed fibre sheath: the skin of aquatic salamanders

Many animal connective tissues are composite materials formed into sheaths containing regularly organized collagen fibres in a crossed, fabric-like array. From a few simple assumption about the interactions between fibres, we construct a model for the effect of such a fabric-like construction on the Poisson's ratio of connective tissue sheaths. Surprisingly, the model predicts high Poisson's ratios (often greater than 1.0) Mdashespecially high given the value of 0.5 that is usually used for primarily aqueous biological tissues (based on assumptions of incompressibility and anisotropy). However, virtually all empirical attempts to measure Poisson's ratio in animal connective tissue sheaths (including our own experiments on salamander skin) reveal similarly high Poisson's ratios. The model also predicts that Poisson's ratio will increase with increasing strain, at a rate dependent on the initial angle of the crossed fibres relative to the direction of strain. Since the Poisson's ratio of a material is directly correlated with the material's stiffness, such strain-dependent changes in Poisson's ratio have important implications for the stiffness properties of connective tissue sheaths. Given the structural support role of connective tissues, stiffness is assumed to be one of their most important qualities, and several examples of how our model might predict the stiffness qualities within the walls of cylinders formed from helically wound crossed fibre sheaths (such as mammalian annular ligament and nematode cuticle) are given.     

Time-Delayed Mutual Information of the Phase as a Measure of Functional Connectivity

We propose a time-delayed mutual information of the phase for detecting nonlinear synchronization in electrophysiological data such as MEG. Palus already introduced the mutual information as a measure of synchronization [1]. To obtain estimates on small data-sets as reliably as possible, we adopt the numerical implementation as proposed by Kraskov and colleagues [2]. An embedding with a parametric time-delay allows a reconstruction of arbitrary nonstationary connective structures – so-called connectivity patterns – in a wide class of systems such as coupled oscillatory or even purely stochastic driven processes [3]. By using this method we do not need to make any assumptions about coupling directions, delay times, temporal dynamics, nonlinearities or underlying mechanisms. For verifying and refining the methods we generate synthetic data-sets by a mutual amplitude coupled network of Rössler oscillators with an a-priori known connective structure. This network is modified in such a way, that the power-spectrum forms a power law, which is also observed in electrophysiological recordings. The functional connectivity measure is tested on robustness to additive uncorrelated noise and in discrimination of linear mixed input data. For the latter issue a suitable de-correlation technique is applied. Furthermore, the compatibility to inverse methods for a source reconstruction in MEG such as beamforming techniques is controlled by dedicated dipole simulations. Finally, the method is applied on an experimental MEG recording.     

A DNA Methylation Network Interaction Measure,and Detection of Network Oncomarkers

Epigenetic processes–including DNA methylation–are increasingly seen as having a fundamental role in chronic diseases like cancer. DNA methylation patterns offer a route to develop prognostic measures based directly on DNA measurements, rather than less-stable RNA measurements. A novel DNA methylation-based measure of the co-ordinated interactive behaviour of genes is developed, in a network context. It is shown that this measure reflects well the co-regulatory behaviour linked to gene expression (at the mRNA level) over the same network interactions. This measure, defined for pairs of genes in a single patient/sample, associates with overall survival outcome independent of known prognostic clinical features, in several independent data sets relating to different cancer types. In total, more than half a billion CpGs in over 1600 samples, taken from nine different cancer entities, are analysed. It is found that groups of gene-pair interactions which associate significantly with survival identify statistically significant subnetwork modules. Many of these subnetwork modules are shown to be biologically relevant by strong correlation with pre-defined gene sets, such as immune function, wound healing, mitochondrial function and MAP-kinase signalling. In particular, the wound healing module corresponds to an increase in co-ordinated interactive behaviour between genes for worse prognosis, and the immune module corresponds to a decrease in co-ordinated interactive behaviour between genes for worse prognosis. This measure has great potential for defining DNA-based cancer biomarkers. Such biomarkers could naturally be developed further, by drawing on the rapidly expanding knowledge base of network science.     

Localization of nuclear matrix core filament proteins at interphase and mitosis.

The gentle removal of chromatin uncovers a nuclear matrix consisting of two parts: a nuclear lamina connected to the intermediate filaments of the cytoskeleton and an internal matrix of thick, polymorphic fibers connecting the lamina to masses in the nuclear interior. This internal nuclear matrix can be further fractionated to uncover a highly branched network of 9 nm and 13 nm core filaments retaining some enmeshed bodies. The core filament network retains most of the nuclear RNA, as well as the fA12RNP antigen, and may be the most basic or core element of internal nuclear structure. One high molecular weight protein component of the core filament network, the H1B2 antigen, is normally masked in the interphase nucleus and is uncovered as the chromatin condenses at mitosis. This protein is associated with a fibrogranular network surrounding and connected to the chromosomes. The core filament-associated fA12 antigen also becomes associated with this perichromosomal network. We propose that the core filament nuclear matrix structure may not completely disassemble at mitosis but, rather, that parts remain as a structural network connected to chromosomes and other mitotic structures. These mitotic networks may, in turn, serve as the core structures on which the nuclear matrices of daughter cells are built.     

Evolution of peptidase diversity

A wide variety of peptidases associate with vital biological pathways, but the origin and evolution of their tremendous diversity are poorly defined. Application of the MEROPS classification to a comprehensive set of genomes yields a simple pattern of peptidase distribution and provides insight into the organization of proteolysis in all forms of life. Unexpectedly, a near ubiquitous core set of peptidases is shown to contain more types than those unique to higher multicellular organisms. From this core group, an array of eukaryote-specific peptidases evolved to yield well known intracellular and extracellular processes. The paucity of peptidase families unique to higher metazoa suggests gains in proteolytic network complexity required a limited number of biochemical inventions. These findings provide a framework for deeper investigation into the evolutionary forces that shaped each peptidase family and a roadmap to develop a timeline for their expansion as an interconnected system.     

Immunolocalization of Fibronectin and Laminin in the Amphibian Intestine During Spontaneous and Triiodothyronine-Induced Metamorphosis

Fibronectin and laminin were detected by indirect immunofluorescence in the intestine of Alytes obstetricans (anuran amphibian) during triiodothyronine (T3)-induced metamorphosis and spontaneous post-embryonic development. Fibronectin was first detected between a small number of connective tissue cells. As T3-treatment and spontaneous development progressed, fibronectin became detectable as a fine network extending throughout the whole thickness of the connective tissue and particularly in the core of the developing epithelial folds. During the first week of T3-treatment and throughout the spontaneous larval period, laminin was present as a linear band within the basement membrane. Between day 6 and 12 of hormonal treatment, an increase in the laminin fluorescent staining was noted. After hormonal treatment for two weeks and at the end of spontaneous metamorphosis, laminin staining was localized within the basement membrane of the folded epithelium and around muscle fibers. These observations indicate that variations in the density and distribution of extracellular matrix molecules are closely related spatiotemporarily to the structural changes occurring in the connective and muscle tissues of the intestine during metamorphosis.     

Radial locations of amino acid residues in a globular protein: correlation with the sequence

The location measure of a residue in a globular protein is defined as the number of C alpha atoms surrounding the residue located within a sphere of the radius of 14 A. This quantity is a measure of the exposure of a residue to solvent, and is related closely to the distance from the center of mass of a protein. In this work, the experimental value for each residue of a protein is obtained from the X-ray crystallographic data, and the quantity is also calculated from the amino acid sequence data by applying an empirical parameter set to it. The correlation between the experimental and computed quantities is as high as 0.50 on the average over 92 proteins of known three-dimensional structure. Therefore, the location measure of every residue in a globular protein is predictable with good accuracy from the sequence.     

A new measure of the robustness of biochemical networks

MOTIVATION: The robustness of a biochemical network is defined as the tolerance of variations in kinetic parameters with respect to the maintenance of steady state. Robustness also plays an important role in the fail-safe mechanism in the evolutionary process of biochemical networks. The purposes of this paper are to use the synergism and saturation system (S-system) representation to describe a biochemical network and to develop a robustness measure of a biochemical network subject to variations in kinetic parameters. Since most biochemical networks in nature operate close to the steady state, we consider only the robustness measurement of a biochemical network at the steady state. RESULTS: We show that the upper bound of the tolerated parameter variations is related to the system matrix of a biochemical network at the steady state. Using this upper bound, we can calculate the tolerance (robustness) of a biochemical network without testing many parametric perturbations. We find that a biochemical network with a large tolerance can also better attenuate the effects of variations in rate parameters and environments. Compensatory parameter variations and network redundancy are found to be important mechanisms for the robustness of biochemical networks. Finally, four biochemical networks, such as a cascaded biochemical network, the glycolytic-glycogenolytic pathway in a perfused rat liver, the tricarboxylic acid cycle in Dictyostelium discoideum and the cAMP oscillation network in bacterial chemotaxis, are used to illustrate the usefulness of the proposed robustness measure.     

On Hydrophobicity and Conformational Specificity in Proteins

In this study we examine the distribution of hydrophobic residues in a nonredundant set of monomeric globular single-domain proteins. We find that the total fraction of hydrophobic residues is roughly constant and has no discernible dependence on protein size. This results in a decrease of the hydrophobicity of the core as the size of proteins increases. Using a normalized measure, and by comparing with sets of randomly reshuffled sequences, we show that this change in the composition of the core is statistically significant and robust with respect to which amino acids are considered hydrophobic and to how buried residues are defined. Comparison with model sequences optimized for stability, while still required to retain their native state as a unique minimum energy conformation, suggests that the size-independence of the total fraction of hydrophobic residues could be a result of requiring proteins to be conformationally specific.     

Microfibril Structure Masks Fibrillin-2 in Postnatal Tissues

Fibrillin microfibrils are polymeric structures present in connective tissues. The importance of fibrillin microfibrils to connective tissue function has been demonstrated by the multiple genetic disorders caused by mutations in fibrillins and in microfibril-associated molecules. However, knowledge of microfibril structure is limited, largely due to their insolubility. Most previous studies have focused on how fibrillin-1 is organized within microfibril polymers. In this study, an immunochemical approach was used to circumvent the insolubility of microfibrils to determine the role of fibrillin-2 in postnatal microfibril structure. Results obtained from studies of wild type and fibrillin-1 null tissues, using monoclonal and polyclonal antibodies with defined epitopes, demonstrated that N-terminal fibrillin-2 epitopes are masked in postnatal microfibrils and can be revealed by enzymatic digestion or by genetic ablation of Fbn1. From these studies, we conclude that fetal fibrillin polymers form an inner core within postnatal microfibrils and that microfibril structure evolves as growth and development proceed into the postnatal period. Furthermore, documentation of a novel cryptic site present in EGF4 in fibrillin-1 underscores the molecular complexity and tissue-specific differences in microfibril structure.     

Functional role of periostin in development and wound repair: implications for connective tissue disease

Integrity of the extracellular matrix (ECM) is essential for maintaining the normal structure and function of connective tissues. ECM is secreted locally by cells and organized into a complex meshwork providing physical support to cells, tissues, and organs. Initially thought to act only as a scaffold, the ECM is now known to provide a myriad of signals to cells regulating all aspects of their phenotype from morphology to differentiation. Matricellular proteins are a class of ECM related molecules defined through their ability to modulate cell-matrix interactions. Matricellular proteins are expressed at high levels during development, but typically only appear in postnatal tissue in wound repair or disease, where their levels increase substantially. Members of the CCN family, tenascin-C, osteopontin, secreted protein acidic rich in cysteine (SPARC), bone sialoprotein, thrombospondins, and galectins have all been classed as matricellular proteins. Periostin, a 90 kDa secreted homophilic cell adhesion protein, was recently added to matricellular class of proteins based on its expression pattern and function during development as well as in wound repair. Periostin is expressed in connective tissues including the periodontal ligament, tendons, skin and bone, and is also prominent in neoplastic tissues, cardiovascular disease, as well as in connective tissue wound repair. This review will focus on the functional role of periostin in tissue physiology. Fundamentally, it appears that periostin influences cell behaviour as well as collagen fibrillogenesis, and therefore exerts control over the structural and functional properties of connective tissues in both health and disease. Periostin is a novel matricellular protein with close homology to Drosophila fasciclin 1. In this review, the functional role of periostin is discussed in the context of connective tissue physiology, in development, disease, and wound repair.