Hierarchical analysis of dependency in metabolic networks

MOTIVATION: Elucidation of metabolic networks for an increasing number of organisms reveals that even small networks can contain thousands of reactions and chemical species. The intimate connectivity between components complicates their decomposition into biologically meaningful sub-networks. Moreover, traditional higher-order representations of metabolic networks as metabolic pathways, suffers from the lack of rigorous definition, yielding pathways of disparate content and size. RESULTS: We introduce a hierarchical representation that emphasizes the gross organization of metabolic networks in largely independent pathways and sub-systems at several levels of independence. The approach highlights the coupling of different pathways and the shared compounds responsible for those couplings. By assessing our results on Escherichia coli (E.coli metabolic reactions, Genetic Circuits Research Group, University of California, San Diego, http://gcrg.ucsd.edu/organisms/ecoli.html, 'model v 1.01. reactions') against accepted biochemical annotations, we provide the first systematic synopsis of an organism's metabolism. Comparison with operons of E.coli shows that low-level clusters are reflected in genome organization and gene regulation. AVAILABILITY: Source code, data sets and supplementary information are available at http://www.mas.ecp.fr/labo/equipe/gagneur/hierarchy/hierarchy.html     

Hierarchical modularity of nested bow-ties in metabolic networks

Background  

The exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. Topological analysis of graph models has often been applied to study the structural characteristics of complex metabolic networks.     

Hierarchical analysis of piecewise affine models of gene regulatory networks

A key point in the analysis of dynamical models of biological systems is to handle systems of relatively high dimensions. In the present paper we propose a method to hierarchically organize a certain type of piecewise affine (PWA) differential systems. This specific class of systems has been extensively studied for the past few years, as it provides a good framework to model gene regulatory networks. The method, shown on several examples, allows a qualitative analysis of the asymptotic behavior of a PWA system, decomposing it into several smaller subsystems. This technique, based on the well-known strongly connected components decomposition, is not new. However, its adaptation to the non-smooth PWA differential equations turns out to be quite relevant because of the strong discrete structure underlying these equations. Its biological relevance is shown on a 7-dimensional PWA system modeling the gene network responsible for the carbon starvation response in Escherichia coli.

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Hierarchical thinking in network biology: the unbiased modularization of biochemical networks

As reconstructed biochemical reaction networks continue to grow in size and scope, there is a growing need to describe the functional modules within them. Such modules facilitate the study of biological processes by deconstructing complex biological networks into conceptually simple entities. The definition of network modules is often based on intuitive reasoning. As an alternative, methods are being developed for defining biochemical network modules in an unbiased fashion. These unbiased network modules are mathematically derived from the structure of the whole network under consideration.     

Hierarchical networks of food exchange in the black garden ant Lasius niger

In most eusocial insects, the division of labor results in relatively few individuals foraging for the entire colony. Thus, the survival of the colony depends on its efficiency in meeting the nutritional needs of all its members. Here, we characterize the network topology of a eusocial insect to understand the role and centrality of each caste in this network during the process of food dissemination. We constructed trophallaxis networks from 34 food-exchange experiments in black garden ants (Lasius niger). We tested the influence of brood and colony size on (i) global indices at the network level (i.e., efficiency, resilience, centralization, and modularity) and (ii) individual values (i.e., degree, strength, betweenness, and the clustering coefficient). Network resilience, the ratio between global efficiency and centralization, was stable with colony size but increased in the presence of broods, presumably in response to the nutritional needs of larvae. Individual metrics highlighted the major role of foragers in food dissemination. In addition, a hierarchical clustering analysis suggested that some domestics acted as intermediaries between foragers and other domestics. Networks appeared to be hierarchical rather than random or centralized exclusively around foragers. Finally, our results suggested that networks emerging from social insect interactions can improve group performance and thus colony fitness.     

Evolution of the reticular formation

The reticular formation of mammals contains numerous nuclei which can be recognized by their projection patterns, cytoarchitectonics, and neuropeptide/neurotransmitter content. We have identified reticular nuclei in representatives from numerous reptilian groups and ascertained presence or absence of these reticular nuclei in an attempt to use neuronal occurrence as a tool to determine phylogenetic relationships. Recently these studies have been extended to two elasmobranchs, a galeomorph shark and a ray. In this report, we concentrate on three medullary spinal projecting reticular nuclei, reticularis gigantocellularis, reticularis magnocellularis, and reticularis paragigantocellularis. We found that all three nuclei were present in rats, lizards, and elasmobranchs, but one nucleus was absent in crocodilians, and two nuclei were absent in turtles. Thus brain organization may give us clues to phylogenetic relationships. Moreover, these three reticular nuclei exhibited remarkably similar cellular morphology in mammals, reptiles, and elasmobranchs.     

Systems of ordering data

Four ordering systems have been used most frequently in taxonomy: (1) special purpose classifications, (2) downward classifications (identification schemes), (3) upward or grouping classifications (traditional), and (4) Hennigian phylogenetic systems. The special properties of these four systems are critically evaluated. Grouping classifications and phylogenetic systems have very different objectives: the former the documentation of similarity and closeness of relationship, the latter of phylogeny. Both are legitimate ordering systems.     

Palladium toning of silver-impregnated reticular fibers

Palladium toning is much less expensive than gold toning. Ten minutes in 0.05% potassium hexachloropalladate in 4 N hydrochloric acid tones silver-impregnated reticular fibers as well as 3 min in 0.2% aqueous gold chloride does. Differences in toning of the background depend on the silver stain.     

Magnetic ordering of phospholipid membranes

Phospholipid bilayers could be homogeneously oriented by application of strong magnetic fields as is demonstrated by means of deuterium and phosphorus nuclear magnetic resonance. The membranes were composed of either Escherichia coli lipids or a mixture of synthetic phosphatidylethanolamine and phosphatidylglycerol. The planes of the bilayer were found to align parallel to the magnetic field.     

Chiral nematic ordering of polysaccharides

In this paper, evidence for the chiral nematic (cholesteric) self-ordering of cellulose-derived materials is reviewed. A wide range of cellulose derivatives, and some other polysaccharides, form chiral nematic phases, both in concentrated solution and in the melt. Solid films and gels retaining the chiral nematic ordering of the polymer chains may be prepared from these liquid crystalline phases. Optical and electron microscopic techniques may be used to elucidate the helicoidal structure of chiral nematic cellulosics in the liquid crystalline phase, and of the films, gels and solids prepared from such phases. Remarkably, dilute aqueous suspensions of cellulose crystallites prepared by acid degradation also show chiral nematic order; the order is preserved in dry films prepared from the suspensions. The structure of some of these samples prepared in vitro shows a marked resemblance to structures observed in vivo.     

Automated ordering of fingerprinted clones

MOTIVATION: A considerable amount of human intervention is currently required to produce high-quality fingerprint-based physical maps for genomic studies. RESULTS: An algorithm has been developed and implemented to automatically order fingerprinted clones within contigs. The resulting software, named CORAL (Clone ORdering ALgorithm), has been tested on maps that have previously been manually edited and on maps derived from in silico simulations. The fingerprint map and DNA sequence of the human genome has provided an additional test to CORAL. Measurements suggest that CORAL performs significantly better than the software currently used by most laboratories to order fingerprinted clones at throughputs far exceeding those that can be achieved manually.     

Time ordering of gene coexpression

Temporal microarray gene expression profiles allow characterization of gene function through time dynamics of gene coexpression within the same genetic pathway. In this paper, we define and estimate a global time shift characteristic for each gene via least squares, inferred from pairwise curve alignments. These time shift characteristics of individual genes reflect a time ordering that is derived from ob- served temporal gene expression profiles. Once these time shift characteristics are obtained for each gene, they can be entered into further analyses, such as clustering. We illustrate the proposed methodology using Drosophila embryonic development and yeast cell-cycle gene expression profiles, as well as simulations. Feasibility is demonstrated through the successful recovery of time ordering. Estimated time shifts for Drosophila maternal and zygotic genes provide excellent discrimination between these two categories and confirm known genetic pathways through the time order of gene expression. The application to yeast cell-cycle data establishes a natural time order of genes that is in line with cell-cycle phases. The method does not require periodicity of gene expression profiles. Asymptotic justifications are also provided.     

Histochemical and morphological characterization of reticular fibers

The results presented in this paper show that collagen fibers can be clearly distinguished from reticular fibers using the picrosirius-polarization method. A morphologic and morphometric study of these two types of fibers with electron microscopy shows that reticular fibers are characterized by the smaller diameter of their fibrillar components and the higher content of interfibrillar material, resulting in a loose arrangement of the fibrils. The evidences presented suggest that the amorphous matrix in which fibrils are embedded is responsible for the silver impregnation of reticular fibers. Our results show that the matrix of reticular fibers is characteristically rich in heparitin sulfate, and that the glycosaminoglycans present show a high interaction with the fibrillar component of these fibers.     

The reticular formation differentiates heterotopic stimuli

The role of the reticular formation (RF) in discriminative functions was studied in experiments on anaesthetized cats. In this association, a) the variability of responses in the RF (bipolarly recorded potential gradients - PG) to the same stimuli, and b) the responses of the RF to different (heterotopic) stimuli were recorded. The PG pattern in electrical stimulation of the same source (a nerve, skin) was constant during the time periods studied (several tens of minutes); even when the functional state of the RF was modified with strychnine, the basic characteristics of the responses usually remained intact. The pattern of PG generated by natural stimulation (tapping) was likewise reproduced with exactness at the level of statistical significance. Responses evoked from reciprocally remote receptor areas were manifestly different, at least in one of the depths investigated. The differences in stimulation of topically close areas were small. The results show that the RF, through its reactions, can differentiate heterotopic stimuli.