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Adaptive reconfiguration of fractal small-world human brain functional networks.

Brain function depends on adaptive self-organization of large-scale neural assemblies, but little is known about quantitative network parameters governing these processes in humans. Here, we describe the topology and synchronizability of frequency-specific brain functional networks using wavelet decomposition of magnetoencephalographic time series, followed by construction and analysis of undirected graphs. Magnetoencephalographic data were acquired from 22 subjects, half of whom performed a finger-tapping task, whereas the other half were studied at rest. We found that brain functional networks were characterized by small-world properties at all six wavelet scales considered, corresponding approximately to classical delta (low and high), , alpha, beta, and gamma frequency bands. Global topological parameters (path length, clustering) were conserved across scales, most consistently in the frequency range 2-37 Hz, implying a scale-invariant or fractal small-world organization. Dynamical analysis showed that networks were located close to the threshold of order/disorder transition in all frequency bands. The highest-frequency gamma network had greater synchronizability, greater clustering of connections, and shorter path length than networks in the scaling regime of (lower) frequencies. Behavioral state did not strongly influence global topology or synchronizability; however, motor task performance was associated with emergence of long-range connections in both beta and gamma networks. Long-range connectivity, e.g., between frontal and parietal cortex, at high frequencies during a motor task may facilitate sensorimotor binding. Human brain functional networks demonstrate a fractal small-world architecture that supports critical dynamics and task-related spatial reconfiguration while preserving global topological parameters.

Brain↗

Information exchange and the robustness of organizational networks.

The dynamics of information exchange is an important but understudied aspect of collective communication, coordination, and problem solving in a wide range of distributed systems, both physical (e.g., the Internet) and social (e.g., business firms). In this paper, we introduce a model of organizational networks according to which links are added incrementally to a hierarchical backbone and test the resulting networks under variable conditions of information exchange. Our main result is the identification of a class of multiscale networks that reduce, over a wide range of environments, the likelihood that individual nodes will suffer congestion-related failure and that the network as a whole will disintegrate when failures do occur. We call this dual robustness property of multiscale networks "ultrarobustness." Furthermore, we find that multiscale networks attain most of their robustness with surprisingly few link additions, suggesting that ultrarobust organizational networks can be generated in an efficient and scalable manner. Our results are directly relevant to the relief of congestion in communication networks and also more broadly to activities, like distributed problem solving, that require individuals to exchange information in an unpredictable manner.

Journal Article↗

A natural class of robust networks.

As biological studies shift from molecular description to system analysis we need to identify the design principles of large intracellular networks. In particular, without knowing the molecular details, we want to determine how cells reliably perform essential intracellular tasks. Recent analyses of signaling pathways and regulatory transcription networks have revealed a common network architecture, termed scale-free topology. Although the structural properties of such networks have been thoroughly studied, their dynamical properties remain largely unexplored. We present a prototype for the study of dynamical systems to predict the functional robustness of intracellular networks against variations of their internal parameters. We demonstrate that the dynamical robustness of these complex networks is a direct consequence of their scale-free topology. By contrast, networks with homogeneous random topologies require fine-tuning of their internal parameters to sustain stable dynamical activity. Considering the ubiquity of scale-free networks in nature, we hypothesize that this topology is not only the result of aggregation processes such as preferential attachment; it may also be the result of evolutionary selective processes.

Biophysical Phenomena↗

Evolution of gene networks by gene duplications: a mathematical model and its implications on genome organization.

Networks of transcriptional regulators have key roles in metazoan development. Important forces in the evolution of these networks are gene duplications and gene deletions, events that may change the spatiotemporal expression pattern of network genes. A measure for the probability of such changes after gene-duplication events is proposed. This measure is based on a simple mathematical model that describes such networks as dynamical systems and on properties of ensembles of these dynamical systems. It is predicted that this probability depends only on the fraction of genes duplicated in a single event and that it is largest if approximately 40% of the genes in a network are duplicated. This property is robust with respect to variations in model parameters. On these grounds, it is argued that (i) evolution of gene networks should preferentially occur either by duplication of single genes or by duplication of all genes involved in a network, and that (ii) tight linkage ("clustering") or strong dispersal are the two evolutionarily most favorable forms of genomic organization of genes forming such networks.

Animals↗

Type IV collagen of the glomerular basement membrane. Evidence that the chain specificity of network assembly is encoded by the noncollagenous NC1 domains.

The ultrafiltration function of the glomerular basement membrane (GBM) of the kidney is impaired in genetic and acquired diseases that affect type IV collagen. The GBM is composed of five (alpha1 to alpha5) of the six chains of type IV collagen, organized into an alpha1.alpha2(IV) and an alpha3.alpha4.alpha5(IV) network. In Alport syndrome, mutations in any of the genes encoding the alpha3(IV), alpha4(IV), and alpha5(IV) chains cause the absence of the alpha3. alpha4.alpha5 network, which leads to progressive renal failure. In the present study, the molecular mechanism underlying the network defect was explored by further characterization of the chain organization and elucidation of the discriminatory interactions that govern network assembly. The existence of the two networks was further established by analysis of the hexameric complex of the noncollagenous (NC1) domains, and the alpha5 chain was shown to be linked to the alpha3 and alpha4 chains by interaction through their respective NC1 domains. The potential recognition function of the NC1 domains in network assembly was investigated by comparing the composition of native NC1 hexamers with hexamers that were dissociated and reconstituted in vitro and with hexamers assembled in vitro from purified alpha1-alpha5(IV) NC1 monomers. The results showed that NC1 monomers associate to form native-like hexamers characterized by two distinct populations, an alpha1.alpha2 and alpha3.alpha4.alpha5 heterohexamer. These findings indicate that the NC1 monomers contain recognition sequences for selection of chains and protomers that are sufficient to encode the assembly of the alpha1.alpha2 and alpha3.alpha4.alpha5 networks of GBM. Moreover, hexamer formation from the alpha3, alpha4, and alpha5 NC1 monomers required co-assembly of all three monomers, suggesting that mutations in the NC1 domain in Alport syndrome may disrupt the assembly of the alpha3.alpha4.alpha5 network by interfering with the assembly of the alpha3.alpha4.alpha5 NC1 hexamer.

Animals↗

The NC1 domain of collagen IV encodes a novel network composed of the alpha 1, alpha 2, alpha 5, and alpha 6 chains in smooth muscle basement membranes.

Type IV collagen, the major component of basement membranes (BMs), is a family of six homologous chains (alpha1-alpha6) that have a tissue-specific distribution. The chains assemble into supramolecular networks that differ in the chain composition. In this study, a novel network was identified and characterized in the smooth muscle BMs of aorta and bladder. The noncollagenous (NC1) hexamers solubilized by collagenase digestion were fractionated by affinity chromatography using monoclonal antibodies against the alpha5 and alpha6 NC1 domains and then characterized by two-dimensional gel electrophoresis and Western blotting. Both BMs were found to contain a novel alpha1.alpha2.alpha5.alpha6 network besides the classical alpha1.alpha2 network. The alpha1.alpha2.alpha5.alpha6 network represents a new arrangement in which a protomer (triple-helical isoform) containing the alpha5 and alpha6 chains is linked through NC1-NC1 interactions to an adjoining protomer composed of the alpha1 and alpha2 chains. Re-association studies revealed that the NC1 domains contain recognition sequences sufficient to encode the assembly of both networks. These findings, together with previous ones, indicate that the six chains of type IV collagen are distributed in three major networks (alpha1.alpha2, alpha3.alpha4.alpha5, and alpha1.alpha2.alpha5.alpha6) whose chain composition is encoded by the NC1 domains. The existence of the alpha1.alpha2.alpha5.alpha6 network provides a molecular explanation for the concomitant loss of alpha5 and alpha6 chains from the BMs of patients with X-linked Alport's syndrome.

Animals↗

Network participation for unpromoted female dentists in relation to psychosocial support.

Studies have shown that female unpromoted general practice (GP) dentists have a taxing work situation with many problems related to their psychosocial work environment. This study aims to describe: 1) the participation of this group in organized network activity (support groups) in a region (Scania) in Sweden, 2) the sense of support compared with another organization and with a nationwide sample of GP dentists, and 3) the covariation of network participation with support. All unpromoted female dentists within the Public Dental Health Service (PDHS) in Scania received a questionnaire and 94% responded. Those participating in network activity < or =4 times a year constituted 12% of respondents. Cooperation between colleagues was lower than in the nationwide sample. Support from the PDHS was experienced as weak. It was not possible to explain why female unpromoted GP dentists participated < or =4 times a year, while those who felt lonely in their work were to a higher degree participants in a network. Almost 9 out of 10 reported being strengthened by the network both as a person and in a professional role. The female dentist was three times more likely to participate in a network if she had a male head of clinic. The main findings are a paucity of inter-colleague contact and a lack of association between support and network participation. The many affirmative comments indicated that network participation might be a good coping strategy for unpromoted female GP dentists.

Adaptation, Psychological↗

Gender differences in HIV risk behaviors among young injectors and their social network members.

Using epidemiological and social network research methods, this study examines gender differences in HIV risk and protective behaviors and social network characteristics among 193 young injection drug users (IDUs) and 127 referred members of their social networks. Respondents reported on their drug use, sexual behavior, and relationships within three types of social networks: hang out (i.e., friendship); drug use; and sexual networks. Most respondents were homeless and had experienced numerous life stressors. Females' social networks consisted more predominantly of drug injectors, and members more frequently appeared multiple networks. Females reported needle sharing more frequently than males, but also reported more protective behaviors such as needle exchange use and carrying clean syringes. Young female IDUs may compound their risk by having sex and injecting with higher risk partners. However, their propensity to practice protective behaviors may provide an opening for interventions to reduce their HIV risk and that of their social network members.

Adult↗

Mouse differentiation-specific keratins 1 and 10 require a preexisting keratin scaffold to form a filament network.

Keratins 1 (K1) and 10 (K10) are the predominant cytoskeletal intermediate filaments of epidermal cells during transition from the proliferative to the terminal differentiation stage. In situ, formation of the K1/K10 intermediate filament network occurs in the cytoplasm of cells with a preexisting cytoskeleton composed of keratins 5 and 14. To define cytoskeletal interactions permissive for formation of the K1/K10 filamentous network, active copies of mouse K1 and K10 genes were introduced into fibroblasts (NIH 3T3) which do not normally express these proteins. Transient and stable transfectants, as well as heterokaryons produced by fusions with epithelial cells, were evaluated for expression of K1 and K10 proteins and filament formation using specific antibodies. In contrast to keratin pairs K5/K14 and K8/K18, the K1/K10 pair failed to form an extensive keratin filament network on its own, although small isolated dense K1/K10 filament bundles were observed throughout the cytoplasm by EM. K1 and K10 filaments integrated only into the preexisting K5/K14 network upon fusion of the NIH 3T3 (K1/K10) cells with epithelial cells expressing endogenous K5/K14 or with NIH 3T3 cells which were transfected with active copies of the K5 and K14 genes. When combinations of active recombinant gene constructs for keratins 1, 5, 10, and 14 were tested in transient NIH 3T3 transfections, the most intact cytokeratin network observed by immunofluorescence was formed by the K5/K14 pair. The K1/K14 pair was capable of forming a cytoskeletal network, but the network was poorly developed, and usually perinuclear. Transfection of K10 in combination with K5 or K1 resulted in cytoplasmic agglomerates, but not a cytoskeleton. These results suggest that the formation of the suprabasal cytoskeleton in epidermis is dependent on the preexisting basal cell intermediate filament network. Furthermore, restrictions on filament formation appear to be more stringent for K10 than for K1.

3T3 Cells↗

Action of cytochalasin D on cytoskeletal networks.

Extraction of SC-1 cells (African green monkey kidney) with the detergent Triton X-100 in combination with stereo high-voltage electron microscopy of whole mount preparations has been used as an approach to determine the mode of action of cytochalasin D on cells. The cytoskeleton of extracted BSC-1 cells consists of substrate-associated filament bundles (stress fibers) and a highly cross-linked network of four major filament types extending throughout the cell body; 10-nm filaments, actin microfilaments, microtubules, and 2- to 3-nm filaments. Actin filaments and 2- to 3-nm filaments form numerous end-to-side contacts with other cytoskeletal filaments. Cytochalasin D treatment severely disrupts network organization, increases the number of actin filament ends, and leads to the formation of filamentous aggregates or foci composed mainly of actin filaments. Metabolic inhibitors prevent filament redistribution, foci formation, and cell arborization, but not disorganization of the three-dimensional filament network. In cells first extracted and then treated with cytochalasin D, network organization is disrupted, and the number of free filament ends is increased. Supernates of preparations treated in this way contain both short actin filaments and network fragments (i.e., actin filaments in end-to-side contact with other actin filaments). It is proposed that the dramatic effects of cytochalasin D on cells result from both a direct interaction of the drug with the actin filament component of cytoskeletal networks and a secondary cellular response. The former leads to an immediate disruption of the ordered cytoskeletal network that appears to involve breaking of actin filaments, rather than inhibition of actin filament-filament interactions (i.e., disruption of end-to-side contacts). The latter engages network fragments in an energy-dependent (contractile) event that leads to the formation of filament foci.

Actins↗

Centrifugation shearing exposes filamentous networks in cortical regions of crane-fly spermatocytes.

Spermatocytes of the crane-fly, Nephrotoma suturalis, were attached to electron microscope grids and then sheared by applying centrifugal force. Transmission electron microscopy of exposed regions of the cell cortex revealed networks containing arrays of filamentous structures. Networks were present in sheared spermatocytes at all stages of meiosis. The networks of dividing spermatocytes (meta- through telophase) were denser and appeared to contain more aggregated material then networks of prophase cells. The appearance of networks in spermatocytes resembled actin-containing networks of sheared and detergent-extracted human erythrocytes. Networks treated with myosin subfragment 1 under conditions in which muscle F-actin was clearly decorated were not distinguishable from those of untreated cells. Exposure to deoxyribonuclease-1 caused the disruption of networks in sheared spermatocytes as well as in erythrocytes. The results of deoxyribonuclease experiments are interpreted as an indication that actin is a component of the cell cortex in crane-fly spermatocytes.

Actins↗

Relationships between the activity of MMP1/TIMP1 enzymes and the TH1/TH2 cytokine network.

The evaluation of the balance between matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs) would appear to be important in cancer patients. Since the activity of these enzymes is regulated at the gene level by cytokines, we studied the serum relationships between MMP1/TIMP1 and the network of TH1/TH2 cytokines in healthy subjects to better understand how the physiological network of cytokines regulates MMP1/TIMP1 activity. Such a study could lead to suggestions for follow-up experiments to create prognostic and diagnostic indices for more efficient disease prevention programs and biotherapeutic treatments of patients. For this purpose, we determined serum levels of MMP1, TIMP1 and interleukin (IL)2, interferon (IFN) gamma, IL4 and IL10 in both healthy men and women (men and women were analyzed separately as hormones are one of the non-cytokine regulatory factors of TH1 or TH2 polarization). These cytokines make up our basic network. Cytokines within the physiological network function simultaneously so mathematical models of multivariate statistical methods were used to study MMP1/TIMP1 and TH1/TH2 network relationships. It has been suggested that mathematical modeling is the only effective way of studying the immune system as a whole. The influence of network activation, antigen presenting cells, antibody response and chemokines on MMP1/TIMP1 balance was also studied. Network activation was evaluated by measuring the levels of soluble IL2 receptors (sIL2R) and sIL6R; the influence of antigen presenting cells was evaluated by measuring serum levels of tumor necrosis factor alpha (TNF alpha) and IL1 beta; antibody response was evaluated by measuring IL5 and IL6 serum levels and the influence of chemokines was evaluated by measuring serum levels of IL8. Our overall results suggest that there are relationships between the activity of MMP1/TIMP1 and the TH1/TH2 network in physiological conditions. These data may be useful in gaining a clearer insight into how the two systems interact and hence regulate the physiological homeostasis. Therefore, this paper provides suggestions for experimental studies on MMP1/TIMp1 enzymes and TH1/TH2 cytokines to create clinical and prognostic markers for patient evaluation.

Adult↗

Pairwise alignment of protein interaction networks.

With an ever-increasing amount of available data on protein-protein interaction (PPI) networks and research revealing that these networks evolve at a modular level, discovery of conserved patterns in these networks becomes an important problem. Although available data on protein-protein interactions is currently limited, recently developed algorithms have been shown to convey novel biological insights through employment of elegant mathematical models. The main challenge in aligning PPI networks is to define a graph theoretical measure of similarity between graph structures that captures underlying biological phenomena accurately. In this respect, modeling of conservation and divergence of interactions, as well as the interpretation of resulting alignments, are important design parameters. In this paper, we develop a framework for comprehensive alignment of PPI networks, which is inspired by duplication/divergence models that focus on understanding the evolution of protein interactions. We propose a mathematical model that extends the concepts of match, mismatch, and gap in sequence alignment to that of match, mismatch, and duplication in network alignment and evaluates similarity between graph structures through a scoring function that accounts for evolutionary events. By relying on evolutionary models, the proposed framework facilitates interpretation of resulting alignments in terms of not only conservation but also divergence of modularity in PPI networks. Furthermore, as in the case of sequence alignment, our model allows flexibility in adjusting parameters to quantify underlying evolutionary relationships. Based on the proposed model, we formulate PPI network alignment as an optimization problem and present fast algorithms to solve this problem. Detailed experimental results from an implementation of the proposed framework show that our algorithm is able to discover conserved interaction patterns very effectively, in terms of both accuracies and computational cost.

Algorithms↗

Biogenesis of nanotubular network in Toxoplasma parasitophorous vacuole induced by parasite proteins.

The intracellular parasite Toxoplasma gondii develops within a nonfusogenic vacuole containing a network of elongated nanotubules that form connections with the vacuolar membrane. Parasite secretory proteins discharged from dense granules (known as GRA proteins) decorate this intravacuolar network after invasion. Herein, we show using specific gene knockout mutants, that the unique nanotubule conformation of the network is induced by the parasite secretory protein GRA2 and further stabilized by GRA6. The vacuolar compartment generated by GRA2 knockout parasites was dramatically disorganized, and the normally tubular network was replaced by small aggregated material. The defect observed in Deltagra2 parasites was evident from the initial stages of network formation when a prominent cluster of multilamellar vesicles forms at a posterior invagination of the parasite. The secretory protein GRA6 failed to localize properly to this posterior organizing center in Deltagra2 cells, indicating that this early conformation is essential to proper assembly of the network. Construction of a Deltagra6 mutant also led to an altered mature network characterized by small vesicles instead of elongated nanotubules; however, the initial formation of the posterior organizing center was normal. Complementation of the Deltagra2 knockout with mutated forms of GRA2 showed that the integrity of both amphipathic alpha-helices of the protein is required for correct formation of the network. The induction of nanotubues by the parasite protein GRA2 may be a conserved feature of amphipathic alpha-helical regions, which have also been implicated in the organization of Golgi nanotubules and endocytic vesicles in mammalian cells.

Animals↗

Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome.

MOTIVATION: Current growth in the field of genomics has provided a number of exciting approaches to the modeling of evolutionary mechanisms within the genome. Separately, dynamical and statistical analyses of networks such as the World Wide Web and the social interactions existing between humans have shown that these networks can exhibit common fractal properties-including the property of being scale-free. This work attempts to bridge these two fields and demonstrate that the fractal properties of molecular networks are linked to the fractal properties of their underlying genomes. RESULTS: We suggest a stochastic model capable of describing the evolutionary growth of metabolic or signal-transduction networks. This model generates networks that share important statistical properties (so-called scale-free behavior) with real molecular networks. In particular, the frequency of vertices connected to exactly k other vertices follows a power-law distribution. The shape of this distribution remains invariant to changes in network scale: a small subgraph has the same distribution as the complete graph from which it is derived. Furthermore, the model correctly predicts that the frequencies of distinct DNA and protein domains also follow a power-law distribution. Finally, the model leads to a simple equation linking the total number of different DNA and protein domains in a genome with both the total number of genes and the overall network topology. AVAILABILITY: MatLab (MathWorks, Inc.) programs described in this manuscript are available on request from the authors. CONTACT: ar345@columbia.edu.

Biological Evolution↗

How to reconstruct a large genetic network from n gene perturbations in fewer than n(2) easy steps.

MOTIVATION: The reconstruction of genetic networks is the holy grail of functional genomics. Its core task is to identify the causal structure of a gene network, that is, to distinguish direct from indirect regulatory interactions among gene products. In other words, to reconstruct a genetic network is to identify, for each network gene, which other genes and their activity the gene influences directly. Crucial to this task are perturbations of gene activity. Genomic technology permits large-scale experiments perturbing the activity of many genes and assessing the effect of each perturbation on all other genes in a genome. However, such experiments cannot distinguish between direct and indirect effects of a genetic perturbation. RESULTS: I present an algorithm to reconstruct direct regulatory interactions in gene networks from the results of gene perturbation experiments. The algorithm is based on a graph representation of genetic networks and applies to networks of arbitrary size and complexity. Algorithmic complexity in both storage and time is low, less than O(n(2)). In practice, the algorithm can reconstruct networks of several thousand genes in mere CPU seconds on a desktop workstation. AVAILABILITY: A perl implementation of the algorithm is given in the Appendix. CONTACT: wagnera@unm.edu

Algorithms↗

Evaluating functional network inference using simulations of complex biological systems.

MOTIVATION: Although many network inference algorithms have been presented in the bioinformatics literature, no suitable approach has been formulated for evaluating their effectiveness at recovering models of complex biological systems from limited data. To overcome this limitation, we propose an approach to evaluate network inference algorithms according to their ability to recover a complex functional network from biologically reasonable simulated data. RESULTS: We designed a simulator to generate data representing a complex biological system at multiple levels of organization: behaviour, neural anatomy, brain electrophysiology, and gene expression of songbirds. About 90% of the simulated variables are unregulated by other variables in the system and are included simply as distracters. We sampled the simulated data at intervals as one would sample from a biological system in practice, and then used the sampled data to evaluate the effectiveness of an algorithm we developed for functional network inference. We found that our algorithm is highly effective at recovering the functional network structure of the simulated system-including the irrelevance of unregulated variables-from sampled data alone. To assess the reproducibility of these results, we tested our inference algorithm on 50 separately simulated sets of data and it consistently recovered almost perfectly the complex functional network structure underlying the simulated data. To our knowledge, this is the first approach for evaluating the effectiveness of functional network inference algorithms at recovering models from limited data. Our simulation approach also enables researchers a priori to design experiments and data-collection protocols that are amenable to functional network inference.

Adaptation, Physiological↗

Functional topology in a network of protein interactions.

MOTIVATION: The building blocks of biological networks are individual protein-protein interactions (PPIs). The cumulative PPI data set in Saccharomyces cerevisiae now exceeds 78 000. Studying the network of these interactions will provide valuable insight into the inner workings of cells. RESULTS: We performed a systematic graph theory-based analysis of this PPI network to construct computational models for describing and predicting the properties of lethal mutations and proteins participating in genetic interactions, functional groups, protein complexes and signaling pathways. Our analysis suggests that lethal mutations are not only highly connected within the network, but they also satisfy an additional property: their removal causes a disruption in network structure. We also provide evidence for the existence of alternate paths that bypass viable proteins in PPI networks, while such paths do not exist for lethal mutations. In addition, we show that distinct functional classes of proteins have differing network properties. We also demonstrate a way to extract and iteratively predict protein complexes and signaling pathways. We evaluate the power of predictions by comparing them with a random model, and assess accuracy of predictions by analyzing their overlap with MIPS database. CONCLUSIONS: Our models provide a means for understanding the complex wiring underlying cellular function, and enable us to predict essentiality, genetic interaction, function, protein complexes and cellular pathways. This analysis uncovers structure-function relationships observable in a large PPI network.

Algorithms↗