Mechanical stimulation has a critical role in the development and maintenance of the skeleton. This function requires the perception of extracellular stimuli as well as their conversion into intracellular biochemical responses. This process is called mechanotransduction and is mediated by a plethora of molecular events that regulate bone metabolism. Indeed, mechanoreceptors, such as integrins, G protein‐coupled receptors, receptor protein tyrosine kinases, and stretch‐activated Ca2+ channels, together with their downstream effectors coordinate the transmission of load‐induced signals to the nucleus and the (...) expression of bone‐related genes. During the past decade, scientists have gained increasing insight into the molecular networks implicated in bone mechanotransduction. In the present paper, we consider the major signaling cascades and transcription factors that control bone and cartilage mechanobiology and discuss the influence of the mechanical microenvironment on the determination of skeletal morphology. (shrink)

Biochemical networks, including those containing signaling pathways, display a wide range of regulatory properties. These include the ability to propagate information across different time scales and to function as switches and oscillators. The mechanisms underlying these complex behaviors involve many interacting components and cannot be understood by experiments alone. The development of computational models and the integration of these models with experiments provide valuable insight into these complex systems‐level behaviors. Here we review current approaches to the development of (...) computational models of biochemical networks and describe the insights gained from models that integrate experimental data, using three examples that deal with ultrasensitivity, flexible bistability and oscillatory behavior. These types of complex behavior from relatively simple networks highlight the necessity of using theoretical approaches in understanding higher order biological functions. BioEssays 24:1110–1117, 2002. © 2002 Wiley‐Periodicals, Inc. (shrink)

The Liver kinase B1 with its downstream target AMP activated protein kinase (LKB1‐AMPK), and the key nutrient sensor mammalian target of rapamycin complex 1 (mTORC1) form two signaling systems that coordinate metabolic and cellular activity with changes in the environment in order to preserve homeostasis. For example, nutritional fluctuations rapidly feed back on these signaling systems and thereby affect cell‐specific functions. Recent studies have started to reveal important roles of these strategic metabolic regulators in Schwann cells for the (...) trophic support and myelination of axons. Because aberrant intermediate metabolism along with mitochondrial dysfunction in Schwann cells is mechanistically linked to nerve abnormalities found in acquired and inherited peripheral neuropathies, manipulation of the LKB1‐AMPK, and mTORC1 signaling hubs may be a worthwhile therapeutic target to mitigate nerve damage in disease. Here, recent advances in our understanding of LKB1‐AMPK and mTORC1 functions in Schwann cells are covered, and future research areas for this key metabolic signaling network are proposed. (shrink)

Recent years have witnessed tremendous growth in the epidermal growth factor (EGF) family of peptide growth factors and the ErbB family of tyrosine kinases, the receptors for these factors. Accompanying this growth has been an increased appreciation for the roles these molecules play in tumorigenesis and in regulating cell proliferation and differentiation during development. Consequently, a significant question has been how diverse biological responses are specified by these hormones and receptors. Here we discuss several characteristics of hormone-receptor interactions and receptor (...) coupling that contribute to specificity: 1) a single EGF family hormone can bind multiple receptors; 2) a single ErbB family receptor can bind multiple hormones; 3) there are three distinct functional groups of EGF family hormones; 4) EGF family hormones can activate receptors in trans, and this heterodimerization diversifies biological responses; 5) ErbB3 requires a receptor partner for signaling; and 6) ErbB family receptors differentially couple to signaling pathways and biological responses. BioEssays 20:41–48, 1998. © 1998 John Wiley & Sons, Inc. (shrink)

Wnt proteins can activate different intracellular signaling cascades in various organisms by interacting with receptors of the Frizzled family. The first identified Wnt signaling pathway, the Wnt/β‐catenin pathway, has been studied in much detail and is highly conserved among species. As to non‐canonical Wnt pathways, the current situation is more nebulous partly because the intracellular mediators of this pathway are not yet fully understood and, in some cases, even identified. However, there are increasing data that prove the existence (...) of non‐canonical Wnt signaling and demonstrate its involvement in different developmental processes. In vertebrates, Wnt‐11 and Wnt‐5A can activate the Wnt/JNK pathway, which resembles the planar cell polarity pathway in Drosophila. The Wnt/Ca2+‐pathway has only been described in Xenopus and zebrafish so far and it is unclear whether it also exists in other organisms. Two recent papers provide us with new insight into non‐canonical Wnt signaling by (1) presenting a new intracellular mediator of non‐canonical signaling in Xenopus1 and (2) implicating the existence of an additional non‐canonical Wnt signaling pathway in flies.2 BioEssays 24:881–884, 2002. © 2002 Wiley Periodicals, Inc. (shrink)

There is an urgent need for novel protection strategies to sustainably secure crop production under changing climates. Studying microbial effectors, defined as microbe‐derived proteins that alter signalling inside plant cells, has advanced our understanding of plant immunity and microbial plant colonisation strategies. Our understanding of effectors in the establishment and beneficial outcome of plant symbioses is less well known. Combining functional and comparative interaction assays uncovered specific symbiont effector targets in highly interconnected plant signalling networks and revealed the potential (...) of effectors in beneficially modulating plant traits. The diverse functionality of symbiont effectors differs from the paradigmatic immuno‐suppressive function of pathogen effectors. These effectors provide solutions for improving crop resilience against climate stress by their evolution‐driven specification in host protein targeting and modulation. Symbiont effectors represent stringent tools not only to identify genetic targets for crop breeding, but to serve as applicable agents in crop management strategies under changing environments. (shrink)

Somatic complementation by fusion of two mutant cells and mixing of their cytoplasms occurs when the genetic defect of one fusion partner is cured by the functional gene product provided by the other. We have found that complementation of mutational defects in the network mediating stimulus‐induced commitment and sporulation of Physarum polycephalum may reflect time‐dependent changes in the signaling state of its molecular building blocks. Network perturbation by fusion of mutant plasmodial cells in different states of activation, and the (...) time‐resolved analysis of somatic complementation effects can be used to systematically probe network structure and dynamics. Time‐resolved somatic complementation quantitatively detects regulatory interactions between the functional modules of a network, independent of their biochemical composition or subcellular localization, and without being limited to direct physical interactions. BioEssays 25:950–960, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

Adaptors are proteins of multi‐modular structure without enzymatic activity. Their capacity to organise large, temporary protein complexes by linking proteins together in a regulated and selective fashion makes them of outstanding importance in the establishment and maintenance of specificity and efficiency in all known signal transduction pathways. This review focuses on the structural and functional characterisation of adaptors involved in tyrosine kinase (TK) signalling. TK‐linked adaptors can be distinguished by their domain composition and binding specificities. However, such structural classifications have (...) proven inadequate as indicators of functional roles. A better way to understand the logic of signalling networks might be to look at functional aspects of adaptor proteins such as signalling specificity, negative versus positive contribution to signal propagation, or their position in the signalling hierarchy. All of these functions are dynamic, suggesting that adaptors have important regulatory roles rather than acting only as stable linkers in signal transduction. BioEssays 28: 465–479, 2006. © 2006 Wiley Periodicals, Inc. (shrink)

Both the quantity of information and the informational content of a signal are defined in the context of signaling games. Informational content is a generalization of standard philosophical notions of propositional content. It is shown how signals that initially carry no information may spontaneously acquire informational content by evolutionary or learning dynamics. It is shown how information can flow through signaling chains or signaling networks.

A comparison of six alternative definitions of the term 'cellular pathway' against the background of ontological realism.

To depict the mechanisms that have enabled the emergence of semantic conventions, philosophers and researchers particularly access a game-theoretic model: the signaling game. In this article I argue that this model is also quite appropriate to analyze not only the emergence of a semantic convention, but also its change. I delineate how the application of signaling games helps to reproduce and depict mechanisms of semantic change. For that purpose I present a model that combines a signaling game (...) with innovative reinforcement learning; in simulation runs I conduct this game repeatedly within a multi-agent setup, where agents are arranged in social network structures. The results of these runs are contrasted with an attested theory from sociolinguistics: the ‘weak tie’ theory. Analyses of the produced data target a deeper understanding of the role of environmental variables for the promotion of semantic change or solidity of semantic conventions. (shrink)

Embryonic development and adult tissue homeostasis are controlled through activation of intracellular signal transduction pathways by extracellular growth factors. In the past, signal transduction has largely been regarded as a linear process. However, more recent data from large‐scale and high‐throughput experiments indicate that there is extensive cross‐talk between individual signaling cascades leading to the notion of a signaling network. The behavior of such complex networks cannot be predicted by simple intuitive approaches but requires sophisticated models and computational (...) simulations. The purpose of such models is to generate experimentally testable hypotheses and to find explanations for unexpected experimental results. Here, we discuss the need for, and the future impact of, mathematical models for exploring signal transduction in different biological contexts such as for example development. BioEssays 30:1110–1125, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

Prostate cancer is the most frequently diagnosed non‐skin cancer and the third leading cause of cancer mortality in men. In the initial stages, prostate cancer is dependent on androgens for growth, which is the basis for androgen ablation therapy. However, in most cases, prostate cancer progresses to a hormone refractory phenotype for which there is no effective therapy available at present. The androgen receptor (AR) is required for prostate cancer growth in all stages, including the relapsed, “androgen‐independent” tumors in the (...) presence of very low levels of androgens. This review focuses on AR function and AR‐target genes and summarizes the major signaling pathways implicated in prostate cancer progression, their crosstalk with each other and with AR signaling. This complex network of interactions is providing a deeper insight into prostate carcinogenesis and may form the basis for novel diagnostic and therapeutic strategies. BioEssays 29:1227–1238, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

We employ the Social Signaling Model and life history of a Western Dani big-man, Tibenuk, to analyze a neglected curiosity in the career of the big-man type. The big-man is renowned as an economic entrepreneur, the master of material displays. In New Guinea, however, big-men had invariably first gained fame and some influence as eminent warriors. The SSM accounts for this two-part career path by proposing that small-scale social organization rests on honest, competitive signaling of individual and collective (...) fighting strength, with leaders being those who excel in these contests. The performances for which big-men are already known, conspicuous ceremonial displays, broadcast this strength indirectly. Explicitly conceptualized as symbolic fighting, they constituted indexical proxies for their sponsors’ individual and collective willingness and ability to fight. Success on the battlefield, though, signaled fighting strength more directly. Men therefore had to demonstrate strength on both the battlefield and the ceremonial ground if they were to become big-men. This was Tibenuk’s achievement. When he was young and at his physical peak, he demonstrated outstanding capability in war. War is a young man’s game, however, and as his physical capacities waned, he shifted to politics, an older man’s game, honing his political talents and developing extensive political networks that allowed him to sponsor massive pig feasts, the principal form of conspicuous ceremonial display. Tibenuk’s career also reveals synergies between warrior and political talents that hitherto have been overlooked in big-man analysis. (shrink)

Cooption and modularity are informative concepts in evolutionary developmental biology. Genes function within complex networks that act as modules in development. These modules can then be coopted in various functional and evolutionary contexts. Hormonal signaling, the main focus of this review, has a modular character. By regulating the activities of genes, proteins and other cellular molecules, a hormonal signal can have major effects on physiological and ontogenetic processes within and across tissues over a wide spatial and temporal scale. (...) Because of this property, we argue that hormones are frequently involved in the coordination of life history transitions (LHTs) and their evolution (LHE). Finally, we promote the usefulness of a comparative, non-model system approach towards understanding how hormones function and guide development and evolution, highlighting thyroid hormone function in echinoids as an example. BioEssays 27:64–75, 2005. © 2004 Wiley Periodicals, Inc. (shrink)

Recent work by Brian Skyrms offers a very general way to think about how information flows and evolves in biological networks—from the way monkeys in a troop communicate to the way cells in a body coordinate their actions. A central feature of his account is a way to formally measure the quantity of information contained in the signals in these networks. In this article, we argue there is a tension between how Skyrms talks of signalling networks and (...) his formal measure of information. Although Skyrms refers to both how information flows through networks and that signals carry information, we show that his formal measure only captures the latter. We then suggest that to capture the notion of flow in signalling networks, we need to treat them as causal networks. This provides the formal tools to define a measure that does capture flow, and we do so by drawing on recent work defining causal specificity. Finally, we suggest that this new measure is crucial if we wish to explain how evolution creates information. For signals to play a role in explaining their own origins and stability, they can’t just carry information about acts; they must be difference-makers for acts. _1_ Signalling, Evolution, and Information _2_ Skyrms’s Measure of Information _3_ Carrying Information versus Information Flow _3.1_ Example 1 _3.2_ Example 2 _3.3_ Example 3 _4_ Signalling Networks Are Causal Networks _4.1_ Causal specificity _4.2_ Formalizing causal specificity _5_ Information Flow as Causal Control _5.1_ Example 1 _5.2_ Examples 2 and 3 _5.3_ Average control implicitly ‘holds fixed’ other pathways _6_ How Does Evolution Create Information? _7_ Conclusion Appendix >. (shrink)

I hypothesize that re-occurring prior experience of complex systems mobilizes a fast response, whose attractor is encoded by their strongly connected network core. In contrast, responses to novel stimuli are often slow and require the weakly connected network periphery. Upon repeated stimulus, peripheral network nodes remodel the network core that encodes the attractor of the new response. This “core-periphery learning” theory reviews and generalizes the heretofore fragmented knowledge on attractor formation by neural networks, periphery-driven innovation, and a number of (...) recent reports on the adaptation of protein, neuronal, and social networks. The core-periphery learning theory may increase our understanding of signaling, memory formation, information encoding and decision-making processes. Moreover, the power of network periphery-related “wisdom of crowds” inventing creative, novel responses indicates that deliberative democracy is a slow yet efficient learning strategy developed as the success of a billion-year evolution. Also see the video abstract here: https://youtu.be/IIjP7zWGjVE. The network core triggers fast responses to previously experienced stimuli. Innovations require the network periphery that encodes a novel attractor by core-remodeling. This core-periphery learning theory is introduced as a general adaptation, learning, decision-making, and forgetting mechanism of all complex systems including protein, metabolic, signaling, neuronal, social networks, and ecosystems. (shrink)

We observe that in certain two-player repeated games of incomplete information, where information may be incomplete on both sides, it is possible for an informed player to signal his status as an informed player to the other without revealing any information about the choice of chance. The key to obtaining such a class of games is to relax the assumption that the players’ moves are observable. We show that in such cases players can achieve a kind of signaling that (...) is “zero-knowledge”, in the sense that the other player becomes convinced that her opponent is informed without ever learning the choice of chance. Moreover, such “zero-knowledge signaling” has all of the statistical properties associated with zero-knowledge proofs in intereactive protocols. In particular, under the general assumption that moves are unobservable, such signaling leads to a class of equilibria in repeated games that are separatingin regard to the status of player 1–informed or uninformed–but only for player 2; any other player in a network, being unable to observe the moves of player 2, remains uncertain as to the status of player 1. (shrink)

In pathological conditions associated with persistent increases in hemodynamic workload (old myocardial infarction, high blood pressure, valvular heart disease), a number of signalling pathways are activated in the heart, all of which promote hypertrophic growth of the heart, characterised at the cellular level by increases in individual cardiac myocyte size. Some of these pathways are required for a successful adaptation to cardiac injury. Other pathways are maladaptive, however, as they lead to progressive contractile dysfunction and heart failure. The free radical (...) gas nitric oxide and natriuretic peptides, both of which are produced in the heart, have emerged as endogenous inhibitors of maladaptive hypertrophy signalling. Overall, it appears that cardiac hypertrophy is controlled by an interplay of pro‐ and antihypertrophic signalling networks. This delicate balance can tip towards adaptation or heart failure. In the future, patients living with cardiac disease may benefit from therapeutic strategies targeting maladaptive hypertrophy signalling pathways. BioEssays 26:608–615, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

Recent work by Brian Skyrms offers a very general way to think about how information flows and evolves in biological networks — from the way monkeys in a troop communicate, to the way cells in a body coordinate their actions. A central feature of his account is a way to formally measure the quantity of information contained in the signals in these networks. In this paper, we argue there is a tension between how Skyrms talks of signalling (...) class='Hi'>networks and his formal measure of information. Although Skyrms refers to both how information flows through networks and that signals carry information, we show that his formal measure only captures the latter. We then suggest that to capture the notion of flow in signalling networks, we need to treat them as causal networks. This provides the formal tools to define a measure that does capture flow, and we do so by drawing on recent work defining causal specificity. Finally, we suggest that this new measure is crucial if we wish to explain how evolution creates information. For signals to play a role in explaining their own origins and stability, they can’t just carry information about acts: they must be difference-makers for acts. (shrink)

The Motin family proteins (Motins) are a class of scaffolding proteins consisting of Angiomotin (AMOT), AMOT‐like protein 1 (AMOTL1), and AMOT‐like protein 2 (AMOTL2). Motins play a pivotal role in angiogenesis, tumorigenesis, and neurogenesis by modulating multiple cellular signaling pathways. Recent findings indicate that Motins are components of the Hippo pathway, a signaling cascade involved in development and cancer. This review discusses how Motins are integrated into the Hippo signaling network, as either upstream regulators or downstream effectors, (...) to modulate cell proliferation and migration. The repression of YAP/TAZ by Motins contributes to growth inhibition, whereas subcellular localization of Motins and their interactions with actin fibers are critical in regulating cell migration. The net effect of Motins on cell proliferation and migration may contribute to their diverse biological functions. (shrink)

We consider how an epistemic network might self-assemble from the ritualization of the individual decisions of simple heterogeneous agents. In such evolved social networks, inquirers may be significantly more successful than they could be investigating nature on their own. The evolved network may also dramatically lower the epistemic risk faced by even the most talented inquirers. We consider networks that self-assemble in the context of both perfect and imperfect communication and compare the behaviour of inquirers in each. This (...) provides a step in bringing together two new and developing research programs, the theory of self-assembling games and the theory of network epistemology. (shrink)

The recent discovery of the medullary circuit driving “hunger responses” – reduced thermogenesis and promoted feeding – has greatly expanded our knowledge on the central neural networks for energy homeostasis. However, how hypothalamic hunger and satiety signals generated under fasted and fed conditions, respectively, control the medullary autonomic and somatic motor mechanisms remains unknown. Here, in reviewing this field, we propose two hypothalamomedullary neural pathways for hunger and satiety signaling. To trigger hunger signaling, neuropeptide Y activates a (...) group of neurons in the paraventricular hypothalamic nucleus (PVH), which then stimulate an excitatory pathway to the medullary circuit to drive the hunger responses. In contrast, melanocortin‐mediated satiety signaling activates a distinct group of PVH neurons, which then stimulate a putatively inhibitory pathway to the medullary circuit to counteract the hunger signaling. The medullary circuit likely contains inhibitory and excitatory premotor neurons whose alternate phasic activation generates the coordinated masticatory motor rhythms to promote feeding. (shrink)

Recent work on the evolution of signaling systems provides a novel way of thinking about genetic information, where information is passed between genes in a regulatory network. I use examples from evolutionary developmental biology to show how information can be created in these networks and how it can be reused to produce rapid phenotypic change.

Hindbrain development is orchestrated by a vertebrate gene regulatory network that generates segmental patterning along the anterior–posterior axis via Hox genes. Here, we review analyses of vertebrate and invertebrate chordate models that inform upon the evolutionary origin and diversification of this network. Evidence from the sea lamprey reveals that the hindbrain regulatory network generates rhombomeric compartments with segmental Hox expression and an underlying Hox code. We infer that this basal feature was present in ancestral vertebrates and, as an evolutionarily constrained (...) developmental state, is fundamentally important for patterning of the vertebrate hindbrain across diverse lineages. Despite the common ground plan, vertebrates exhibit neuroanatomical diversity in lineage‐specific patterns, with different vertebrates revealing variations of Hox expression in the hindbrain that could underlie this diversification. Invertebrate chordates lack hindbrain segmentation but exhibit some conserved aspects of this network, with retinoic acid signaling playing a role in establishing nested domains of Hox expression. (shrink)

In species capable of learning, including our own, individuals can modify their behavior by some adaptive process. Important classes of behavior - mating, predation, coalitions, trade, signaling, and division of labor - involve interactions between individuals. The agents involved learn two things: with whom to interact and how to act. That is to say that adaptive dynamics operates both on structure and strategy.

Most land plants associate with mycorrhizal fungi that can connect roots of neighboring plants in common mycelial networks (CMNs). Recent evidence shows that CMNs transfer warning signals of pathogen and aphid attack between plants. However, we do not know how defence‐related signaling via CMNs operates or how ubiquitous it is. Nor do we know what the ecological relevance and fitness consequences are, particularly from the perspective of the mycorrhizal fungus. Here, we focus on the potential fitness benefits for (...) mycorrhizal fungi and outline hypothetical scenarios in which signal transfer via CMNs is modulated in order to acquire the most benefit for the fungus (i.e. acquisition of carbon) for minimal cost. We speculate that the signal may be quantitative and may elicit plant defence responses on different levels depending on the distance the signal is transferred. Finally, we discuss the possibility of practical applications of this phenomenon for crop protection. (shrink)

Reproduction and immunity are energy intensive, intimately linked processes in most organisms. In women, pregnancy is associated with widespread immunological adaptations that alter immunity to many diseases, whereas, immune dysfunction has emerged as a major cause for infertility in both men and women. Deciphering the molecular bases of this dynamic association is inherently challenging in mammals. This relationship has been traditionally studied in fast‐living, invertebrate species, often in the context of resource allocation between life history traits. More recently, these studies (...) have advanced our understanding of the mechanistic underpinnings of the immunity‐fertility dialogue. Here, we review the molecular connections between reproduction and immunity from the perspective of human pregnancy to mechanistic discoveries in laboratory organisms. We focus particularly on recent invertebrate studies identifying conserved signaling pathways and transcription factors that regulate resource allocation and shape the balance between reproductive status and immune health. (shrink)

Through statistical analysis of datasets describing single cell shape following systematic gene depletion, we have found that the morphological landscapes explored by cells are composed of a small number of attractor states. We propose that the topology of these landscapes is in large part determined by cell‐intrinsic factors, such as biophysical constraints on cytoskeletal organization, and reflects different stable signaling and/or transcriptional states. Cell‐extrinsic factors act to determine how cells explore these landscapes, and the topology of the landscapes themselves. (...) Informational stimuli primarily drive transitions between stable states by engaging signaling networks, while mechanical stimuli tune, or even radically alter, the topology of these landscapes. As environments fluctuate, the topology of morphological landscapes explored by cells dynamically adapts to these fluctuations. Finally we hypothesize how complex cellular and tissue morphologies can be generated from a limited number of simple cell shapes. (shrink)

A categorical, higher dimensional algebra and generalized topos framework for Łukasiewicz–Moisil Algebraic–Logic models of non-linear dynamics in complex functional genomes and cell interactomes is proposed. Łukasiewicz–Moisil Algebraic–Logic models of neural, genetic and neoplastic cell networks, as well as signaling pathways in cells are formulated in terms of non-linear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks. An algebraic formulation of variable ‘next-state functions’ is extended (...) to a Łukasiewicz–Moisil Topos with an n-valued Łukasiewicz–Moisil Algebraic Logic subobject classifier description that represents non-random and non-linear network activities as well as their transformations in developmental processes and carcinogenesis. The unification of the theories of organismic sets, molecular sets and Robert Rosen’s (M,R)-systems is also considered here in terms of natural transformations of organismal structures which generate higher dimensional algebras based on consistent axioms, thus avoiding well known logical paradoxes occurring with sets. Quantum bionetworks, such as quantum neural nets and quantum genetic networks, are also discussed and their underlying, non-commutative quantum logics are considered in the context of an emerging Quantum Relational Biology. (shrink)

As a result of the time‐ and context‐dependency of gene expression, gene regulatory and signaling pathways undergo dynamic changes during development. Creating a model of the dynamics of molecular interaction networks offers enormous potential for understanding how a genome orchestrates the developmental processes of an organism. The dynamic nature of pathway topology calls for new modeling strategies that can capture transient molecular links at the runtime. The aim of this paper is to present a brief and informative, but (...) not all‐inclusive, viewpoint on the computational aspects of modeling and simulation of a non‐static molecular network. BioEssays 26:68–72, 2004. © 2003 Wiley Periodicals, Inc. (shrink)

Although Caenorhabditis and Drosophila proved invaluable in unraveling the molecular mechanisms of apoptosis, it is now clear that these animals are of limited value for understanding the evolution of apoptotic systems. Whereas data from these invertebrates led to the assumption that the extrinsic apoptotic pathway is restricted to vertebrates, recent data from cnidarians and sponges indicate that this pathway predates bilaterian origins. Here we review the phylogenetic distribution of caspase‐8, the initiator caspase of the extrinsic apoptotic pathway, its paralogs and (...) other components of the network. The ancestral caspase‐8 gave rise to four paralogs early in vertebrate evolution, and these have been maintained in many tetrapods. However, eutherians have lost caspase‐18 and myomorph rodents have lost caspase‐10, these losses suggesting functional redundancy amongst caspase‐8 paralogs. The apoptotic network of the eumetazoan ancestor appears to have been complex and vertebrate like, and is only now being revealed by studying simple animals. (shrink)

This paper examines and contrasts two closely related evolutionary explanations in human behaviour: signalling theory, and the theory of Credibility Enhancing Displays. Both have been proposed to explain costly, dangerous, or otherwise ‘extravagant’ social behaviours, especially in the context of religious belief and practice, and each have spawned significant lines of empirical research. However, the relationship between these two theoretical frameworks is unclear, and research which engages both of them is largely absent. In this paper we seek to address this (...) gap at the theoretical level, examining the core differences between the two approaches and prospects and conditions for future empirical testing. We clarify the dynamical and mechanistic bases of signalling and CREDs as explanatory models and contrast the previous uses to which they have been put in the human sciences. Because of idiosyncrasies regarding those uses, several commonly supposed differences and comparative advantages are actually misleading and not in fact generalisable. We also show that signalling and CREDs theories as explanatory models are not interchangeable, because of deep structural differences. As we illustrate, the proposed causal networks of each theory are distinct, with important differences in the endogeneity of various phenomena within each model and their explanatory targets. As a result, they can be seen as complementary rather than in competition. We conclude by surveying the current state of the literature and identifying the differential predictions which could underpin more comprehensive empirical comparison in future research. (shrink)

When imposing traffic congestion pricing around downtown commercial centers, there is a concern that commercial activities will have to consider relocating due to reduced demand, at a cost to merchants. Concerns like these were important in the debates before the introductions of congestion charges in both London and Stockholm and influenced the final policy design choices. This study introduces a sequential experimental game to study reactions to congestion pricing in the commercial sector. In the game, merchants first make location choices. (...) Consumers, who drive to do their shopping, subsequently choose where to shop. Initial responses to the introduction of congestion pricing and equilibrium selection adjustments over time are observed. These observations are compared to responses and adjustments in a condition where congestion pricing is reduced from an initially high level. Payoffs are non-linear and non-transparent, making it less than obvious that the efficient equilibrium will be selected, and introducing possibilities that participants need to discover their preferences and anchor on past experiences. We find that initial responses reflect standard inverse price–demand relations, and that adjustments over time rely on signaling by consumers leading to the efficient equilibrium. There is also evidence that priming from initial experiences influence play somewhat. We confirm that commercial activities relocate following the introduction of congestion pricing and that the adjustment process is costly to merchants. (shrink)

The Golgi apparatus in vertebrate cells consists of individual Golgi stacks fused together in a continuous ribbon structure. The ribbon structure per se is not required to mediate the classical functions of this organelle and the relevance of the “ribbon” structure has been a mystery since first identified ultrastructurally in the 1950s. Recent advances recognize a role for the Golgi apparatus in a range of cellular processes, some mediated by signaling networks which are regulated at the Golgi. Here (...) we review the cellular processes and signaling events regulated by the Golgi apparatus and, in particular, explore an emerging theme that the ribbon structure of the Golgi contributes directly to the regulation of these higher order functions. The Golgi apparatus has recently emerged as a signaling hub for co-ordinating cellular processes. Here we explore the concept that the Golgi ribbon structure is critical in regulating higher order processes. Changes in Golgi ribbon morphology, that is, fragmentation into mini-stacks, modulate cellular processes, and are associated with diseases including neurodegeneration and cancer. (shrink)

Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to cell biology to lend a new perspective on the evolved designs of cells' underlying reaction networks. We present a catalog of 21 design patterns divided into three categories: creational patterns describe processes that build the cell, structural patterns describe the layouts of reaction networks, and (...) behavioral patterns describe reaction network function. Applying this pattern language to the E. coli central metabolic reaction network, the yeast pheromone response signaling network, and other examples lends new insights into these systems. (shrink)

How is a disease contracted, and how does it progress through the body? Answers to these questions are fundamental to understanding both basic biology and medicine. Advances in the biomedical sciences continue to provide more tools to address these fundamental questions and to uncover questions that have not been thought of before. Despite these major advances, we are still facing conceptual and technical challenges when learning about the etiology of disease, especially for genetic diseases. In this review, we illustrate this (...) point by discussing the causal links between molecular mechanisms and systems-level phenotypes in molecular diseases. We begin with an examination of sickle cell anemia, and how mechanisms of the disease have been comprehended over the last century. While sickle cell anemia involves a mutation in a single protein in a single cell type, other diseases involve mutations in networks with many protein interactions and in diverse cell types. We introduce the challenges that result from these differences and illustrate the current obstacles by discussing the RASopathies, a recently discovered class of developmental syndromes that result from mutations in signaling networks. Methods to study mutant genotypes that lead to mutant phenotypes are discussed, particularly the use of model organisms and mutant proteins to study protein interactions that may be important for development of disease. These studies will point toward the future of diagnosing and treating genetic disease. (shrink)

Vascular Endothelial Growth Factor (VEGF) is the most potent and ubiquitous vascular growth factor known to date. Yet, prior to its description as a secreted mitogen for endothelial cells, it was identified as a vascular permeability factor. These seemingly disparate avenues of discovery highlight VEGF's ability to control many distinct aspects of endothelial cell behaviour, including proliferation, migration, specialisation and survival. The versatility of VEGF as a patterning molecule is likely linked to its association with various signalling receptor complexes, but (...) also its expression in several isoforms with a differential affinity for heparan sulfate proteoglycans in the extracellular matrix. In contrast to the absolute requirement for all known VEGF receptors, the presence of only a single VEGF isoform is sufficient for vascular development. However, the isoforms serve as exquisite tools for the fine patterning of growing vessel networks during embryogenesis and in postnatal life. BioEssays 25:1052–1060, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

Reactive oxygen species (ROS) are known as toxic metabolic products in plants and other aerobic organisms. An elaborate and highly redundant plant ROS network, composed of antioxidant enzymes, antioxidants and ROS-producing enzymes, is responsible for maintaining ROS levels under tight control. This allows ROS to serve as signaling molecules that coordinate an astonishing range of diverse plant processes. The specificity of the biological response to ROS depends on the chemical identity of ROS, intensity of the signal, sites of production, (...) plant developmental stage, previous stresses encountered and interactions with other signaling molecules such as nitric oxide, lipid messengers and plant hormones. Although many components of the ROS signaling network have recently been identified, the challenge remains to understand how ROS-derived signals are integrated to eventually regulate such biological processes as plant growth, development, stress adaptation and programmed cell death. (shrink)

In this paper we explore the organizational conditions underlying the emergence of organisms at the multicellular level. More specifically, we shall propose a general theoretical scheme according to which a multicellular organism is an ensemble of cells that effectively regulates its own development through collective mechanisms of control of cell differentiation and cell division processes. This theoretical result derives from the detailed study of the ontogenetic development of three multicellular systems and, in particular, of their corresponding cell-to-cell signaling (...) class='Hi'>networks. The case study supports our claim that a specific type of functional integration among the cells of a multicellular ensemble , is required for it to qualify as a proper organism. Finally, we argue why a multicellular system exhibiting this type of functionally differentiated and integrated developmental organization becomes a self-determining collective entity and, therefore, should be considered as a second-order autonomous system. (shrink)

It is well known that microbial pathogens are able to subvert the host immune system in order to increase microbial replication and propagation. Recent research indicates that another arm of the immune response, that of the chemokine system, is also subject to this sabotage, and is undermined by a range of microbial pathogens, including viruses, bacteria, and parasites. Currently, it is known that the chemokine system is being challenged by a number of mechanisms, and still more are likely to be (...) discovered with further research. Here we first review the general mechanisms by which microbial pathogens bypass mammalian chemokine defences. Broadly, these can be grouped as viral chemokine interacting proteins, microbial manipulation of host chemokine and chemokine receptor expression, microbial blockade of host chemokine receptor signalling, and the largely hypothetical mechanisms of microbial enhancement of host anti‐chemokine networks (including digestion, antagonism, and neutralisation of host chemokines and chemokine receptors). We then discuss the potential results of these interactions in terms of outcome of infection. BioEssays 25:478–488, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

Chloroplasts and other plastids are plant cell organelles that account for major biochemical functions. They contain their own gene expression system but are integrated into the signaling network of the entire cell. Both nuclear and plastid genes are involved in chloroplast biogenesis, and the gene expression pathways both inside and outside the organelle are subject to developmental and environmental control. The plastid transcription apparatus reflects this general scheme, with a basic organelle‐encoded enzymatic machinery surrounded by factors that may be (...) encoded by nuclear genes. Among the transcription regulatory mechanisms thought to play a role during plastid development are: (1) differential usage of promoter elements; (2) phosphorylation of transcription factors by a protein kinase, which is itself subject to phosphorylation and redox control; (3) dynamic changes in the composition of the transcription apparatus. In etioplasts, the dominating polymerase ‘B’ is a bacterial‐type enzyme, whereas the major chloroplast polymerase ‘A’ is a much larger enzyme reminiscent of those in the nucleus. These two enzyme forms may share common components and recruit others during development. (shrink)

Context can determine whether a given gene acts as an oncogene or a tumor suppressor. Deubiquitinating enzymes (DUBs) regulate the stability of many components of the pathways dictating cell fate so it would be expected that alterations in the levels or activity of these enzymes may have oncogenic or tumor suppressive consequences. In the current review we survey publications reporting that genes encoding DUBs are oncogenes or tumor suppressors. For many DUBs both claims have been made. For such “double agents,” (...) the effects of gain or loss of function will depend on the overall status of a complex of molecular signaling networks subject to extensive crosstalk. As the TGF‐β paradox makes clear context is critical in cell fate decisions, and the disconnect between experimental findings and patient survival outcomes can in part be attributed to disparities between culture conditions and the microenvironment in vivo. Convincing claims for oncogene or tumor suppressor roles require the documentation of gene alterations in patient samples; survival curves are alone inadequate. (shrink)

In this article, we argue, first, that there are very different research projects that fall under the heading of “systems biology of cancer.” While they share some general features, they differ in their aims and theoretical commitments. Second, we argue that some explanations in systems biology of cancer are concerned with properties of signaling networks and how they may play an important causal role in patterns of vulnerability to cancer. Further, some systems biological explanations are compelling illustrations of (...) how “top-down” and “bottom-up” approaches to the same phenomena may be integrated. (shrink)

The defense of plants against herbivores and pathogens involves the participation of an enormous range of different metabolites, some of which act directly as defensive weapons against enemies (toxins or deterrents) and some of which act as components of the complex internal signaling network that insures that defense is timed to enemy attack. Recent work reveals a surprising trend: The same compounds may act as both weapons and signals of defense. For example, two groups of well‐studied defensive weapons, glucosinolates (...) and benzoxazinoids, trigger the accumulation of the protective polysaccharide callose as a barrier against aphids and pathogens. In the other direction, several hormones acting in defense signaling (and their precursors and products) exhibit activity as weapons against pathogens. Knowing which compounds are defensive weapons, which are defensive signals and which are both is vital for understanding the functioning of plant defense systems. (shrink)