Abstraction in perceptual symbol systems

After reviewing six senses of abstraction, this article focuses on abstractions that take the form of summary representations. Three central properties of these abstractions are established: ( i ) type-token interpretation; (ii) structured representation; and (iii) dynamic realization. Traditional theories of representation handle interpretation and structure well but are not sufficiently dynamical. Conversely, connectionist theories are exquisitely dynamic but have problems with structure. Perceptual symbol systems offer an approach that implements all three properties naturally. Within this framework, a loose collection of property and relation simulators develops to represent abstractions. Type-token interpretation results from binding a property simulator to a region of a perceived or simulated category member. Structured representation results from binding a configuration of property and relation simulators to multiple regions in an integrated manner. Dynamic realization results from applying different subsets of property and relation simulators to category members on different occasions. From this standpoint, there are no permanent or complete abstractions of a category in memory. Instead, abstraction is the skill to construct temporary online interpretations of a category's members. Although an infinite number of abstractions are possible, attractors develop for habitual approaches to interpretation. This approach provides new ways of thinking about abstraction phenomena in categorization, inference, background knowledge and learning.     

A conceptual framework for the spatial analysis of functional trait diversity

Functional trait diversity is a popular tool in modern ecology, mainly used to infer assembly processes and ecosystem functioning. Patterns of functional trait diversity are shaped by ecological processes such as environmental filtering, species interactions and dispersal that are inherently spatial, and different processes may operate at different spatial scales. Adding a spatial dimension to the analysis of functional trait diversity may thus increase our ability to infer community assembly processes and to predict change in assembly processes following disturbance or land‐use change. Richness, evenness and divergence of functional traits are commonly used indices of functional trait diversity that are known to respond differently to large‐scale filters related to environmental heterogeneity and dispersal and fine‐scale filters related to species interactions (competition). Recent developments in spatial statistics make it possible to separately quantify large‐scale patterns (variation in local means) and fine‐scale patterns (variation around local means) by decomposing overall spatial autocorrelation quantified by Moran's coefficient into its positive and negative components using Moran eigenvector maps (MEM). We thus propose to identify the spatial signature of multiple ecological processes that are potentially acting at different spatial scales by contrasting positive and negative components of spatial autocorrelation for each of the three indices of functional trait diversity. We illustrate this approach with a case study from riparian plant communities, where we test the effects of disturbance on spatial patterns of functional trait diversity. The fine‐scale pattern of all three indices was increased in the disturbed versus control habitat, suggesting an increase in local scale competition and an overall increase in unexplained variance in the post‐disturbance versus control community. Further research using simulation modeling should focus on establishing the proposed link between community assembly rules and spatial patterns of functional trait diversity to maximize our ability to infer multiple processes from spatial community structure.     

A role for systems epidemiology in tuberculosis research

Despite being a curable disease, tuberculosis (TB) killed more people in 2009 than during any previous year in history. Progress in TB research has been slow, and remains burdened by important gaps in our knowledge of the basic biology of Mycobacterium tuberculosis, the causative agent of TB, and its interaction with the human host. Fortunately, major systems biology initiatives have recently been launched that will help fill some of these gaps. However, to fully comprehend TB and control this disease globally, current systems biological approaches will not suffice. The influence of host and pathogen diversity, changes in human demography, and socioeconomic and environmental factors will also need to be considered. Such a multidisciplinary approach might be best described as 'systems epidemiology' in an effort to overcome the traditional boundaries between basic biology and classical epidemiology.     

A role for brain stress systems in addiction

Drug addiction is a chronically relapsing disorder characterized by compulsion to seek and take drugs and has been linked to dysregulation of brain regions that mediate reward and stress. Activation of brain stress systems is hypothesized to be key to the negative emotional state produced by dependence that drives drug seeking through negative reinforcement mechanisms. This review explores the role of brain stress systems (corticotropin-releasing factor, norepinephrine, orexin [hypocretin], vasopressin, dynorphin) and brain antistress systems (neuropeptide Y, nociceptin [orphanin FQ]) in drug dependence, with emphasis on the neuropharmacological function of extrahypothalamic systems in the extended amygdala. The brain stress and antistress systems may play a key role in the transition to and maintenance of drug dependence once initiated. Understanding the role of brain stress and antistress systems in addiction provides novel targets for treatment and prevention of addiction and insights into the organization and function of basic brain emotional circuitry.     

Accuracy of alternative representations for integrated biochemical systems

The Michaelis-Menten formalism often provides appropriate representations of individual enzyme-catalyzed reactions in vitro but is not well suited for the mathematical analysis of complex biochemical networks. Mathematically tractable alternatives are the linear formalism and the power-law formalism. Within the power-law formalism there are alternative ways to represent biochemical processes, depending upon the degree to which fluxes and concentrations are aggregated. Two of the most relevant variants for dealing with biochemical pathways are treated in this paper. In one variant, aggregation leads to a rate law for each enzyme-catalyzed reaction, which is then represented by a power-law function. In the other, aggregation produces a composite rate law for either net rate of increase or net rate of decrease of each system constituent; the composite rate laws are then represented by a power-law function. The first variant is the mathematical basis for a method of biochemical analysis called metabolic control, the latter for biochemical systems theory. We compare the accuracy of the linear and of the two power-law representations for networks of biochemical reactions governed by Michaelis-Menten and Hill kinetics. Michaelis-Menten kinetics are always represented more accurately by power-law than by linear functions. Hill kinetics are in most cases best modeled by power-law functions, but in some cases linear functions are best. Aggregation into composite rate laws for net increase or net decrease of each system constituent almost always improves the accuracy of the power-law representation. The improvement in accuracy is one of several factors that contribute to the wide range of validity of this power-law representation. Other contributing factors that are discussed include the nonlinear character of the power-law formalism, homeostatic regulatory mechanisms in living systems, and simplification of rate laws by regulatory mechanisms in vivo.     

Chaos theory: the transforming role of functional systems

The review of applications of chaos theory in physiology shows, that this theory makes possible to get quantitative measure of degree of the order for such processes as neuronal activity, heart rate, electroencephalogram etc. The basic concepts of chaos theory--fractal dimension. Liapunov exponents, entropy, some algorithms for obtaining of quantitative characteristics of degree of the order for different processes--have been considered in this paper. The main areas for application chaos theory in physiology and medicine have been revealed and some examples of practical and theoretical achievements in this new region of investigation are given, as well as existing limitations and problems with results interpretation. Entirely new possibilities for understanding of the order in physiological processes are shown when estimation is made from the point of view of the functional system theory.     

A role for oligonucleotide-based RNA-knock down technologies in functional genomics

Functional genomics is inundating the pharmaceutical industry with large numbers of potential gene targets from several sources such as gene expression profiling experiments (DNA microchips, proteomics) or database mining. Oligonucleotide-based RNA-knock down technologies such as antisense or RNA interference can aid in the filtering and prioritization of target candidates in the drug discovery process.     

Evidence for dissociation between the perceptual and visuomotor systems in humans

When a visual stimulus is continuously moved behind a small stationary window, the window appears displaced in the direction of motion of the stimulus. In this study we showed that the magnitude of this illusion is dependent on (i) whether a perceptual or visuomotor task is used for judging the location of the window (ii) the directional signature of the stimulus, and (iii) whether or not there is a significant delay between the end of the visual presentation and the initiation of the localization measure. Our stimulus was a drifting sinusoidal grating windowed in space by a stationary, two-dimensional, Gaussian envelope (sigma=1 cycle of sinusoid). Localization measures were made following either a short (200 ms) or long (4.2 s) post-stimulus delay. The visuomotor localization error was up to three times greater than the perceptual error for a short delay. However, the visuomotor and perceptual localization measures were similar for a long delay. Our results provide evidence in support of the hypothesis that separate cortical pathways exist for visual perception and visually guided action and that delayed actions rely on stored perceptual information.     

Abstract representations of biological systems in supercategories

An abstract representation of biological systems from the standpoint of the theory of supercategories is presented. The relevance of such representations forG-relational biologies is suggested. In section A the basic concepts of our representation, that is class, system, supercategory and measure are introduced. Section B is concerned with the mathematical representation starting with some axioms and principles which are natural extensions of the current abstract representations in biology. Likewise, some extensions of the principle of adequate design are introduced in section C. Two theorems which present the connection between categories and supercategories are proved. Two other theorems concerning the dynamical behavior of biological and biophysical systems are derived on the basis of the previous considerations. Section D is devoted to a general study of oscillatory behavior in enzymic systems, some general quantitative relations being derived from our representation. Finally, the relevance of these results for a quantum theoretic approach to biology is discussed.     

A conceptual and statistical framework for adaptive radiations with a key role for diversity dependence

Abstract In this article we propose a new framework for studying adaptive radiations in the context of diversity-dependent diversification. Diversity dependence causes diversification to decelerate at the end of an adaptive radiation but also plays a key role in the initial pulse of diversification. In particular, key innovations (which in our definition include novel traits as well as new environments) may cause decoupling of the diversity-dependent dynamics of the innovative clade from the diversity-dependent dynamics of its ancestral clade. We present a likelihood-based inference method to test for decoupling of diversity dependence using molecular phylogenies. The method, which can handle incomplete phylogenies, identifies when the decoupling took place and which diversification parameters are affected. We illustrate our approach by applying it to the molecular phylogeny of the North American clade of the legume tribe Psoraleeae (47 extant species, of which 4 are missing). Two diversification rate shifts were previously identified for this clade; our analysis shows that the first, positive shift can be associated with decoupling of two Pediomelum subgenera from the other Psoraleeae lineages, while we argue that the second, negative shift can be attributed to speciation being protracted. The latter explanation yields nonzero extinction rates, in contrast to previous findings. Our framework offers a new perspective on macroevolution: new environments and novel traits (ecological opportunity) and diversity dependence (ecological limits) cannot be considered separately.     

A functional role for VAP-33 in insulin-stimulated GLUT4 traffic

Soluble N-ethylmaleimide sensitive factor attachment protein receptors (SNAREs) are critical proteins in membrane fusion, in both regulated and constitutive vesicular traffic. In addition, proteins that interact with the SNAREs are thought to regulate fusion. Vesicle-associated membrane protein-2 (VAMP-2) is a SNARE protein involved in insulin-dependent glucose transporter 4 (GLUT4) traffic. VAMP-2 is required for productive GLUT4 incorporation into the plasma membrane. VAMP-associated protein of 33 kDa (VAP-33) is an integral membrane protein that binds VAMPs in vitro , and is hypothesized to be a regulator of VAMPs. In L6 skeletal myoblasts, which display insulin-dependent traffic of GLUT4, we show that VAP-33 colocalized significantly with VAMP-2 using indirect confocal immunofluorescence and biochemical cosegregation. Overexpression of wild-type VAP-33 in L6 myoblasts attenuated the insulin-dependent incorporation of myc-tagged GLUT4 into the plasma membrane, and this response was restored by co-overexpression of VAMP-2 linked to green fluorescent protein. Antibodies to VAP-33 microinjected into 3T3-L1 adipocytes abrogated the insulin-stimulated translocation of GLUT4 to the plasma membrane, as measured in adhered plasma membrane lawns. Immunopurified VAMP-2-containing compartments from L6 myotubes and 3T3-L1 adipocytes showed significant levels of VAP-33. We propose that VAP-33 may be a regulator of VAMP-2 availability for GLUT4 traffic and other vesicle fusion events.     

A functional role for Nlrp6 in intestinal inflammation and tumorigenesis

The nucleotide-binding oligomerization domain-like receptor (NLR) family member, Nlrp6, has been implicated in inflammasome signaling to activate caspase-1, which is essential for the production of mature IL-1β and IL-18. However, a function for Nlrp6 in vivo has never been demonstrated. Due to the relative high expression of Nlrp6 in intestinal tissue, we hypothesized that Nlrp6 has a role in intestinal homeostasis. Indeed, Nlrp6-deficient mice are more susceptible to chemically induced colitis as well as colitis-induced tumorigenesis than wild-type (WT) mice. Nlrp6-deficient mice exhibited significantly more inflammation within the colon than WT mice after dextran sulfate sodium treatment. Their inability to resolve inflammation and repair damaged epithelium as efficiently as WT mice resulted in prolonged increases in epithelial proliferative activity that likely underlie the increased propensity for tumors in these mice during chronic inflammation. We further show that the activity of Nlrp6 in hematopoietic cells is critical for protection against inflammation-related colon tumorigenesis. This study highlights the importance of NLR function in maintaining intestinal homeostasis to prevent the development of aberrant inflammation and tumor development within the colon.     

A role for cAMP in the development of functional neuromuscular transmission

We have found that the incidence of functionally connected neuron-myotube pairs in chick ciliary-myotube cultures increases from 58% to more than 90% when the cells are treated for several hours with 8-bromo-cyclic adenosine monophosphate (8-br-cAMP) or with agents known to increase intracellular cAMP. The increase in connectivity was not accompanied by a change in neuron survival, or in the length of neurite-myotube contact. Moreover, there was no change in the shape of the presynaptic action potential, in mean end plate potential (epp) amplitude or in the sensitivity of postsynaptic acetylcholine receptors (AChRs). One interpretation of these results in that a cAMP-dependent phosphorylation acts as a trigger to activate a previously "silent" synapse.     

A common framework for perceptual learning

In this review, we summarize recent evidence that perceptual learning can occur not only under training conditions but also in situations of unattended and passive sensory stimulation. We suggest that the key to learning is to boost stimulus-related activity that is normally insufficient exceed a learning threshold. We discuss how factors such as attention and reinforcement have crucial, permissive roles in learning. We observe, however, that highly optimized stimulation protocols can also boost responses and promote learning. This helps to reconcile observations of how learning can occur (or fail to occur) in seemingly contradictory circumstances, and argues that different processes that affect learning operate through similar mechanisms that are probably based on, and mediated by, neuromodulatory factors.     

A functional role for Anopheles gambiae Arrestin1 in olfactory signal transduction

Insect sensory arrestins act to desensitize visual and olfactory signal transduction pathways, as evidenced by the phenotypic effects of mutations in the genes encoding both Arr1 and Arr2 in Drosophila melanogaster. To assess whether such arrestins play similar roles in other, more medically relevant dipterans, we examined the ability of Anopheles gambiae sensory arrestin homologs AgArr1 and AgArr2 to rescue phenotypes associated with an olfactory deficit observed in D. melanogaster arrestin mutants. Of these, only AgArr1 facilitated significant phenotypic rescue of the corresponding Drosophila arr mutant olfactory phenotype, consistent with the view that functional orthology is shared by these Arr1 homologs. These results represent the first step in the functional characterization of AgArr1, which is highly expressed in olfactory appendages of An. gambiae in which it is likely to play an essential role in olfactory signal transduction. In addition to providing insight into the common elements of the peripheral olfactory system of dipterans, this work validates the importance of AgArr1 as a potential target for novel anti-malaria strategies that focus on olfactory-based behaviors in An. gambiae.     

A functional role for death proteases in s-Myc- and c-Myc-mediated apoptosis.

Upon activation, cell surface death receptors, Fas/APO-1/CD95 and tumor necrosis factor receptor-1 (TNFR-1), are attached to cytosolic adaptor proteins, which in turn recruit caspase-8 (MACH/FLICE/Mch5) to activate the interleukin-1 beta-converting enzyme (ICE)/CED-3 family protease (caspase) cascade. However, it remains unknown whether these apoptotic proteases are generally involved in apoptosis triggered by other stimuli such as Myc and p53. In this study, we provide lines of evidence that a death protease cascade consisting of caspases and serine proteases plays an essential role in Myc-mediated apoptosis. When Rat-1 fibroblasts stably expressing either s-Myc or c-Myc were induced to undergo apoptosis by serum deprivation, a caspase-3 (CPP32)-like protease activity that cleaves a specific peptide substrate, Ac-DEVD-MCA, appeared in the cell lysates. Induction of s-Myc- and c-Myc-mediated apoptotic cell death was effectively prevented by caspase inhibitors such as Z-Asp-CH2-DCB and Ac-DEVD-CHO. Furthermore, exposing the cells to a serine protease inhibitor, 4-(2-aminoethyl)benzenesulfonyl fluoride (AEBSF), also significantly inhibited s-Myc- and c-Myc-mediated apoptosis and the appearance of the caspase-3-like protease activity in vivo. However, AEBSF did not directly inhibit caspase-3-like protease activity in the apoptotic cell lysates in vitro. Together, these results indicate that caspase-3-like proteases play a critical role in both s-Myc- and c-Myc-mediated apoptosis and that caspase-3-like proteases function downstream of the AEBSF-sensitive step in the signaling pathway of Myc-mediated apoptosis.