Primate visual signals in noisy environments

Most animals and plants need to send signals and rely on some sort of response. For an active receptor of signals, virtually all the signal transmissions that litter the environment, bar those that are functional at any given moment, can be described as 'noise'. I concentrate here on some primate examples where loud calls combine with 'loud' colouring and patterns, to suggest that increasing the intensity of signals can help overcome the problem of 'noise'. I also present evidence that certain ecological conditions favour use of the visual channel. I use some examples, drawn from African guenons, to suggest that visual patterns broadcast on this channel have evolved and have, effectively, been elaborated to conform with certain optical principles. These optical properties minimize ambiguity and enhance species-specific (or at least population-specific) distinctiveness. The abilities of ancestral forest primates to discriminate between functional signals and visual 'noise' may have played an important part in providing the basis for our own hominin ancestors' visual proficiencies.     

Conformational sampling of peptides in cellular environments

Biological systems provide a complex environment that can be understood in terms of its dielectric properties. High concentrations of macromolecules and cosolvents effectively reduce the dielectric constant of cellular environments, thereby affecting the conformational sampling of biomolecules. To examine this effect in more detail, the conformational preference of alanine dipeptide, poly-alanine, and melittin in different dielectric environments is studied with computer simulations based on recently developed generalized Born methodology. Results from these simulations suggest that extended conformations are favored over alpha-helical conformations at the dipeptide level at and below dielectric constants of 5-10. Furthermore, lower-dielectric environments begin to significantly stabilize helical structures in poly-alanine at epsilon = 20. In the more complex peptide melittin, different dielectric environments shift the equilibrium between two main conformations: a nearly fully extended helix that is most stable in low dielectrics and a compact, V-shaped conformation consisting of two helices that is preferred in higher dielectric environments. An additional conformation is only found to be significantly populated at intermediate dielectric constants. Good agreement with previous studies of different peptides in specific, less-polar solvent environments, suggest that helix stabilization and shifts in conformational preferences in such environments are primarily due to a reduced dielectric environment rather than specific molecular details. The findings presented here make predictions of how peptide sampling may be altered in dense cellular environments with reduced dielectric response.     

Integration of flowering signals in winter-annual Arabidopsis

Photoperiod is the primary environmental factor affecting flowering time in rapid-cycling accessions of Arabidopsis (Arabidopsis thaliana). Winter-annual Arabidopsis, in contrast, have both a photoperiod and a vernalization requirement for rapid flowering. In winter annuals, high levels of the floral inhibitor FLC (FLOWERING LOCUS C) suppress flowering prior to vernalization. FLC acts to delay flowering, in part, by suppressing expression of the floral promoter SOC1 (SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1). Vernalization leads to a permanent epigenetic suppression of FLC. To investigate how winter-annual accessions integrate signals from the photoperiod and vernalization pathways, we have examined activation-tagged alleles of FT and the FT homolog, TSF (TWIN SISTER OF FT), in a winter-annual background. Activation of FT or TSF strongly suppresses the FLC-mediated late-flowering phenotype of winter annuals; however, FT and TSF overexpression does not affect FLC mRNA levels. Rather, FT and TSF bypass the block to flowering created by FLC by activating SOC1 expression. We have also found that FLC acts as a dosage-dependent inhibitor of FT expression. Thus, the integration of flowering signals from the photoperiod and vernalization pathways occurs, at least in part, through the regulation of FT, TSF, and SOC1.     

Computational models of molecular self-organization in cellular environments

The cellular environment creates numerous obstacles to efficient chemistry, as molecular components must navigate through a complex, densely crowded, heterogeneous, and constantly changing landscape in order to function at the appropriate times and places. Such obstacles are especially challenging to self-organizing or self-assembling molecular systems, which often need to build large structures in confined environments and typically have high-order kinetics that should make them exquisitely sensitive to concentration gradients, stochastic noise, and other non-ideal reaction conditions. Yet cells nonetheless manage to maintain a finely tuned network of countless molecular assemblies constantly forming and dissolving with a robustness and efficiency generally beyond what human engineers currently can achieve under even carefully controlled conditions. Significant advances in high-throughput biochemistry and genetics have made it possible to identify many of the components and interactions of this network, but its scale and complexity will likely make it impossible to understand at a global, systems level without predictive computational models. It is thus necessary to develop a clear understanding of how the reality of cellular biochemistry differs from the ideal models classically assumed by simulation approaches and how simulation methods can be adapted to accurately reflect biochemistry in the cell, particularly for the self-organizing systems that are most sensitive to these factors. In this review, we present approaches that have been undertaken from the modeling perspective to address various ways in which self-organization in the cell differs from idealized models.     

myo-inositol metabolites as cellular signals

The discovery of the second-messenger functions of inositol 1,4,5-trisphosphate and diacylglycerol, the products of hormone-stimulated inositol phospholipid hydrolysis, marked a turning point in studies of hormone function. This review focuses on the myo-inositol moiety which is involved in an increasingly complex network of metabolic interconversions, myo-Inositol metabolites identified in eukaryotic cells include at least six glycerophospholipid isomers and some 25 distinct inositol phosphates which differ in the number and distribution of phosphate groups around the inositol ring. This apparent complexity can be simplified by assigning groups of myo-inositol metabolites to distinct functional compartments. For example, the phosphatidylinositol 4-kinase pathway functions to generate inositol phospholipids that are substrates for hormone-sensitive forms of inositol-phospholipid phospholipase C, whilst the newly discovered phosphatidylinositol 3-kinase pathway generates lipids that are resistant to such enzymes and may function directly as novel mitogenic signals. Inositol phosphate metabolism functions to terminate the second-messenger activity of inositol 1,4,5-trisphosphate, to recycle the latter's myo-inositol moiety and, perhaps, to generate additional signal molecules such as inositol 1,3,4,5-tetrakisphosphate, inositol pentakisphosphate and inositol hexakisphosphate. In addition to providing a more complete picture of the pathways of myo-inositol metabolism, recent studies have made rapid progress in understanding the molecular basis underlying hormonal stimulation of inositol-phospholipid-specific phospholipase C and inositol 1,4,5-trisphosphate-mediated Ca2+ mobilisation.     

Regulation of cellular signals by G-proteins

Extracellular signals are transduced across the cell by the cell surface receptors, with the aid of G-proteins, which act at a critical point of signal transduction and cellular regulation. Structurally, G-proteins are heterotrimeric consisting α, β and γ subunits but in functionally active state they dissociate into α subunit coupled to GTP and as βγ dimer. G-proteins can be broadly divided into two classes based on their sensitivity to pertussis toxin and cholera toxin. Existence of various forms of each of the subunit allows molecular diversity in the subunit species of G-proteins. These subunits interact with a wide range of receptors and effectors, facilitated by post translational modification of their subunits. Different types of G-proteins mediate several signalling events in different parts of the body. This review summarizes the features of (i) structural and functional heterogenity among different subunits of G-proteins, (ii) interaction of G-proteins and their subunits with effectors with specific cases of G-protein mediated signalling in olfaction, phototransduction in the retina, ras andras related transduction and (iii) disease conditions associated with malfunctioning of G-proteins.     

Integration of light and plastid signals

Light and plastid signals promote chloroplast biogenesis and are among the most potent inducers and repressors of photosynthesis-related gene expression, respectively. These signals can be likened to a 'gas and brake system' that promotes efficient chloroplast biogenesis and function. Recent findings indicate that a particular plastid signal can 'rewire' a light signaling network, converting it from an inducer into a repressor of particular photosynthesis-related genes. Therefore, a plastid signal appears to be an endogenous regulator of light signaling rather than a signal acting independently from light. This integration of light and plastid signals may allow plants to proactively manage chloroplast dysfunction when performing chloroplast biogenesis and maintenance in adverse light conditions.     

Evolutionary dynamics of cellular automata-based self-replicators in hostile environments

In this paper we investigate population dynamics, genealogy and complexity-increase of locally interacting populations of cellular automata-based evolving self-replicating loops (evoloops). We outline experiments indicating that the evolutionary growth in complexity, known to be achievable in principle given the complete genetic accessibility granted by universal construction, may be achievable in practice using much simpler replicating structures. By introducing evoloop populations to hostile environments, we demonstrate that selection pressures toward smaller species can be mediated to enable evolutionary accessibility to larger species, which themselves roam a much more vast portion of genetic state-space. We show that this growth in size results from intrinsically biased genealogy inherent in the rules of the evoloop CA, normally suppressed by selection pressures from direct competition favouring the smallest species. This shows that, in populations of simple self-replicating structures, a limited form of complexity-increase may result from a process which is driven by biased genealogical connectivity--a purely emergent property arising out of bottom-up evolutionary dynamics--and not just by adaptation . Implications of this result are discussed and contrasted with other self-replication studies in Artificial Life and Biology.     

Field-effect devices for detecting cellular signals

The integration of living cells together with silicon field-effect devices challenges a new generation of biosensors and bioelectronic devices. Cells are representing highly organised complex systems, optimised by millions of years of evolution and offering a broad spectrum of bioanalytical receptor “tools” such as enzymes, nucleic acids proteins, etc. Their combination with semiconductor-based electronic chips allows the construction of functional hybrid systems with unique functional and electronic properties for both fundamental studies and biosensoric applications. This review article summarises recent advances and trends in research and development of cell/transistor hybrids (cell-based field-effect transistors) as well as light-addressable potentiometric sensors.     

Flexibility in animal signals facilitates adaptation to rapidly changing environments

Charles Darwin posited that secondary sexual characteristics result from competition to attract mates. In male songbirds, specialized vocalizations represent secondary sexual characteristics of particular importance because females prefer songs at specific frequencies, amplitudes, and duration. For birds living in human-dominated landscapes, historic selection for song characteristics that convey fitness may compete with novel selective pressures from anthropogenic noise. Here we show that black-capped chickadees (Poecile atricapillus) use shorter, higher-frequency songs when traffic noise is high, and longer, lower-frequency songs when noise abates. We suggest that chickadees balance opposing selective pressures by use low-frequency songs to preserve vocal characteristics of dominance that repel competitors and attract females, and high frequency songs to increase song transmission when their environment is noisy. The remarkable vocal flexibility exhibited by chickadees may be one reason that they thrive in urban environments, and such flexibility may also support subsequent genetic adaptation to an increasingly urbanized world.     

Engineering small molecule specificity in nearly identical cellular environments

Methotrexate (MTX), an inhibitor of dihydrofolate reductase, was tethered to an FKBP12 ligand (SLF), and the resulting bifunctional molecule (MTXSLF) potently inhibits either enzyme but not both simultaneously. MTXSLF is cytotoxic to fibroblasts derived from FKBP12-null mice but is detoxified 40-fold by FKBP12 in wild-type fibroblasts. These studies demonstrate that non-target proteins in an otherwise identical genetic background can be used to predictably regulate the biological activity of synthetic molecules.     

Sphingomyelin and derivatives as cellular signals.

This comprehensive review was necessitated by recent observations suggesting that sphingomyelin and derivatives may serve second messenger functions. It has attempted to remain true to the theme of cellular signalling. Hence, it has focussed on the lipids involved primarily with respect to their metabolism and properties in mammalian systems. The enzymology involved has been emphasized. An attempt was made to define directions in which signals may be flowing. However, the evidence presented to date is insufficient to conclusively designate the mechanisms of stimulated lipid metabolism. Hence, the proposed pathways must be viewed as preliminary. Further, the biologic functions of these lipids is for the most part uncertain. Thus, it is difficult to presently integrate this sphingomyelin pathway into the greater realm of cell biology. Nevertheless, the present evidence appears to suggest that a sphingomyelin pathway is likely to possess important bioregulatory functions. Hopefully, interest in this novel pathway will grow and allow a more complete understanding of the roles of these sphingolipids in physiology and pathology.     

Influence of traffic variations on exposure to wireless signals in realistic environments

In this article, the general public daily exposure to broadcast signals and Global System for Mobile Communications (GSM) or Universal Mobile Telecommunications System (UMTS) mobile telephone signals in indoor areas is investigated. Temporal variations and traffic distributions during a day at different indoor sites in urban and rural zones are presented. The goal is to analyze the real exposure compared to the maximum assessment imposed by radio protection standards and to characterize the ratio between daily and maximum theoretical values. Hence, a realistic maximum is proposed based on the statistical analysis performed using measurements. Broadcast signals remain constant over the day so they are best fitted with a Normal distribution while the mobile telephone signals depend on the traffic demand during the day so they fit a three‐Gaussian distribution model. A general mask is also constructed for underlining the maximum equivalent active traffic for different periods in the day. Also, relations between the mean values over 24 h, the realistic maximal values (at 99%) and the maximal theoretical values are presented. The realistic maximum is also presented with a sliding time average of 6 min applied to the measurements in accordance with international standards. An extrapolation factor is given for the different systems to easily assess the maximum values starting from an instantaneous measurement. The extrapolation factor is also given for a broadband measurement to estimate the maximum potential exposure during the day. Bioelectromagnetics 33:288–297, 2012. © 2011 Wiley Periodicals, Inc.     

Extracellular signals, transcriptional responses and cellular specificity

The expression of a relatively small set of common primary response genes is frequently induced, in a variety of cellular responses, by growth factors, protein hormones and neurotransmitters. The characterization of these genes and their products may provide clues to the mechanisms by which ligand- and cell-specific responses may be generated.     

Biphasic responses, quantal signals and cellular behaviour

It is commonplace to think of thresholds in biological systems. Biphasic responses, with both thresholds and upper limits, or lintels, are also surprisingly common. In this paper we show that they are found in many systems in which an aspect of cellular behaviour is controlled by chemical signals. In some cases the biphasic response can lead to the partitioning of a tissue into regions expressing different behaviours and, therefore, in principle able to take different developmental and evolutionary paths within the same organism. Several other features are common; these include brief, all-or-nothing responses and the expression of different behaviours evoked by a signal of a single chemical species in one or more cell types, but over different concentration ranges. Such behaviour is illustrated very clearly by the differentiation of cells in the mammalian immune system as well as by developing slime mould cells, so the underlying principle is widespread. We suggest that the interaction of unitary behaviours with chemical signals showing such non-linear concentration dependences will account for the complexity of development.     

Integration of NPY, AGRP, and melanocortin signals in the hypothalamic paraventricular nucleus: evidence of a cellular basis for the adipostat

Energy stores are held relatively constant in many mammals. The circuitry necessary for maintaining energy homeostasis should (1) sense the amount of energy stored in adipose tissue, (2) sense and integrate the multiple opposing signals regarding nutritional state, and (3) provide output regulating energy intake and expenditure to maintain energy homeostasis. We demonstrate that individual neurons within the paraventricular nucleus of the hypothalamus (PVH) are capable of detection and integration of orexigenic (neuropeptide Y [NPY]) and anorexigenic (melanocortin) signals, that NPY and melanocortins are functional antagonists of each other within the PVH in the regulation of feeding behavior, and that melanocortin administration within the PVH regulates both feeding behavior and energy expenditure. These data provide a cellular basis for the adipostat within neurons in the PVH that appear to be jointly regulated by NPY- and melanocortin-responsive neurons.     

Image motion environments: background noise for movement-based animal signals

Understanding the evolution of animal signals has to include consideration of the structure of signal and noise, and the sensory mechanisms that detect the signals. Considerable progress has been made in understanding sounds and colour signals, however, the degree to which movement-based signals are constrained by the particular patterns of environmental image motion is poorly understood. Here we have quantified the image motion generated by wind-blown plants at 12 sites in the coastal habitat of the Australian lizard Amphibolurus muricatus. Sampling across different plant communities and meteorological conditions revealed distinct image motion environments. At all locations, image motion became more directional and apparent speed increased as wind speeds increased. The magnitude of these changes and the spatial distribution of image motion, however, varied between locations probably as a function of plant structure and the topographic location. In addition, we show that the background motion noise depends strongly on the particular depth-structure of the environment and argue that such microhabitat differences suggest specific strategies to preserve signal efficacy. Movement-based signals and motion processing mechanisms, therefore, may reveal the same type of habitat specific structural variation that we see for signals from other modalities.