How similar are nut-cracking and stone-flaking? A functional approach to percussive technology

Various authors have suggested similarities between tool use in early hominins and chimpanzees. This has been particularly evident in studies of nut-cracking which is considered to be the most complex skill exhibited by wild apes, and has also been interpreted as a precursor of more complex stone-flaking abilities. It has been argued that there is no major qualitative difference between what the chimpanzee does when he cracks a nut and what early hominins did when they detached a flake from a core. In this paper, similarities and differences between skills involved in stone-flaking and nut-cracking are explored through an experimental protocol with human subjects performing both tasks. We suggest that a ‘functional’ approach to percussive action, based on the distinction between functional parameters that characterize each task and parameters that characterize the agent''s actions and movements, is a fruitful method for understanding those constraints which need to be mastered to perform each task successfully, and subsequently, the nature of skill involved in both tasks.     

How many replicates of arrays are required to detect gene expression changes in microarray experiments? A mixture model approach

Background  

It has been recognized that replicates of arrays (or spots) may be necessary for reliably detecting differentially expressed genes in microarray experiments. However, the often-asked question of how many replicates are required has barely been addressed in the literature. In general, the answer depends on several factors: a given magnitude of expression change, a desired statistical power (that is, probability) to detect it, a specified Type I error rate, and the statistical method being used to detect the change. Here, we discuss how to calculate the number of replicates in the context of applying a nonparametric statistical method, the normal mixture model approach, to detect changes in gene expression.     

How to model the events in cutaneous fibrosis?

Skin fibrosis is classically seen as the consequence of chronic inflammation and altered healing response that is characterized by the differentiation of fibroblasts into secretory myofibroblasts and accumulation of connective tissue. Although fibrosis severely affects organ function and causes esthetic defects, no effective therapy is currently available to attenuate the fibrogenic process probably because the fibrogenic process is more complex than previously thought. Indeed, it might involve several interacting and mutually dependent cell types (fibroblasts, keratinocytes, endothelial cells, inflammatory cells), numerous paracrine factors, bio-active molecules and micro-environmental stimuli (growth factors, vasoactive peptides, balance between pro- and anti-inflammatory cytokines, coagulation system, reactive oxygen species, extracellular matrix...). In this perspective, the traditional approach that model individual cell response in simple cell culture system is probably inadequate and too simplistic. This article reviews the new models used to study skin fibrosis in vitro, in organotypic culture systems and in vivo and examines how these different models might be used to identify new molecular pathways involved in fibrogenesis. The monolayer cultures allow the study of fibrogenic signals induced by a single factor on a single cell type. Isolation of cells from fibrotic tissue allows to define the fibrogenic differentiation acquired in vivo. The organotypic models allow cell to cell and cell to matrix interaction and the experimental models in pigs and mice allowed studies in integrated physiological systems. These various and complementary models would also provide new tools to develop and test new drugs and treatments.     

How universal are reserve design rules? A test using butterflies and their life history traits

We used butterfly species lists available for a set of 125 Czech Republic National Nature Reserves and Monuments, the highest small‐sized conservation category in the country encompassing practically all biotope types existing in central Europe, to test the validity of generally agreed “reserve design rules” using multivariate ordination analyses. Further, we used ordination analysis of butterfly life history traits to seek for biological mechanisms responsible for butterfly community responses to essentially geometric reserves characteristics. Reserve area, relative perimeter, within reserve habitat heterogeneity, and surrounding landscape compositional and configurational heterogeneity all affected the composition of butterfly assemblages after controlling for effects of geographical position and prevailing biotope type. Species inclining towards large reserves displayed low mobility and high local population density, probably because they require large habitat areas to maintain self‐sustaining populations; such species tend to have restricted distribution in the country and threatened status. Reserves with relatively long boundaries hosted species with high mobility, broad trophic range and long adult period; faunas of such reserves contain high proportions of widespread generalists. Species with narrow trophic ranges inclined towards reserves containing diverse habitats, probably due to requirements for high floristic diversity. Species with short adult flight, low generations number and overwintering in early stages inclined towards reserves situated amidst diverse landscapes, perhaps because such species require finely‐grained mosaics for metapopulation dynamics. Commonly agreed reserve design rules thus hold for Central European butterflies, but different design characteristics are important for individual species, depending on their life histories.     

Rad3 and Sty1 function in Schizosaccharomyces pombe: an integrated response to DNA damage and environmental stress?

In Schizosaccharomyces pombe , the Ataxia Telangiectasia-mutated (Atm)/Atm and Rad 3 Related (Atr) homologue Rad3 is an essential regulator of the response to DNA damage and stalled replication forks. Rad3 activates the downstream kinases Chk1 and Cds1. These kinases in turn inhibit cell cycle progression by mediating Cdc2 phosphorylation. Studies in both yeast and mammalian cells suggest additional roles for Rad3 in regulating cellular responses to environmental stress. In S. pombe , cellular responses to various environmental stresses are regulated primarily through the stress-activated MAP kinase p38 homologue Sty1. An important function of Sty1 is to drive cells rapidly through mitosis by facilitating the accumulation of Cdc25. Interestingly, Sty1 is activated simultaneously with Rad3 following exposure to UV radiation or ionizing radiation (IR). Similarly, exposure to environmental stresses induces the expression of rad3 ⁺, cds1 ⁺ and other checkpoint regulator genes. It is currently unclear how the pathways regulated by Sty1 and Rad3 and their opposing effects on mitosis are integrated. Recent studies suggest that Sty1 and Rad3 function together to regulate the expression of several stress response genes following exposure to IR. In this review, we discuss current knowledge on the interaction of Rad3/Atm and Sty1/p38 in regulating cellular responses to environmental stress and DNA damage.     

Classifying the fire‐response traits of plants: How reliable are species‐level classifications?

Plant species in fire‐prone environments possess specific traits which allow them to survive fire. Species are commonly classified according to whether they survive fire and resprout or whether they are killed by fire and regenerate from seed. However, different populations of the same species have been shown to vary in their responses. Therefore, the classification of a species into a single category based on fire‐response traits may not necessarily be representative of every population under every circumstance. This study examined the extent of within‐species variation in fire‐response traits of woody plants in south‐eastern Australia after the 2003 fires. Species were then classified using two approaches: (i) using data from a field survey of fire‐response traits, taking into account within‐species variation; and (ii) using species' fire responses listed in a pre‐existing fire‐response database compiled from a variety of primary sources. Field data showed that the majority of species in the study area resprouted after fire with around one in 10 species variable in their resprouting response. Almost half of all species varied from site to site according to whether they regenerated from seed, either solely or in addition to resprouting. The numbers of species classified as resprouters and seed regenerators varied according to the classification method used. Differences were also found between the classification method when calculating the mean proportion of resprouters and seed regenerators across sites. The fire‐response traits for some species from the database were found to differ from the observed field responses. This study demonstrated that the application of a fire‐response trait, reported in a trait database, to an entire species, may not adequately represent the actual fire responses of the populations of interest. Rather than considering the fire‐response traits of a species, accurate prediction may be better achieved by considering how different populations of plants will respond to fire.     

Can behavioral and personality traits influence the success of unintentional species introductions?

Unintentional species invasions are instigated by human-mediated dispersal of individuals beyond their native range. Although most introductions fail at the first hurdle, a select subset pass through each stage of the introduction process (i.e., transport, introduction, establishment and spread) to become successful invaders. Efforts to identify the traits associated with invasion success have predominately focused on deliberate introductions, which essentially bypass the initial introduction stage. Here, we highlight how behavior influences the success or failure of unintentional species introductions across each stage of the introduction process, with a particular focus on transportation and initial establishment. In addition, we emphasize how recent advances in understanding of animal personalities and individual-level behavioral variation can help elucidate the mechanisms underlying the success of stowaways.     

A mathematical model to predict the tissue response to parthenin — An allelochemical

Parthenin — a sesquiterpene lactone fromParthenium hysterophorus L. is an allelochemical that prevents the germination ofPhaseolus aureus Roxb. cv. ML-5 seeds. The response of the seed has been attributed to the inhibition of the respiratory electron transport ability of its embryo. It has been shown to depend directly not only upon concentration of parthenin, but simultaneously on the duration of exposure of the seeds to the chemical as well. A strong correlation exists between the quantum of the response and the product of the period of exposure and the concentration of parthenin. In order to predict the maximum possible germination ability of the seed exposed for a given period to a given concentration of parthenin, an expression X = 10000 Y³ / [e^Y/0.31-1] was formulated from the equation X = AY³/[e^Y/Y0-1], where X represents values of maximum respiratory activity, Y represents the product of concentration and time in units mg cn^-3 h, A represents a dimensional constant. The trend and nature of response that is calculated on the basis of formulation coincides with that of measured response through spectrophotometry.     

The application of generalizability theory to surface electromyographic measurements during psychophysiological stress testing: How many measurements are needed?

Generalizability theory is an extension of classical reliability theory that allows multiple sources of measurement error in an experimental design to be investigated simultaneously. In the present study, generalizability theory was used to evaluate measurement error in psychophysiological test procedures used to differentiate tension headache patients from normal controls based upon measures of electromyographic (EMG) responding. Thirty-three subjects who met diagnostic criteria for tension-type headache and 40 normal control subjects who rarely or never experienced headache participated in two laboratory sessions. EMG activity of head and neck muscles was recorded while subjects performed baseline, relaxation, choice reaction time, psychomotor tracking, and cold pressor tasks. Variance components were computed for an experimental design having subjects nested within experimenters and crossed with sessions and replications. Generalizability coefficients were computed for combinations of various numbers of sessions and replications. The generalizability of EMG measures was highly variable, depending on the experimental conditions in force. The largest sources of measurement error were attributed to the unique responsiveness of individual subjects under a particular set of treatment conditions. For some stress tests currently in use, data from several testing sessions may need to be averaged in order to achieve acceptable levels of generalizability. Generalizability greater than 0.80 can be expected only rarely when data are collected during a single session. In the research setting, low generalizability may account for the failure of EMG-based stress tests to differentiate tension headache patients from controls during stressful task performance. In the clinical setting, the generalizability of information derived from stress profiling or muscle scanning techniques, which depend on results obtained during a single testing session, is doubtful.This research was supported by NIH under grant No. R01-NS-25114.     

Simulating winning in the wild — The behavioral and hormonal response of black redstarts to single and repeated territorial challenges of high and low intensity

In many vertebrates testosterone increases during aggressive interactions and the surges in this hormone may be responsible for the winner effect. So far studies on this relationship have been done in captivity only, because simulating a winning situation for a territory owner in the field is difficult. However, an increasing number of studies show that territorial aggression is not necessarily accompanied by elevated testosterone after a single simulated territorial intrusion (STI) and therefore it has been proposed that STIs may even create a losing experience. We examined whether free-living male black redstarts (Phoenicurus ochruros) show changes in androgens, corticosterone and behavior following repeated STIs of high or low intensity and in contrast to being challenged only once. Repeated intrusions had no influence on androgen and corticosterone levels regardless of intrusion intensity. In contrast, the behavioral response changed over days depending on the intensity of the intrusion. Only birds challenged with high-level intruders approached the decoy significantly faster during the third intrusion than during the first one, stayed closer to the decoy, and sang more songs than males challenged with low-level intruders. Thus, although black redstarts reacted differently to STIs varying in frequency and intensity, these behavioral differences were not reflected in androgen or corticosterone levels. Our data show that it is unlikely that STIs induce a losing experience. Furthermore, they indicate that a hormonal effect of winning an encounter may not be universal in vertebrates and may depend on the ecological or life-history context.     

Are human endogenous retroviruses pathogenic? An approach to testing the hypothesis

A number of observations have led researchers to postulate that, despite being replication‐defective, human endogenous retroviruses (HERVs) may have retained the potential to cause or contribute to disease. However, mechanisms of HERV pathogenicity might differ substantially from those of modern infectious retroviruses or of the infectious precursors of HERVs. Therefore, novel pathways of HERV involvement in disease pathogenesis should be investigated. Recent technological advances in sequencing and bioinformatics are making this task increasingly feasible. The accumulating knowledge of HERV biology may also facilitate the definition and general acceptance of criteria that establish HERV pathogenicity. Here, we explore possible mechanisms whereby HERVs may cause disease and examine the evidence that either has been or should be obtained in order to decisively address the pathogenic potential of HERVs.     

How many freshwater diatoms are pH specialists? A response to Pither & Aarssen (2005)

Pither & Aarssen (2005) propose a null model approach to assess the proportion of niche specialist taxa along ecological gradients. They apply this methodology to a large data set of lacustrine diatom assemblages and conclude that a majority of the taxa are generalists on a pH gradient. This conflicts with previous work, which shows that many diatom taxa have a statistically significant relationship with pH. We demonstrate the methods used by Pither & Aarssen (2005) have a high Type II error for rare taxa, and that this problem is compounded by the non-uniform sampling of the pH gradient which effectively precludes acid-lake specialist diatoms from being recognized as such. We re-analyse the data used by Pither & Aarssen (2005) and show that most of the diatoms have a statistically significant relationship with pH, and we thus refute their conclusions that few diatom species are specialists.     

How to lift a model for individual behaviour to the population level?

The quick answer to the title question is: by bookkeeping; introduce as p(opulation)-state a measure telling how the individuals are distributed over their common i(ndividual)-state space, and track how the various i-processes change this measure. Unfortunately, this answer leads to a mathematical theory that is technically complicated as well as immature. Alternatively, one may describe a population in terms of the history of the population birth rate together with the history of any environmental variables affecting i-state changes, reproduction and survival. Thus, a population model leads to delay equations. This delay formulation corresponds to a restriction of the p-dynamics to a forward invariant attracting set, so that no information is lost that is relevant for long-term dynamics. For such equations there exists a well-developed theory. In particular, numerical bifurcation tools work essentially the same as for ordinary differential equations. However, the available tools still need considerable adaptation before they can be practically applied to the dynamic energy budget (DEB) model. For the time being we recommend simplifying the i-dynamics before embarking on a systematic mathematical exploration of the associated p-behaviour. The long-term aim is to extend the tools, with the DEB model as a relevant goal post.     

JNK, cytoskeletal regulator and stress response kinase? A Drosophila perspective

c-Jun N-terminal kinases (JNKs) are intracellular stress-activated signalling molecules, which are controlled by a highly evolutionarily conserved signalling cascade. In mammalian cells, JNKs are regulated by a wide variety of cellular stresses and growth factors and have been implicated in the regulation of remarkably diverse biological processes, such as cell shape changes, immune responses and apoptosis. How can such different stimuli activate the JNK pathway and what roles does JNK play in vivo? Molecular genetic analysis of the Drosophila JNK gene has started to provide answers to these questions, confirming the role of this molecule in development and stress responses and suggesting a conserved function for JNK signalling in processes such as wound healing. Here, we review this work and discuss how future experiments in Drosophila should reveal the cell type-specific mechanisms by which JNKs perform their diverse functions.     

Interactions of heat shock protein 47 with collagen and the stress response: an unconventional chaperone model?

Heat shock proteins (HSPs) are upregulated and manifested upon cellular stress and possess chaperoning functions. HSP47 is an endoplasmic reticulum (ER)-resident, collagen-specific chaperone and plays a key role in collagen biosynthesis and its structural assembly. The collagen scaffold is a primary structural target of recent interest due to its applications in tissue engineering and drug delivery and in treatment of clinical disorders. This review highlights the fundamental aspects of HSPs in protein folding and quality control, in the elicitation of a stress response in connective tissue and in the characterization of HSP47 in collagen folding and assembly. The significant features of HSP47 which are distinct in its cellular capabilities are discussed. We propose that targeting the stress response is a key factor in identifying connective tissue biomarkers. We also address the issues and strategies involved in the stress response of connective tissue diseases. In conclusion, we describe the prospects of collagen biochemistry in correlation to the science of HSPs.