View from the top: hierarchies and reverse hierarchies in the visual system

We propose that explicit vision advances in reverse hierarchical direction, as shown for perceptual learning. Processing along the feedforward hierarchy of areas, leading to increasingly complex representations, is automatic and implicit, while conscious perception begins at the hierarchy's top, gradually returning downward as needed. Thus, our initial conscious percept--vision at a glance--matches a high-level, generalized, categorical scene interpretation, identifying "forest before trees." For later vision with scrutiny, reverse hierarchy routines focus attention to specific, active, low-level units, incorporating into conscious perception detailed information available there. Reverse Hierarchy Theory dissociates between early explicit perception and implicit low-level vision, explaining a variety of phenomena. Feature search "pop-out" is attributed to high areas, where large receptive fields underlie spread attention detecting categorical differences. Search for conjunctions or fine discriminations depends on reentry to low-level specific receptive fields using serial focused attention, consistent with recently reported primary visual cortex effects.     

Size and fecundity hierarchies in an herbaceous perennial

Summary Inequalities in size in populations have potentially important effects on fitness but have rarely been examined in natural populations. I measured size (number of culms) and fecundity (number of spikelets) in five populations of the grass Danthonia spicata from 1981 to 1985. The populations were in sites in a Pinus-Quercus-Populus forest in northern lower Michigan, USA comprising a secondary succession sequence. The sites had been burned in 1980, 1954, 1948, 1936, and 1911, respectively. Mean sizes and fecundities and the amount of hierarchy in size and fecundity, measured by the Gini coefficient, were compared between the YOUNG population, 1980 burn site, and the OLD populations, 1954, 1948, 1936, and 1911 burn sites. I found large differences in mean size and fecundity between the YOUNG and OLD populations with much larger individuals in the YOUNG population. No differences in size hierarchies were found in either the first year of measurement or after five years. The fecundity hierarchies showed no significant difference among the populations in the first year but after five years the YOUNG population showed a significant decrease in amount of inequality. The longterm patterns of size and fecundity hierarchies differed because fecundity was a cumulative trait while size was not. Size inequalities may not always be a good measure of fecundity inequalities. Short-term measures of inequality in perennials may not be a good indicator of long-term values. In contrast to greenhouse studies, habitat light levels did not affect size hierarchies although they did affect fecundity hierarchies.     

Database searching with DNA and protein sequences: an introduction

This review of sequence database searching aims to set out current practice in the area, in order to give practical guidelines to the experimental biologist. It describes the basic principles behind the programs and enumerates the range of databases available in the public domain. Of these, the most important are the equivalent DNA databases European Molecular Biology Laboratory (EMBL), GenBank and DNA Databank of Japan (DDBJ), and the protein databases Swiss-Prot and TrEMBL. The commonly used BLAST and FASTA algorithms are described in detail and alternative approaches mentioned briefly. Scoring matrices used to compare amino acid types during protein database searches are compared, with an emphasis on the PAM and BLOSUM series of observed substitution matrices.     

Disgust as an adaptive system for disease avoidance behaviour

Disgust is an evolved psychological system for protecting organisms from infection through disease avoidant behaviour. This 'behavioural immune system', present in a diverse array of species, exhibits universal features that orchestrate hygienic behaviour in response to cues of risk of contact with pathogens. However, disgust is also a dynamic adaptive system. Individuals show variation in pathogen avoidance associated with psychological traits like having a neurotic personality, as well as a consequence of being in certain physiological states such as pregnancy or infancy. Three specialized learning mechanisms modify the disgust response: the Garcia effect, evaluative conditioning and the law of contagion. Hygiene behaviour is influenced at the group level through social learning heuristics such as 'copy the frequent'. Finally, group hygiene is extended symbolically to cultural rules about purity and pollution, which create social separations and are enforced as manners. Cooperative hygiene endeavours such as sanitation also reduce pathogen prevalence. Our model allows us to integrate perspectives from psychology, ecology and cultural evolution with those of epidemiology and anthropology. Understanding the nature of disease avoidance psychology at all levels of human organization can inform the design of programmes to improve public health.     

Liposuction abdominoplasty: an evolving concept

Liposuction abdominoplasty-liposuction of abdominal subcutaneous tissue deep and superficial to Scarpa's fascia, with excision of excess abdominal skin and, when indicated, plication of the anterior rectus sheath without undermining-is an effective, low-risk approach to minimizing abdominal flap undermining. The technique allows aggressive thinning and "sculpting" of full-thickness abdominal subcutaneous tissue and achieves a natural (not featureless) abdominal contour. It minimizes the creation of "dead space," which often leads to postoperative complications, as well as preserves sensory nerve and blood supply to the abdominal skin. The operation may be performed with the patient under local anesthesia, which probably diminishes the risk for deep vein thrombosis. Moreover, additional procedures can be conducted safely and the postoperative course is short, uneventful, and without restrictions; patients return to normal activity within a week or so. New evaluation criteria for abdominoplasty are discussed in this article, the most important of which is the assessment of intraabdominal fat content and its impact on surgical outcome and the decision to perform anterior rectus sheath plication. The concept of a sliding, mobile, sensate abdominal flap, created by liposuction and sustained by multiple neurovascular mesenteries, is also offered.     

The disruption of dominance hierarchies by a non-native species: an individual-based analysis

We studied the effects of the exotic rainbow trout (Oncorhynchus mykiss) on the performance and the dominance hierarchy of native Atlantic salmon (Salmo salar) at the group and individual level using laboratory and semi-natural experiments. At the group level, we compared the effects of interspecific and intraspecific competition (substitutive and additive design) on behavioural responses and growth of young-of-the-year Atlantic salmon. At the individual level, the same design was used to evaluate: (1) the temporal consistency of behavioural responses, dominance hierarchy and growth rate of Atlantic salmon; (2) the pattern of correlations between behaviours; and (3) the relationship between individual growth rate and behaviour. In the laboratory, group-level analyses revealed a weak but similar effect of rainbow trout and intraspecific competition on the behaviour and growth of Atlantic salmon. In contrast, individual-based analyses demonstrated that rainbow trout (but not intraspecific competition) strongly affected behavioural strategy, dominance hierarchy and growth trajectory of individual Atlantic salmon. Specifically, behaviours, dominance status and growth rate of salmon were temporally consistent in the intraspecific environment, while these patterns were disrupted when rainbow trout were present. Similarly, we found that rainbow trout strongly affected behavioural correlations and the relationships between individual growth rate and behaviour. The semi-natural experiments confirmed these results as interspecific competition affected relationships between individual growth rate of salmon, initial weight and activity index. Overall, individual-based analyses highlighted important mechanisms that were concealed at the group level, and that may be crucial to understand ecological and evolutionary consequences of exotic species. Moreover, these results demonstrated that competition with an exotic species disrupts the hierarchical relationship among native individuals and may therefore represent a potential for a shift in selective pressure.     

Modeling the adaptive immune system: predictions and simulations

MOTIVATION: Immunological bioinformatics methods are applicable to a broad range of scientific areas. The specifics of how and where they might be implemented have recently been reviewed in the literature. However, the background and concerns for selecting between the different available methods have so far not been adequately covered. SUMMARY: Before using predictions systems, it is necessary to not only understand how the methods are constructed but also their strength and limitations. The prediction systems in humoral epitope discovery are still in their infancy, but have reached a reasonable level of predictive strength. In cellular immunology, MHC class I binding predictions are now very strong and cover most of the known HLA specificities. These systems work well for epitope discovery, and predictions of the MHC class I pathway have been further improved by integration with state-of-the-art prediction tools for proteasomal cleavage and TAP binding. By comparison, class II MHC binding predictions have not developed to a comparable accuracy level, but new tools have emerged that deliver significantly improved predictions not only in terms of accuracy, but also in MHC specificity coverage. Simulation systems and mathematical modeling are also now beginning to reach a level where these methods will be able to answer more complex immunological questions.     

Mimotopes: realization of an unlikely concept

Theoretically it seems highly unlikely that relatively small peptides could mimic functionally discontinuous epitopes of antigens. Nevertheless various recent reports show this to be the case. Peptide mimics of protein-, polysaccharide- and DNA-epitopes have been shown to be able to replace the native epitope. Moreover, some of them are able to induce, when used in a vaccine, antibodies with the same activity as that of the antibody used as a template. These mimics, called mimotopes, can be used in vaccines and diagnostics and can be developed more or less systematically using solely antibodies and random, semi-random and dedicated peptide arrays or libraries. Furthermore, the mimotope concept which seems to have proven itself for antibody and antigen interaction can be applied equally well to many receptor ligand interactions and thus may form a new generic approach to the development of drugs. Ltd.     

Heterochronic hierarchies: Application and theory in evolution

Heterochrony is an abundant mode of evolution that is not limited to minor allometric changes, contrary to common belief. This misconception, along with confusion over terminology, has resulted from historically restricting our view to timing and rate changes that occur late in ontogeny and affect only major organs. By focusing on finer scales of space and time, at cellular levels and changes early in ontogeny, much of the confusion over heterochrony is eliminated. Heterochrony is redefined: change in the timing and rate of dialogue during cellular self‐assembly. Therefore it naturally follows that temporally‐related spatial nesting of growth fields occurs during ontogeny. Local allometric changes, as well as major morphological “leaps”; may be explained by such alterations. Following a fossil example of hierarchical heterochronic change, a nomenclatural classification is presented along with branching tree models to illustrate the processes.     

The metabotrophic NGF and BDNF: an emerging concept

The field of neurotrophins, particularly, nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF), has witnessed a number of breakthroughs in recent years. There is evidence now that NGF and BDNF mediate multiple biological phenomena, ranging from the Rita Levi Montalcini's neurotrophic through immunotrophic to epitheliotrophic and nociceptive effects. In 2003 we, for the first time, enriched the "NGFome" with one more expression presented in our concept of NGF metabotrophicity, also that of BDNF. This envisages that these two factors may operate as metabotrophins, that is, involved in the maintenance of cardiometabolic homeostasis (glucose and lipid metabolism as well as energy balance, cardioprotection, and wound healing). Recent results also demonstrated that the circulating and/or tissue levels of NGF and BDNF are altered in cardiometabolic diseases (atherosclerosis, obesity, type 2 diabetes, metabolic syndrome, and type 3 diabetes). Altogether, a hypothesis of metabotrophic deficit due to the reduction of NGF/BDNF availability and/or utilization was raised, and implicated in the pathogenesis of cardiometabolic diseases. This may cultivate a novel pathogenic and therapeutic thinking for these diseases.     

A complex allorecognition system in a reef-building coral: delayed responses,reversals and nontransitive hierarchies

A highly polymorphic and complex allorecognition system in the coral Stylophora pistillata was revealed in the field by assaying branch pair combinations among 11 colonies (181 assays) for 24 months. Replicates of between-colony combinations exhibited consistent outcomes, in both time scale and type of response. Different allogeneic combinations exhibited one of two main outcomes, either unilateral rejection, or an array of other incompatible reactions following a state of non-fusion. These responses were partially linked with color morphs (purple dominated yellow). An additional 22 isogeneic grafts resulted in complete fusion. Unilateral rejection occurred 1–7 months following initial contact. Nonfusion usually developed into skeletal suture barriers after 3–9 months, and then into unilateral colony-specific overgrowths at 6–23 months with some reversals in direction at 18–22 months. During this process, small lesions usually developed on the tissue of the subordinate partner, which were either overgrown by the dominant partner or healed. After two years, a network of overgrowths among colonies was established with essentially hierarchial properties, but some nontransitive interactions also occurred. The colonies segregated into three distinct histocompatibility groups; within each group, colonies engaged in nonfusion. Between groups, colonies exhibited nonfusion or rejected each other in a group-specific manner. Based on the results, we discuss the terminology used for fusion versus rejection phenomena in scleractinian corals, the possible genetic background for self-nonself recognition in Stylophora, and the methodological artifacts associated with the use of short-term allorecognition assays. Correspondence to: B. Rinkevich     

Nutritional antioxidants and adaptive cell responses: an update

Many plant antioxidants, intaken through the daily diet or plant-derived dietary supplements, have been shown able to prevent free radical-related diseases by counteracting cell oxidative stress. However, it is now considered that the in vivo beneficial effects of these phytochemicals are unlikely to be explained just by their antioxidant capability. Several plant antioxidants exhibit hormetic properties, by acting as 'low-dose stressors' that may prepare cells to resist more severe stress. In fact, low doses of these phytochemicals activate cell signaling pathways (being the most prominent examples the modulation of the Nrf2/Keap1 pathway, the NF-κB pathway and the Sirtuin-FOXO pathway) but high doses are cytotoxic. Herein we review the adaptive responses induced by the most known plant hormetic antioxidants, which are sulforaphane, resveratrol, curcumin, flavonoids, green tea catechins and diallylsulphides, as well as the molecular mechanisms involved in such responses. Furthermore, this review outlines that the hormetic properties of these bioactive plant antioxidants might be successfully employed for realizing health-promoting dietary interventions especially in the field of neurodegenerative diseases and cancer.