Towards a definition of ecological disturbance

The terms disturbance, perturbation, and stress have been used in various ecological contexts, often synonymously, inconsistently and ambiguously. Consequently, the meaning of these terms lack any ecological rigor upon which to construct a coherent theory of ecosystem response to disturbance. Herein are some of the semantic and conceptual problems involved in defining disturbance, perturbation and stress, and proposals of working definitions as a basis for further discussion.     

Towards an integrated cellular and molecular: definition of breast cancers

Breast cancer is a major health problem as well as scientifically poorly understood. Our knowledge of breast cancer is however rapidly progressing in several directions. First, genomic studies are establishing a new molecular classification of breast cancers. Molecular subtypes have been identified and are being associated with the histoclinical forms of breast cancers. Second, genetic alterations are discovered and classified, generating new potential therapeutical targets. Third, mammary stem cells have been identified in the normal mammary epithelium. Their altered counterparts have been identified in tumors and are being characterized. These combined studies allow a new integrated cellular and molecular definition of breast cancers and a conceptual basis that will help the management of the disease.     

Towards a definition of a crop wild relative

Crop wild relatives are an important socio-economic resource that is currently being eroded or even extinguished through careless human activities. If the Conference of the Parties (COP) to the CBD 2010 Biodiversity Target of achieving a significant reduction in the current rate of loss is to be achieved, we must first define what crop wild relatives are and how their conservation might be prioritised. A definition of a crop wild relative is proposed and illustrated in the light of previous Gene Pool concept theory. Where crossing and genetic diversity information is unavailable, the Taxon Group concept is introduced to assist recognition of the degree of crop wild relative relatedness by using the existing taxonomic hierarchy.     

Towards a chemical definition of idiotypy.

The idiotypic determinants have been precisely located to the variable regions of immunoglobulin polypeptide chains. Both chains are generally required to express the idiotype. The major idiotypic determinants are the result of the amino acid sequence of the hypervaiable regions, although some idiotypic determinants reside outside the antibody combining site and these so called "framework idiotypes" are important markers. In my view the hypervariable regions are spatially disposed so as to present adequate antigenic stimulation, and they display enough structural heterogeneity to account for the uniqueness of the idiotype in the general population of immunoglobulin molecules. Hypervariable regions, the antibody combining site, and the idiotypic determinants thus amalgamate three formerly diverse concepts into a unified theoretical construct.     

Towards a phylogeny and definition of species at the molecular level within the genus Mycobacterium

16S rRNA sequences from Mycobacterium tuberculosis, M. avium, M. gastri, M. kansasii, M. marinum, M. chelonae, M. smegmatis, M. terrae, M. gordonae, M. scrofulaceum, M. szulgai, M. intracellulare, M. nonchromogenicum, M. xenopi, M. malmoense, M. simiae, M. flavescens, M. fortuitum, and M. paratuberculosis were determined and compared. The sequence data were used to infer a phylogenetic tree, which provided the basis for a systematic phylogenetic analysis of the genus Mycobacterium. The groups of slow- and fast-growing mycobacteria could be differentiated as distinct entities. We found that M. simiae occupies phylogenetically an intermediate position between these two groups. The phylogenetic relatedness within the slow-growing species did not reflect the Runyon classification of photochromogenic, scotchromogenic, and nonchromogenic mycobacteria. In general, the phylogenetic units identified by using rRNA sequences confirmed the validity of phenotypically defined species; an exception was M. gastri, which was indistinguishable from M. kansasii when this kind of analysis was used.     

Towards a quantitative definition of plant hormone sensitivity

Abstract A definition of plant hormone sensitivity is proposed which is based on the initial rates of responses at different hormone concentrations. By analogy with enzyme kinetics, it is concluded that simple concentration-response curves can be described by a function containing three ‘sensitivity parameters’. Objective methods for determining the values of these parameters and for comparing curves are described. These methods are used to describe the responses of Commelina communis L. stomata to abscisic acid. If certain assumptions are valid, the sensitivity parameters can be assigned physicochemical meanings. To validate the assumptions, certain experimental criteria must be fulfilled and these are discussed.     

Circular reasoning rather than cyclic expression

A response to Combined analysis reveals a core set of cycling genes by Y Lu, S Mahony, PV Benos, R Rosenfeld, I Simon, LL Breeden and Z Bar-Joseph. Genome Biol 2007, 8:R146.     

Putting together rather than taking apart

The town of Ascona in Switzerland, nestled on the northern shore of Lago Maggiore, hosted the 112 participants in the first systems biology meeting focused on developmental biology. The EMBO workshop was held between 16 and 20 August and brought together a multidisciplinary group of scientists who use systems approaches to understand how the size and shape of multicellular organisms and organs are determined.     

Towards a modern definition of vitamin E-evidence for a quinone hypothesis

We report on the synthesis, biological and pharmacological activity of the tocoquinone natural product, α-tocopherol quinone (ATQ); an oxidative metabolite of α-tocopherol. ATQ is a potent cellular protectant against oxidative stress, whose biological activity is dependent upon its ability to undergo reversible two-electron redox cycling. ATQ is orally bioavailable, with a favorable pharmacokinetic profile and has demonstrated a beneficial clinical response in patients with Friedreich's ataxia. ATQ is a member of a broader class of vitamin E derived quinone metabolites which may be ascribable in whole or in part to the activity of vitamin E.     

Linear-no-threshold is a radiation-protection standard rather than a mechanistic effect model

The linear-no-threshold (LNT) controversy covers much more than the mere discussion whether or not “the LNT hypothesis is valid”. It is shown that one cannot expect to find only one or even the only one dose–effect relationship. Each element within the biological reaction chain that is affected by ionizing radiation contributes in a specific way to the final biological endpoint of interest. The resulting dose–response relationship represents the superposition of all these effects. Till now there is neither a closed and clear picture of the entirety of radiation action for doses below some 10 mSv, nor does clear epidemiological evidence exist for an increase of risk for stochastic effects, in this dose range. On the other hand, radiation protection demands for quantitative risk estimates as well as for practicable dose concepts. In this respect, the LNT concept is preferred against any alternative concept. However, the LNT concept does not necessarily mean that the mechanism of cancer induction is intrinsically linear. It could hold even if the underlying multi-step mechanisms act in a non-linear way. In this case it would express a certain “attenuation” of non-linearities. Favouring LNT against threshold-, hyper-, or sub-linear models for radiation-protection purposes on the one hand, but preferring one of these models (e.g. for a specific effect) because of biological considerations for scientific purposes on the other hand, does not mean a contradiction.     

Towards a molecular understanding of cytokinesis

In this review, we focus on recent discoveries regarding the molecular basis of cleavage furrow positioning and contractile ring assembly and contraction during cytokinesis. However, some of these mechanisms might have different degrees of importance in different organisms. This synthesis attempts to uncover common themes and to reveal potential relationships that might contribute to the biochemical and mechanical aspects of cytokinesis. Because the information about cytokinesis is still fairly rudimentary, our goal is not to present a definitive model but to present testable hypotheses that might lead to a better mechanistic understanding of the process.     

Stomatococcus mucilaginosus produces a mannose-containing lipoglycan rather than lipoteichoic acid

Five strains of Stomatococcus mucilaginosus were investigated to determine whether the organism produces a lipoteichoic acid or a lipoglycan. Crude phenol extracts were purified by hydrophobic interaction chromatography and shown to contain lipoglycan. The major carbohydrate component present was mannose, indicating that the macroamphiphile is a lipomannan. The fatty acid composition of the lipoglycan was similar to that of stomatococcal whole cells. These data provide additional chemotaxonomic evidence supporting the suprageneric classification of the genus Stomatococcus within a group of actinomycete genera that also includes the genus Micrococcus.Abbreviations LTA Lipoteichoic acid - HIC Hydrophobic interaction chromatography - FAMEs Fatty acid methyl esters     

'Nasty neighbours' rather than 'dear enemies' in a social carnivore

Territorial animals typically respond less aggressively to neighbours than to strangers. This 'dear enemy effect' has been explained by differing familiarity or by different threat levels posed by neighbours and strangers. In most species, both the familiarity and the threat-level hypotheses predict a stronger response to strangers than to neighbours. In contrast, the threat-level hypothesis predicts a stronger response to neighbours than to strangers in species with intense competition between neighbours and with residents outnumbering strangers, as commonly found in social mammals such as the banded mongoose (Mungos mungo). The familiarity hypothesis predicts reduced aggression towards neighbours also in these species. We exposed free-living banded mongoose groups to translocated scent marks of neighbouring groups and strangers. Groups vocalized more and inspected more samples in response to olfactory cues of the neighbours than to the strangers. Our results support the threat-level hypothesis and contradict the familiarity hypothesis. We suggest that increased aggression towards neighbours is more common in social species with intense competition between neighbours, as opposed to reduced aggression towards neighbours typical for most solitary species.     

Intrinsic disorder accelerates dissociation rather than association

The intrinsically disordered protein (IDP) has distinct properties both physically and biologically: it often becomes folded when binding to the target and is frequently involved in signal transduction. The physical property seems to be compatible with the biological property where fast association and dissociation between IDP and the target are required. While fast association has been well studied, fueled by the fly‐casting mechanism, the dissociation kinetics has received less attention. We here study how the intrinsic disorder affects the dissociation kinetics, as well as the association kinetics, paying attention to the interaction strength at the binding site (i.e., the quality of the “fly lure”). Coarse‐grained molecular dynamics simulation of the pKID‐KIX system, a well‐studied IDP system, shows that the association rate becomes larger as the disorder‐inducing flexibility that was imparted to the model is increased, but the acceleration is marginal and turns into deceleration as the quality of the fly lure is worsened. In contrast, the dissociation rate is greatly enhanced as the disorder is increased, indicating that intrinsic disorder serves for rapid signal switching more effectively through dissociation than association. Proteins 2016; 84:1124–1133. © 2016 Wiley Periodicals, Inc.