Sustained oscillations in glycolysis: an experimental and theoretical study of chaotic and complex periodic behavior and of quenching of simple oscillations

We report sustained oscillations in glycolysis conducted in an open system (a continuous-flow, stirred tank reactor; CSTR) with inflow of yeast extract as well as glucose. Depending on the operating conditions, we observe simple or complex periodic oscillations or chaos. We report the response of the system to instantaneous additions of small amounts of several substrates as functions of the amount added and the phase of the addition. We simulate oscillations and perturbations by a kinetic model based on the mechanism of glycolysis in a CSTR. We find that the response to particular perturbations forms an efficient tool for elucidating the mechanism of biochemical oscillations.     

Reciprocity and Ethical Tuberculosis Treatment and Control

This paper explores the notion of reciprocity in the context of active pulmonary and laryngeal tuberculosis (TB) treatment and related control policies and practices. We seek to do three things: First, we sketch the background to contemporary global TB care and suggest that poverty is a key feature when considering the treatment of TB patients. We use two examples from TB care to explore the role of reciprocity: isolation and the use of novel TB drugs. Second, we explore alternative means of justifying the use of reciprocity through appeal to different moral and political theoretical traditions (i.e., virtue ethics, deontology, and consequentialism). We suggest that each theory can be used to provide reasons to take reciprocity seriously as an independent moral concept, despite any other differences. Third, we explore general meanings and uses of the concept of reciprocity, with the primary intention of demonstrating that it cannot be simply reduced to other more frequently invoked moral concepts such as beneficence or justice. We argue that reciprocity can function as a mid-level principle in public health, and generally, captures a core social obligation arising once an individual or group is burdened as a result of acting for the benefit of others (even if they derive a benefit themselves). We conclude that while more needs to be explored in relation to the theoretical justification and application of reciprocity, sufficient arguments can be made for it to be taken more seriously as a key principle within public health ethics and bioethics more generally.     

Treatment- and population-dependent activity patterns of behavioral and expression QTLs

Genetic control of gene expression and higher-order phenotypes is almost invariably dependent on environment and experimental conditions. We use two families of recombinant inbred strains of mice (LXS and BXD) to study treatment- and genotype-dependent control of hippocampal gene expression and behavioral phenotypes. We analyzed responses to all combinations of two experimental perturbations, ethanol and restraint stress, in both families, allowing for comparisons across 8 combinations of treatment and population. We introduce the concept of QTL activity patterns to characterize how associations between genomic loci and traits vary across treatments. We identified several significant behavioral QTLs and many expression QTLs (eQTLs). The behavioral QTLs are highly dependent on treatment and population. We classified eQTLs into three groups: cis-eQTLs (expression variation that maps to within 5 Mb of the cognate gene), syntenic trans-eQTLs (the gene and the QTL are on the same chromosome but not within 5 Mb), and non-syntenic trans-eQTLs (the gene and the QTL are on different chromosomes). We found that most non-syntenic trans-eQTLs were treatment-specific whereas both classes of syntenic eQTLs were more conserved across treatments. We also found there was a correlation between regions along the genome enriched for eQTLs and SNPs that were conserved across the LXS and BXD families. Genes with eQTLs that co-localized with the behavioral QTLs and displayed similar QTL activity patterns were identified as potential candidate genes associated with the phenotypes, yielding identification of novel genes as well as genes that have been previously associated with responses to ethanol.     

Evolution and applications of plant pathway resources and databases

Plants are important sources of food and plant products are essential for modern human life. Plants are increasingly gaining importance as drug and fuel resources, bioremediation tools and as tools for recombinant technology. Considering these applications, database infrastructure for plant model systems deserves much more attention. Study of plant biological pathways, the interconnection between these pathways and plant systems biology on the whole has in general lagged behind human systems biology. In this article we review plant pathway databases and the resources that are currently available. We lay out trends and challenges in the ongoing efforts to integrate plant pathway databases and the applications of database integration. We also discuss how progress in non-plant communities can serve as an example for the improvement of the plant pathway database landscape and thereby allow quantitative modeling of plant biosystems. We propose Good Database Practice as a possible model for collaboration and to ease future integration efforts.     

不同风化程度钾长石表面矿物分解细菌的筛选及遗传多样性

【目的】不同风化程度钾长石表面矿物分解细菌生物多样性研究将有助于了解矿物生物风化、生物成矿和土壤形成的演化规律和机理。【方法】采用纯培养法自南平钾矿区高、中、低风化度钾长石以及矿区土壤样品中分离矿物分解细菌,通过摇瓶释硅实验比较不同菌株分解矿物能力,采用16SrDNA限制性酶切多态性分析(Amplified rDNA Restriction Analysis,ARDRA)研究了供试菌株的遗传多样性。【结果】分离筛选到35株生长良好的矿物分解细菌,与对照相比,接菌处理发酵液中有效硅增加了101～206%;所有供试菌株可分为11个OTU,分别属于5个门,6个科,7个属。多数菌株(74%)属于γ-变形杆菌纲(γ-Proteobacteria)。泛菌属(Pantoea),沙雷氏菌属(Serratia),假单胞菌属(Pseudomonas)为优势种群。【结论】南平钾矿区矿物分解细菌具有丰富的微生物种群多样性,且γ-变形杆菌纲(γ-Proteobacteria)细菌在钾长石风化过程中可能起了重要的作用。     

Complexity and stability revisited

Since Robert May's work on random community matrices it has been known that stability tends to decrease with complexity. Recently, it was shown that this is not necessarily true in competitive ecosystems. We investigated the stability of random ecosystems and found that it can largely be predicted by simple matrix statistics such as the mean and the variance of the interaction coefficients. We use this to explain why stability can increase as well as decrease with complexity in ecological communities. We argue that the variance, and to a lesser extent the mean, of the interaction coefficients go a long way in explaining patterns in the stability of ecosystems.     

Extending the concept of keystone species to communities and ecosystems

Keystone species are defined as having disproportionate importance in their community. This concept has proved useful and is now often used in conservation ecology. Here, we introduce the concept of keystone communities (and ecosystems) within metacommunities (and metaecosystems). We define keystone and burden communities as communities with impacts disproportionately large (positive or negative respectively) relative to their weight in the metacommunity. We show how a simple metric, based on the effects of single‐community removals, can characterise communities along a ‘keystoneness’ axis. We illustrate the usefulness of this approach with examples from two different theoretical models. We further distinguish environmental heterogeneity from species trait heterogeneity as determinants of keystoneness. We suggest that the concept of keystone communities/ecosystems will be highly beneficial, not only as a fundamental step towards understanding species interactions in a spatial context, but also as a tool for the management of disturbed landscapes.     

Antimicrobial properties of nitric oxide and its application in antimicrobial formulations and medical devices

This review describes the antimicrobial properties of nitric oxide (NO) and its application as an antimicrobial agent in different formulations and medical devices. We depict the eukaryotic biosynthesis of NO and its physiologic functions as a cell messenger and as an antimicrobial agent of the cell-mediated immune response. We analyze the antimicrobial activity of NO and the eukaryotic protective mechanisms against NO for the purpose of delineating the therapeutic NO dosage range required for an efficacious and safe antimicrobial activity. We also examine the role of NO produced by virulent bacteria in lessening the efficacy of traditional antimicrobials. In addition, we discuss the efficacy of NO in the healing of infected wounds, describing different NO-producing devices by category, analyzing therapeutic levels, duration of NO production, as well as commercial considerations. Finally, we provide current and future prospects for the design and use of NO-producing devices.     

Manufacturing flexibility and performance: bridging the gap between theory and practice

How firms scan and interpret their environments has implications for the flexibility strategy that they choose, as well as for the performance of that strategy. We extend Daft and Weick’s (Acad Manage Rev 9(2):284–295, 1984) model of firms as interpretation systems into a theoretical model of flexibility performance through extended iterations between observations of a failed flexibility initiative and relevant literature. We test the model using well-known teaching cases. We argue that the use of an iterative process that involves cases and theory both stimulates creativity in integrating theory and lays an initial foundation for evidence-based practice.     

Developmental instability and phenotypic evolution in a small and isolated bear population

We explored fluctuating asymmetry (FA) and morphological integration (MI) in the skull of the small, highly inbred and divergent Apennine bear (Ursus arctos marsicanus), to explore its uniqueness and investigate any potential effects of inbreeding depression. We used 3D geometric morphometrics contrasting Apennine bears with other two large outbred bear populations from Scandinavia and Kamchatka as controls. Shape divergence and variability were explored by a principal component analysis on aligned coordinates of 39 landmarks. Procrustes ANOVA, morphological disparity and the global integration index were used to explore FA, shape variance and MI. By remarking Apennine bears as a highly divergent phenotype, we recorded the highest FA and deviation from self-similarity compared with the other two control populations. We conclude that Apennine bears are likely facing developmental instability as a consequence of inbreeding depression, whereas the divergent trait covariance pattern may represent a potential source of evolutionary novelties. We discuss the implications for the conservation and management of this imperiled taxon.     

Testing alien plant distribution and habitat invasibility in mountain ecosystems: growth form matters

Most studies focused on understanding habitat invasibility use the current levels of invasion as a direct proxy of habitat invasibility. This has shown to be biased by the influence of propagule pressure and climate. We suggest that plant growth forms need to be considered as an extra factor, as habitat preferences might not be equal for all potential invaders. We test the influence of propagule pressure, climate and habitat characteristics on the current level of invasion and habitat invasibility, specifically addressing whether an analysis focused on growth forms evidence different patterns than the total pool of alien species. We used 499 floristic vegetation plots located in Córdoba Mountains. We used proportional alien richness of the total pool and for each growth form as response variables. We identified models that best explained current levels of invasion. We used the residuals of the models with propagule pressure and climate as the response variable. Then, we performed linear models to test the relationship between habitat characteristics and the residuals of the models. We found different drivers of current alien distribution patterns for the total pool and each growth form. Habitat invasibility was not equal when quantified for the total pool or growth forms. Shrublands and outcrops were recorded as less susceptible to woody invasion, while grasslands and native woodlands were resistant to the invasion of grasses and none habitat type was resistant to the invasion of forbs. We highlight that the current level of invasion and habitat invasibility are highly growth form dependent.     

Plants and climate change: complexities and surprises

Background Anthropogenic climate change (ACC) will influence all aspects of plant biology over coming decades. Many changes in wild species have already been well-documented as a result of increased atmospheric CO₂ concentrations, warming climate and changing precipitation regimes. A wealth of available data has allowed the use of meta-analyses to examine plant–climate interactions on more sophisticated levels than before. These analyses have revealed major differences in plant response among groups, e.g. with respect to functional traits, taxonomy, life-history and provenance. Interestingly, these meta-analyses have also exposed unexpected mismatches between theory, experimental, and observational studies.Scope We reviewed the literature on species’ responses to ACC, finding ∼42 % of 4000 species studied globally are plants (primarily terrestrial). We review impacts on phenology, distributions, ecophysiology, regeneration biology, plant–plant and plant–herbivore interactions, and the roles of plasticity and evolution. We focused on apparent deviations from expectation, and highlighted cases where more sophisticated analyses revealed that unexpected changes were, in fact, responses to ACC.Conclusions We found that conventionally expected responses are generally well-understood, and that it is the aberrant responses that are now yielding greater insight into current and possible future impacts of ACC. We argue that inconclusive, unexpected, or counter-intuitive results should be embraced in order to understand apparent disconnects between theory, prediction, and observation. We highlight prime examples from the collection of papers in this Special Issue, as well as general literature. We found use of plant functional groupings/traits had mixed success, but that some underutilized approaches, such as Grime''s C/S/R strategies, when incorporated, have improved understanding of observed responses. Despite inherent difficulties, we highlight the need for ecologists to conduct community-level experiments in systems that replicate multiple aspects of ACC. Specifically, we call for development of coordinating experiments across networks of field sites, both natural and man-made.     

The cholera epidemics and the development of public health in Meiji Japan. 2. Strength and weakness of public health politics

We present here the beginnings of public health politics in Meiji Japan (1868-1912). Due to a two century isolation of Japan, public health concepts developed in the West from the end of the 18th century were foreign in premodern Japan. Due to its isolation, Japan was also relatively preserved from some acute infectious diseases such as cholera. In this paper, we investigate the role of cholera epidemics in the emergence of public health concepts in the peculiar context of Meiji Japan. We show that chronic diseases such as tuberculosis and leprosy were neglected for a long time and that the Meiji government set priority on acute infectious diseases that were considered as long as they disturbed public order. Nevertheless, some physicians and government officials considered issues of welfare and poverty. We also review some emerging concepts of social medicine. We try to show that in Japan as well as in western nations public health politics were not exempt of contradictions and paradoxes and a permanent tension existed between coercitive policies and conceptions of welfare and rights to health.     

Geometric robustness theory and biological networks

We provide a geometric framework for investigating the robustness of information flows over biological networks. We use information measures to quantify the impact of knockout perturbations on simple networks. Robustness has two components, a measure of the causal contribution of a node or nodes, and a measure of the change or exclusion dependence, of the network following node removal. Causality is measured as statistical contribution of a node to network function, wheras exclusion dependence measures a distance between unperturbed network and reconfigured network function. We explore the role that redundancy plays in increasing robustness, and how redundacy can be exploited through error-correcting codes implemented by networks. We provide examples of the robustness measure when applied to familiar boolean functions such as the AND, OR and XOR functions. We discuss the relationship between robustness measures and related measures of complexity and how robustness always implies a minimal level of complexity.     

Neutral mutations and repetitive DNA

We have previously shown that computer simulations of processes that generate selectively advantageous changes together with random duplications and deletions give rise to genomes with many different genes embedded in a large amount of dispensable DNA sequence. We now explore the consequences of neutral changes on the evolution of genomes. We follow the consequences of sequence divergences that are neutral when they occur in dispensable sequences or extra copies of genes present in multigene families. We find that when divergence occurs at about the same frequency as duplication/deletion events, genomes carry repetitive sequences in proportion to their size. Inspection of the genomes as they evolved showed that multigene families were generated by relatively recent duplications of single genes and so would be expected to be highly homogeneous.     

'Axogenic' and 'somagenic' neurodegenerative diseases: definitions and therapeutic implications.

Neurodegenerative diseases are characterized by a relentless loss of specific groups of neuronal subtypes. Many of these diseases share similar molecular mechanisms and extracellular mediators of neuronal loss. We now suggest that neurodegeneration originating in the neuronal cell bodies (e.g. in Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis) should be distinguished from that originating in the axons (e.g. in glaucoma, certain peripheral neuropathies and spinal stenosis). We propose that the former group of diseases be defined as 'somagenic' and the latter as 'axogenic'. Although axogenic disorders may share common symptoms and mediators of toxicity with somagenic disorders, they have distinct temporal, subcellular and signal-transduction features. We further suggest that, by adopting this classification of disorders based on pathophysiological processes, we will come to recognize additional diseases (in particular, those defined as axogenic) as being neurodegenerative and therefore possibly amenable to neuroprotective therapy.     

Vav GEFs regulate macrophage morphology and adhesion-induced Rac and Rho activation

The Vav family of proteins have the potential to act as both signalling adapters and GEFs for Rho GTPases. They have therefore been proposed as regulators of the cytoskeleton in various cell types. We have used macrophages from mice deficient in all three Vav isoforms to determine how their function affects cell morphology and migration. Macrophages lacking Vav proteins adopt an elongated morphology and have enhanced migratory persistence in culture. To investigate the pathways through which Vav proteins exert their effects we analysed the responses of macrophages to the chemoattractant CSF-1 and to adhesion. We found that morphological and signalling responses of macrophages to CSF-1 did not require Vav proteins. In contrast, adhesion-induced cell spreading, RhoA and Rac1 activation and cell signalling were all dependent on Vav proteins. We propose that Vav proteins affect macrophage morphology and motile behaviour by coupling adhesion receptors to Rac1 and RhoA activity and regulating adhesion signalling events such as paxillin and ERK1/2 phosphorylation by acting as adapters.     

Analysis of single protoplasts and regenerated plants by PCR and RAPD technology

Summary We investigated the use of the polymerase chain reaction (PCR) and the associated random amplification of polymorphic DNA (RAPD) technique in the analysis of DNA and specific genes in plant cells at different stages of regeneration in in vitro cultures. We demonstrate that both procedures can be used to differentiate reproducibly between closely related species as well as to reveal levels of DNA polymorphism in regenerated plants. We also demonstrate that both procedures, using protocols that we have developed, are applicable at all tissue culture stages, from single isolated protoplasts to regenerated plants. Possible explanations for the variation levels detected in regenerated wheat plants are advanced.