The importance of growing up: juvenile environment influences dispersal of individuals and their neighbours

Dispersal is a key ecological process that is strongly influenced by both phenotype and environment. Here, we show that juvenile environment influences dispersal not only by shaping individual phenotypes, but also by changing the phenotypes of neighbouring conspecifics, which influence how individuals disperse. We used a model system (Tribolium castaneum, red flour beetles) to test how the past environment of dispersing individuals and their neighbours influences how they disperse in their current environment. We found that individuals dispersed especially far when exposed to a poor environment as adults if their phenotype, or even one‐third of their neighbours’ phenotypes, were shaped by a poor environment as juveniles. Juvenile environment therefore shapes dispersal both directly, by influencing phenotype, as well as indirectly, by influencing the external social environment. Thus, the juvenile environment of even a minority of individuals in a group can influence the dispersal of the entire group.     

Comparison of the performance of one stage and two stage sequential anaerobic-aerobic biological processes for the treatment of reactive-azo-dye-containing synthetic wastewaters

In the present study the performance of anaerobic-aerobic one and two stage processes for the biological treatment of synthetic wastewaters containing Reactive Black 5 (RB5) were studied and compared with each other. In both processes the majority of colour removal by biodegradation occurred under anaerobic environment. The colour change under aerobic conditions was correlated with extent of anaerobic decolourisation in the preceding phase/stage of the process. Partial mineralisation of the anaerobic dye metabolites, roughly to the same extent, was achieved aerobically in both one stage and two stage processes. The majority of COD was removed in the anaerobic stage for two stage processes and aerobic stage in one stage processes. In one stage processes, the exposure of anaerobic sludge to alternating anaerobic-aerobic environment decreased anaerobic decolourisation efficiency and COD removal; when employing activated sludge, the same exposure enhanced anaerobic substrate utilisation whereas the effect on the anaerobic decolourisation efficiency depended on RB5 concentration. The comparative performance of one and two stage processes in terms of overall dye decolourisation depended on RB5 concentration. Both types of processes brought about similar overall COD removal. Increase in RB5 concentration, in the range studied, resulted in decrease in overall COD removal for both processes.     

Pollen limitation or mate search need not induce an Allee effect

When a process modelling the availability of gametes is included explicitly in population models a critical depensation or Allee effect usually results. Non-spatial models cannot describe clumping and so small populations must be assumed very diffuse. Consequently individuals in small populations experience low contact rates and so reproduction is limited. In Nature invasions into new territory are unlikely to be as diffuse as those described by non-spatial models. We develop pair approximations to a probabilistic cellular automata model with independent pollination and seed setting processes (equivalently mate search and reproduction processes). Each process can be either global (population-wide) or local (within a small neighbourhood) or a mixture of the two. When either process is global the resulting model recaptures the Allee effect found in non-spatial models. However, if both processes are at least partially local we obtain a model in which Allee effects can be avoided altogether if individuals are suitably strong pollinators and colonisers. The Allee effect disappears because small populations are dramatically more clumped when colonisation is local and less wasteful of pollen when pollination is local.     

The Structure of the Two Ecological Paradigms

Ecological theory is built upon assumptions about the fundamental nature of organism-environment interactions. We argue that two mutually exclusive sets of such assumptions are available and that they have given rise to alternative approaches to studying ecology. The fundamentally different premises of these approaches render them irreconcilable with one another. In this paper, we present the first logical formalisation of these two paradigms.The more widely-accepted approach - which we label the demographic paradigm - includes both population ecology and community ecology (synecology). Demographic ecology assumes that the environment is relatively stable and that biotic processes, governed predominantly by resource availability, are the most important of ecological and evolutionary influences. Moreover, ecological processes are assumed to translate into directional selection pressures that drive significant evolutionary change on a local scale through the process of optimisation.Serious deficiencies in aspects of the demographic approach have been identified over the past few decades by various ecologists, including Gleason, Andrewartha and Birch, White, Den Boer, Strong, Simberloff, and others. Short-term evolutionary optimisation has also been seriously questioned.The development of the alternative approach (autecology) has been subverted by the prominence of demographic ecology. Moreover, it has not been recognised that autecology is underpinned by robust principles and that they are independent of the underlying demographic principles. Components of the autecological approach have been developed to some extent, but they have not been integrated with ancillary fields of study. We therefore articulate the assumptions from which autecology is derived, and use this as a basis for integrating the various spheres of autecological research.We add to the ongoing development of autecology by linking autecological understanding, in so far as it is developed, with the evolutionary justification for species' characteristics being stable in an environment that is continuously dynamic in space and time. The ecology of organisms is essentially an ongoing matching of their species-specific characteristics to the prevailing environmental factors and dynamics. We thus provide a consistent logic through the following subject areas; climate and climate change, spatial and temporal environmental heterogeneity and dynamic theory, physiology, behaviour, migration, and evolution. We demonstrate why adaptation cannot be an ongoing process, but takes place only when organisms are prevented, by incidental influences, from matching the overall dynamics of the environment.     

The highs and lows of plant life: temperature and light interactions in development

Plants must constantly respond to changes in the environment whilst maintaining developmental and growth processes if they are to survive into the next generation. A complex network of signals from temperature and light must correctly converge to achieve successful development, through vegetative to reproductive growth. Temperature can be thought of as an environmental factor that provides both 'inductive' and 'maintenance' signals in development. It can stimulate developmental processes such as seed dormancy release, germination and vernalization. However, when temperature is not regarded as inductive, an accommodating network of genes work in concert to ensure growth responses occur regardless of fluctuating microclimate conditions. Many of the temperature-regulated developmental pathways are intimately linked with light signaling. For example, light-temperature interactions are major determinants in the timing of reproductive development. Indeed, the ability to process and react to complex environmental cues is crucial for both normal and adaptive development in a changing environment. These responses are frequently mediated by manipulating the phytohormone network, which serves as a powerful, yet adaptable controller of development. This paper illustrates the influential role temperature perception plays throughout plant development and the close interaction between temperature, light and hormone signaling.     

城市景观格局视角下空气微生物研究进展

城市化进程将原有自然生态系统改造为以不透水面为主的人工景观,这种变化影响了空气微生物群落的生存环境及其时空异质性。空气微生物受城市化的影响程度与其生态功能的发挥关系密切,微生物群落特征的改变会在一定程度上影响当地生态环境质量并给人群健康带来潜在威胁。城市化进程和空气微生物群落动态分属两个时空尺度差异巨大的生态过程,二者的联合分析已成为目前生态安全与环境健康领域的研究热点。从空气微生物的来源及其组成特征、空气微生物群落的时空异质性及其影响因素以及空气微生物的生态环境效应三个方面系统梳理和总结了近年来探索城市化和空气微生物群落动态之间关系的研究,从宏观视角探讨了当前空气微生物研究的不足,并引入社会-经济-自然复合生态系统、景观格局与过程等相关理论和方法来分析城市化对空气微生物群落特征的影响,旨在明确城市景观格局作用下的空气微生物群落对人群健康的潜在威胁程度,为快速城市化过程中的人居环境的改善提供参考。     

Could melatonin unbalance the equilibrium between autophagy and invasive processes?

The Syrian hamster Harderian gland (HG) is a juxtaorbital organ exhibiting marked gender-associated morphological differences. Regarding contents of porphyrins, this gland is a good model for studying physiological oxidative stress effects, since both sexes present strong (in females) and moderate (in males) levels of this stress in normal conditions. We have recently showed that autophagic processes are in the Syrian hamster HG as the first result of an elevated porphyrin metabolism observed in both sexes. In this case, autophagy is not a cell death mechanism per se but a constant renovation system which allows to continuing with the normal gland activity. Moreover, we have also reported that this gland presents invasive processes, resembling to tumoral progression, and are, additionally, a consequence of a strong oxidative stress environment that is mainly observed in female Syrian hamster HG and in minor proportion in male HG. Here, we present additional data and discuss a model of melatonin action on these cited processes by which melatonin would be able to destroy the equilibrium between both detoxifying actions. We postulate that melatonin reduces oxidative stress level into HG as direct antioxidant. This decrease of free radicals produces the autophagy inhibition due to outbreak signal disappearance in HG. Under these events and regarding the huge contents of porphyrins that this gland supports, the invasive process triggers.     

A Bayesian approach to the evolution of social learning

There has been much interest in understanding the evolution of social learning. Investigators have tried to understand when natural selection will favor individuals who imitate others, how imitators should deal with the fact that available models may exhibit different behaviors, and how social and individual learning should interact. In all of this work, social learning and individual learning have been treated as alternative, conceptually distinct processes. Here we present a Bayesian model in which both individual and social learning arise from a single inferential process. Individuals use Bayesian inference to combine social and nonsocial cues about the current state of the environment. This model indicates that natural selection favors individuals who place heavy weight on social cues when the environment changes slowly or when its state cannot be well predicted using nonsocial cues. It also indicates that a conformist bias should be a universal aspect of social learning.     

Process Monitoring Strategies for Surface Mount Manufacturing Processes

Establishing reliable surface mount assemblies requires robust design and assembly practices, including stringent process control schemes for achieving high yield processes and high quality solder interconnects. Conventional Shewhart-based process control charts prevalent in today's complex surface mount manufacturing processes are found to be inadequate as a result of autocorrelation, high false alarm probability, and inability to detect process deterioration. Hence, new strategies are needed to circumvent the shortcomings of traditional process control techniques. In this article, the adequacy of Shewhart models in a surface mount manufacturing environment is examined and some alternative solutions and strategies for process monitoring are discussed. For modeling solder paste deposition process data, a time series analysis based on neural network models is highly desirable for both controllability and predictability. In particular, neural networks can be trained to model the autocorrelated time series, learn historical process behavior, and forecast future process performance with low prediction errors. This forecasting ability is especially useful for early detection of solder paste deterioration, so that timely remedial actions can be taken, minimizing the impact on subsequent yields of downstream processes. As for the automated component placement process where very low fraction nonconforming frequently occurs, control-charting schemes based on cumulative counts of conforming items produced prior to detection of nonconforming items is more sensitive in flagging process deterioration. For the reflow soldering and wave-soldering processes, the use of demerit control charts is appealing as it provides not only better control when various defects with a different degree of severity are encountered, but also leads to an improved ARL performance. Illustrative examples of actual process data are presented to demonstrate these approaches.     

Integrating across life-history stages: consequences of natal habitat effects on dispersal

Ecological and evolutionary processes are affected by forces acting at both local and regional scales, yet our understanding of how these scales interact has remained limited. These processes are fundamentally linked through individuals that develop as juveniles in one environment and then either remain in the natal habitat or disperse to new environments. Empirical studies in a diverse range of organisms have demonstrated that the conditions experienced in the natal habitat can have profound effects on the adult phenotype. This environmentally induced phenotypic variation can in turn affect the probability that an individual will disperse to a new environment and the ecological and evolutionary impact of that individual in the new environment. We synthesize the literature on this process and propose a framework for exploring the linkage between local developmental environment and dispersal. We then discuss the ecological and evolutionary implications of dispersal asymmetries generated by the effects of natal habitat conditions on individual phenotypes. Our review indicates that the influence of natal habitat conditions on adult phenotypes may be a highly general mechanism affecting the flow of individuals between populations. The wealth of information already gathered on how local conditions affect adult phenotype can and should be integrated into the study of dispersal as a critical force in ecology and evolution.     

Synaptic and voltage-gated currents in interplexiform cells of the tiger salamander retina

We have correlated the membrane properties and synaptic inputs of interplexiform cells (IPCs) with their morphology using whole-cell patch-clamp and Lucifer yellow staining in retinal slices. Three morphological types were identified: (a) a bistratified IPC with descending processes ramifying in both sublaminas a and b of the inner plexiform layer (IPL), and an ascending process that branched in the outer plexiform layer (OPL) and originated from the soma, (b) another bistratified IPC with descending processes ramifying in both sublaminas a and b, and an ascending process that branched in the OPL and originated directly from IPC processes in the IPL, and (c) a monostratified IPC with a descending process ramifying over large lateral extents within the most distal stratum of the IPL, and sending an ascending process to the OPL with little branching. Similar voltage- gated currents were measured in all three types including: (a) a transient inward sodium current, (b) an outward potassium current, and (c) an L-type calcium current. All cells generated multiple spikes with frequency increasing monotonically with the magnitude of injected current. The IPCs that send their descending processes into both sublaminas of the IPL (bistratified) receive excitatory synaptic inputs at both light ON and OFF that decay with a time constant of approximately 1.3 s. Slowly decaying excitation at both ON and OFF suggests that bistratified IPCs may spike continuously in the presence of a dynamic visual environment.     

Interactively illustrating polymerization using three-level model fusion

Background

Research in cell biology is steadily contributing new knowledge about many aspects of physiological processes, both with respect to the involved molecular structures as well as their related function. Illustrations of the spatio-temporal development of such processes are not only used in biomedical education, but also can serve scientists as an additional platform for in-silico experiments.

Results

In this paper, we contribute a new, three-level modeling approach to illustrate physiological processes from the class of polymerization at different time scales. We integrate physical and empirical modeling, according to which approach best suits the different involved levels of detail, and we additionally enable a form of interactive steering, while the process is illustrated. We demonstrate the suitability of our approach in the context of several polymerization processes and report from a first evaluation with domain experts.

Conclusion

We conclude that our approach provides a new, hybrid modeling approach for illustrating the process of emergence in physiology, embedded in a densely filled environment. Our approach of a complementary fusion of three systems combines the strong points from the different modeling approaches and is capable to bridge different spatial and temporal scales.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-345) contains supplementary material, which is available to authorized users.     

Identification of key genes responsible for cytokine-induced erythroid and myeloid differentiation and switching of hematopoietic stem cells by RAGE

We utilized a unique culture system to analyze the expression patterns of gene, protein, and cell surface antigen, and the biological process of the related genes in erythroid and myeloid differentiation and switching of hematopoietic stem cells （HSCs） in response to cytokine alterations. Gene-specific fragments （266） identified from five populations of cytokine-stimulated HSCs were categorized into three groups： （1） expressed specifically in a single cell population; （2） expressed in two cell populations, and （3） expressed in three or more populations. Of 145 defined cDNAs, three （2%） were novel genes. Protein two-dimensional gel electrophoresis and flow cytometry analyses showed overlapped and distinguished protein expression profiles in the cell populations studied. Biological process mapping of mRNAs expressed in erythroid and myeloid lineages indicated that mRNAs shared by both lineages attended ＇core processes,＇ whereas genes specifically expressed in either lineage alone were related to specific processes or cellular maturation. Data from this study support the hypothesis that committed HSCs （El4 or G14） cells can still be redirected to develop into myeloid or erythroid cells when erythropoietin （EPO） is replaced with granulocyte-colony stimulating factor （G-CSF） under erythroid-cultured condition or G-CSF with EPO in myeloid-cultured environment, respectively. Our results suggest that genes or proteins co-expressed in erythroid and myeloid lineages may be essential for the lineage maintenance and switching in hematopoiesis.     

Markov-modulated Markov chains and the covarion process of molecular evolution.

The covarion (or site specific rate variation, SSRV) process of biological sequence evolution is a process by which the evolutionary rate of a nucleotide/amino acid/codon position can change in time. In this paper, we introduce time-continuous, space-discrete, Markov-modulated Markov chains as a model for representing SSRV processes, generalizing existing theory to any model of rate change. We propose a fast algorithm for diagonalizing the generator matrix of relevant Markov-modulated Markov processes. This algorithm makes phylogeny likelihood calculation tractable even for a large number of rate classes and a large number of states, so that SSRV models become applicable to amino acid or codon sequence datasets. Using this algorithm, we investigate the accuracy of the discrete approximation to the Gamma distribution of evolutionary rates, widely used in molecular phylogeny. We show that a relatively large number of classes is required to achieve accurate approximation of the exact likelihood when the number of analyzed sequences exceeds 20, both under the SSRV and among site rate variation (ASRV) models.     

Sex‐specific survival to maturity and the evolution of environmental sex determination

Four decades ago, it was proposed that environmental sex determination (ESD) evolves when individual fitness depends on the environment in a sex‐specific fashion—a form of condition‐dependent sex allocation. Many biological processes have been hypothesized to drive this sex asymmetry, yet a general explanation for the evolution of sex‐determining mechanisms remains elusive. Here, we develop a mathematical model for a novel hypothesis of the evolution of ESD, and provide a first empirical test using data across turtles. ESD is favored when the sex‐determining environment affects annual survival rates equivalently in males and females, and males and females mature at different ages. We compare this hypothesis to alternative hypotheses, and demonstrate how it captures a crucially different process. This maturation process arises naturally from common life histories and applies more broadly to condition‐dependent sex allocation. Therefore, it has widespread implications for animal taxa. Across turtle species, ESD is associated with greater sex differences in the age at maturity compared to species without ESD, as predicted by our hypothesis. However, the effect is not statistically significant and will require expanded empirical investigation. Given variation among taxa in sex‐specific age at maturity, our survival‐to‐maturity hypothesis may capture common selective forces on sex‐determining mechanisms.     

Laccase-mediated system pretreatment to enhance the effect of hydrogen peroxide bleaching of cotton fabric

This study evaluates the bleaching efficiency of the hydrogen peroxide bleaching process combined with laccase-mediated system pretreatment (LMS-HPBP) in the treatment of scoured cotton fabric. By changing the factors of laccase-mediated system pretreatment and the hydrogen peroxide bleaching process and examining the subsequent whiteness value and retained tensile strength of the samples, we find three LMS-HPBP processes that are more environment friendly than the conventional hydrogen peroxide bleaching process (CHPBP): (i) bleaching with lower dosage of hydrogen peroxide; (ii) bleaching at reduced temperature; (iii) bleaching for shortened duration. Whiteness, retained tensile strength and K/S values of cotton fabric samples treated by i-iii processes were similar to or higher than those by CHPBP. X-ray diffraction (XRD) analysis also demonstrated that the three processes rendered fabric of both lower crystallinity and bigger crystallite size than those by CHPBP. In addition, the "green" short-flow process was developed to treat cotton fabric and the results obtained shows this method is feasible as a new energy-saving process.     

Strong species‐environment feedback shapes plant community assembly along environmental gradients

An aim of community ecology is to understand the patterns of competing species assembly along environmental gradients. All species interact with their environments. However, theories of community assembly have seldom taken into account the effects of species that are able to engineer the environment. In this modeling study, we integrate the species' engineering trait together with processes of immigration and local dispersal into a theory of community assembly. We quantify the species' engineering trait as the degree to which it can move the local environment away from its baseline state towards the optimum state of the species (species‐environment feedback). We find that, in the presence of immigration from a regional pool, strong feedback can increase local species richness; however, in the absence of continual immigration, species richness is a declining function of the strength of species‐environment feedback. This shift from a negative effect of engineering strength on species richness to a positive effect, as immigration rate increases, is clearer when there is spatial heterogeneity in the form of a gradient in environmental conditions than when the environment is homogeneous or it is randomly heterogeneous. Increasing the scale over which local dispersal occurs can facilitate species richness when there is no species‐environment feedback or when the feedback is weak. However, increases in the spatial scale of dispersal can reduce species richness when the species‐environment feedback is strong. These results expand the theoretical basis for understanding the effects of the strength of species‐environment feedback on community assembly.     

The role of growth stop as a morphogenetic factor in Mastomys natalensis (Rodentia: Muridae)

The present study investigated growth patterns under three different environmental conditions in a single population of the rodent Mastomys natalensis (Rodentia, Muridae) in Morogoro, Tanzania. The study aimed to test whether and how post-weaning ontogenetic processes are affected by different environmental conditions. Morogoro is characterized by a bimodal rainfall pattern, with unreliable peaks occurring in November/December of some years and reliable ones in February to May. We recognized three different generation types. In the first one, the α generation, growth occurred during the dry second half of the year in years when the November/December rains were very poor. The second group (β generation) grew under conditions when these rains were abundant. Finally, the γ generation, consisted of animals that were born in the middle of the rainy season in years when there was a continuity between both rainfall peaks. Analyses of size and shape following both Huxley–Jolicoeur and Gould–Mosimann approaches revealed that the three groups differ significantly both in size and shape. In both cases, the importance of the environment in assessing growth trajectories during post-natal ontogenetic processes is apparent.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 791–800.     

Quantum-like model of brain's functioning: decision making from decoherence

We present a quantum-like model of decision making in games of the Prisoner's Dilemma type. By this model the brain processes information by using representation of mental states in a complex Hilbert space. Driven by the master equation the mental state of a player, say Alice, approaches an equilibrium point in the space of density matrices (representing mental states). This equilibrium state determines Alice's mixed (i.e., probabilistic) strategy. We use a master equation in which quantum physics describes the process of decoherence as the result of interaction with environment. Thus our model is a model of thinking through decoherence of the initially pure mental state. Decoherence is induced by the interaction with memory and the external mental environment. We study (numerically) the dynamics of quantum entropy of Alice's mental state in the process of decision making. We also consider classical entropy corresponding to Alice's choices. We introduce a measure of Alice's diffidence as the difference between classical and quantum entropies of Alice's mental state. We see that (at least in our model example) diffidence decreases (approaching zero) in the process of decision making. Finally, we discuss the problem of neuronal realization of quantum-like dynamics in the brain; especially roles played by lateral prefrontal cortex or/and orbitofrontal cortex.