Exploring survival strategies of African Savanna trees by partial ordering techniques

The resilience of savanna ecosystems to climate and land-use changes is an important ecological and management question. The term ‘resilience’ is used to refer to the ability of a tree species to survive in a specific location, even under changing environmental conditions. In this study, vectors of functional traits of selected savanna tree species are studied by applying partial order algorithms to them. Some ecological interpretations are obtained and are compared to published research. One finding is the high rates of nitrogen fixation for the leaves of Acacia nigrescens. In opposition to this well-known fact, we discovered that Sclerocarya birrea has a bigger average leaf area than the other four tree species. Additionally, we found high carbonate values within the leaf from Colophospermum mopane, Combretum apiculatum, and Terminalis sericea. These results correspond to different ecological strategies for the tree species in question. It became obvious that geometric structures gained from partial ordering show a very good correspondence to ecological strategies of these tree species. Concepts of partial order theory may therefore be helpful in ecosystem research.     

Biological systems of cellular organization and their computer models

The interactions of self-organizing systems possessing at least two hierarchical levels with the environment are dealt with. The dynamical deliberations taking place at the lower level Q of the organism are modelled by a finite state controlled Markov chain. The transitional probability matrix is parametrized on control variables which are related to the probabilities of “pay off” in an underlying two-agent “game” described in the paper.The environment is envisaged as another Markov chain with fixed transitional probabilities. The higher hierarchical level W plays the role of a controller which receives from the lower level Q collective properties which measure (a) the percentage of occupancy of a “homeostatic” state and (b) the cross-correlation between the dynamical processes at the level Q and the environment.The design of the controller is set up as a two-objective control problem having to do with the maximization of the long term average of an appropriately weighted sum of the conflicting terms: probability of the homeostatic state and cross-correlation with the environment.Optimal strategies are found through computing simulation which determine the efferent controls precipitated from the level W to the level Q. The relevance of the model to a number of problems related to the adaptability of hierarchical structures is discussed. Finally some extentions of the present work to do with the communication process between two multihierarchical systems are mentioned.     

Near optimal manufacturing flow controller design

Flow control of flexible manufacturing systems (FMSs) addresses an important real-time scheduling requirement of modern manufacturing facilities, which are prone to failures and other controllable or stochastic discrete events affecting production capacity, such as change of setup and maintenance scheduling. Flow controllers are useful both in the coordination of interconnected flexible manufacturing cells through distributed scheduling policies and in the hierarchical decomposition of the planning and scheduling problem of complex manufacturing systems. Optimal flow-control policies are hedging-point policies characterized by a generally intractable system of stochastic partial differential equations. This article proposes a near optimal controller whose design is computationally feasible for realistic-size systems. The design exploits a decomposition of the multiple-part-type problem to many analytically tractable one-part-type problems. The decomposition is achieved by replacing the polyhedra production capacity sets with inscribed hypercubes. Stationary marginal densities of state variables are computed iteratively for successive trial controller designs until the best inscribed hypercubes and the associated optimal hedging points are determined. Computational results are presented for an illustrative example of a failureprone FMS.     

Molecular Specificity,Convergence and Constraint Shape Adaptive Evolution in Nutrient-Poor Environments

One of the central goals of evolutionary biology is to explain and predict the molecular basis of adaptive evolution. We studied the evolution of genetic networks in Saccharomyces cerevisiae (budding yeast) populations propagated for more than 200 generations in different nitrogen-limiting conditions. We find that rapid adaptive evolution in nitrogen-poor environments is dominated by the de novo generation and selection of copy number variants (CNVs), a large fraction of which contain genes encoding specific nitrogen transporters including PUT4, DUR3 and DAL4. The large fitness increases associated with these alleles limits the genetic heterogeneity of adapting populations even in environments with multiple nitrogen sources. Complete identification of acquired point mutations, in individual lineages and entire populations, identified heterogeneity at the level of genetic loci but common themes at the level of functional modules, including genes controlling phosphatidylinositol-3-phosphate metabolism and vacuole biogenesis. Adaptive strategies shared with other nutrient-limited environments point to selection of genetic variation in the TORC1 and Ras/PKA signaling pathways as a general mechanism underlying improved growth in nutrient-limited environments. Within a single population we observed the repeated independent selection of a multi-locus genotype, comprised of the functionally related genes GAT1, MEP2 and LST4. By studying the fitness of individual alleles, and their combination, as well as the evolutionary history of the evolving population, we find that the order in which these mutations are acquired is constrained by epistasis. The identification of repeatedly selected variation at functionally related loci that interact epistatically suggests that gene network polymorphisms (GNPs) may be a frequent outcome of adaptive evolution. Our results provide insight into the mechanistic basis by which cells adapt to nutrient-limited environments and suggest that knowledge of the selective environment and the regulatory mechanisms important for growth and survival in that environment greatly increase the predictability of adaptive evolution.     

Recent advances in the metabolic engineering of microorganisms for the production of 3-hydroxypropionic acid as C3 platform chemical

Development of sustainable technologies for the production of 3-hydroxypropionic acid (3HP) as a platform chemical has recently been gaining much attention owing to its versatility in applications for the synthesis of other specialty chemicals. Several proposed biological synthesis routes and strategies for producing 3HP from glucose and glycerol are reviewed presently. Ten proposed routes for 3HP production from glucose are described and one of which was recently constructed successfully in Escherichia coli with malonyl–Coenzyme A as a precursor. This resulted in a yield still far from the required level for industrial application. On the other hand, strategies employing engineered E. coli and Klebsiella pneumoniae capable of producing 3HP from glycerol are also evaluated. The titers produced by these recombinant strains reached around 3 %. At its current state, it is evident that a bulk of engineering works is yet to be done to acquire a biosynthesis route for 3HP that is acceptable for industrial-scale production.     

Digital image analysis of different crown shape of Platycladus orientalis

Platycladus orientalis (L.) Franco is a beautifully crown-shaped evergreen tree species used for ornamental cultivation. These trees are also important afforestation plants at hill sites containing calcareous parent rocks and exhibit high tolerance to drought and barren sites. However, Platycladus orientalis trees with abnormal crowns, such as fusiform and torch-form, have been identified at sites with extreme drought and barren hills in Shandong, China, although the abnormal crowns does not reduce the ornamental value of these trees. In the present study, we used the RGB imaging and geographical statistical analyses through the construction of meteorological indices. The results indicate that variations of abnormal Platycladus orientalis crowns are associated with both the internal metabolism of these trees and the external environment. Crown shapes are strongly affected by the local dry, hot and windy meteorological environment, particularly individuals planted at poor hill site conditions. In response to extreme events of drought, high temperature and strong winds, the twigs and scale leaves of Platycladus orientalis typically wilt from the lower part to the upper part of the crown. The fusiform and torch-form crowns are formed through the wilting of partial twigs and scale leaves to avoid the entire wilt of the trees, thereby saving the life of the tree at the expense of partial twigs and scale leaves.     

Does frequency-dependence determine male morph survival in the bulb mite Rhizoglyphus robini?

Alternative reproductive phenotypes (ARPs) represent discrete morphological variation within a single sex; as such ARPs are an excellent study system to investigate the maintenance of phenotypic variation. ARPs are traditionally modelled as a mixture of pure strategies or as a conditional strategy. Most male dimorphisms are controlled by a conditional strategy, where males develop into a particular phenotype as a result of their condition which allows them to reach a certain threshold. Individuals that are unable to reach the threshold of a conditional strategy are considered to ‘make the best of a bad job’; however, these individuals can have their own fitness merits. Given these fitness merits, condition-dependent selection alone is not sufficient to maintain a conditionally determined male dimorphism and other mechanisms, most likely frequency-dependent selection, are required. We studied in an experiment, the male dimorphic bulb mite Rhizoglyphus robini—where males are fighters that can kill other males or benign scramblers—to assess the strength of frequency-dependent survival in a high and low-quality environment. We found that male survival was frequency-dependent in the high-quality environment but not the low-quality environment. In the high-quality environment the survival curves of the two morphs crossed but the direction of frequency-dependence was opposite to what theory predicts.     

Severe constraints for sound communication in a frog from the South American temperate forest

The efficiency of acoustic communication depends on the power generated by the sound source, the quality of the environment across which signals propagate, the environmental noise and the sensitivity of the intended receivers. Eupsophus calcaratus, an anuran from the temperate austral forest, communicates by means of an advertisement call of weak intensity in a sound-attenuating environment. To estimate the range over which these frogs communicate effectively, we conducted measurements of sound level and degradation patterns of propagating advertisement calls in the field, and measurements of auditory thresholds to pure tones and to natural calls in laboratory conditions. The results show that E. calcaratus produces weak advertisement calls of about 72 dB sound pressure level (SPL) at 0.25 m from the caller. The signals are affected by attenuation and degradation patterns as they propagate in their native environment, reaching average values of 61 and 51 dB SPL at 1 and 2 m from the sound source, respectively. Midbrain multi-unit recordings show a relatively low auditory sensitivity, with thresholds of about 58 dB SPL for conspecific calls, which are likely to restrict communication to distances shorter than 2 m, a remarkably short range as compared to other anurans.     

Conservation implications of small population size and habitat fragmentation in an endangered lupine

Conservation measures to preserve critically endangered species aim to maintain healthy and self-sustaining populations and often involve reintroductions. Effective introductions must take into account the genetic structure and diversity remaining in the species to inform choices of germplasm for introduction strategies. Lupinus aridorum (McFarlin ex Beckner; Fabaceae) is an endangered plant found on two disjunct ridge systems in central Florida. All plants are found in areas that are favored for human development and agriculture. Few options exist for introduction locations, so the most informed strategies must be used to preserve this species. We used ten microsatellite loci, developed for this species, to determine genetic diversity and genetic differentiation among populations, and to compare L. aridorum with two closely related congeners. Our results show a low level of diversity remaining in the species in comparison with a more abundant congener and similar levels of variability among each L. aridorum population. At least three L. aridorum populations exhibit a genetic signal of partial selfing. Hybridization with a closely-related congener was not apparent; however, additional crossing trials are needed to fully assess the possibility of hybridization. Although some sources list the taxonomy of L. aridorum as a variety of a Florida panhandle species, L. westianus (Small), the genetic differences revealed by our data support listing these two species as separate entities. Our findings can be used to guide sampling strategies for ex situ conservation such as providing a mixture of source populations to improve the probability of successful introductions.     

Several different strategies for obtaining animal resources in the late Middle Pleistocene: The case of level XII at Bolomor Cave (Valencia,Spain)

Bolomor Cave, located in Tavernes de la Valldigna (Valencia, Spain), contains a sedimentary deposit composed of seventeen stratigraphic levels ranging from MIS 9 to MIS 5e. This extensive sequence allows us to ask different questions about how the human groups of this chronological period related to their environment. We report several different strategies by which animal resources were obtained from level XII faunal assemblage (MIS 6). These practices range from scavenging to the complex hunting techniques, such as multiple predation. This practice is inferred in the case of horses (Equus ferus) on the basis of: (1) the proportional representation of skeletal elements (elements with high marrow content, such as stylopodials and zeugopodials); (2) age at death of these animals (from infantile to advanced adult); (3) the position and function of cutmarks and toothmarks (mainly oblique and longitudinal incisions on limb bones diaphyses); (4) archaeostratigraphic distribution of their remains in the assemblage; and (5) presence of refits among the bones located at this archaeostratigraphical line. Evidence of anthropogenic processing of small prey (Oryctolagus cuniculus and Cygnus olor) is also identified at level XII. These discoveries imply the development of techniques different from those used to capture large and medium ungulates. From this perspective, a variety of strategies to obtain animal food can be documented at Bolomor Cave. This phenomenon can be related to the highly adaptive subsistence strategies of these hominids, who could take advantage of the benefits offered by a diverse and rich environment. In general, the aim of this study is to provide data about the subsistence strategies of human groups from Bolomor Cave and contribute to knowledge about the human groups’ way of life of in the late Middle Pleistocene.     

Ecological impacts of parasitic chytrids,syndiniales and perkinsids on populations of marine photosynthetic dinoflagellates

Parasitism is a widespread interaction that plays significant roles in ecosystem balance and evolution. Historically the biology of zoosporic parasites is often a neglected field when studying aquatic ecological dynamics, especially in marine ecosystems. In the marine environment, dinoflagellates represent a significantly large component of primary production, and may be infected by a variety of fungal and fungus-like parasites including chytrids, syndiniales, and perkinsids as well as other microorganisms. The relationship between these organisms and their dinoflagellate hosts constitutes a highly significant pathosystem given the increasing importance of aquaculture. Because of their small size and lack of morphological characteristics these organisms are difficult to identify. This review compares the taxonomy, life cycle, host range, infection strategies, and ecological roles of species of Parvilucifera, Amoebophrya and Dinomyces which are parasites of dinoflagellates. Most of these species have only been described recently. Implications for environmental management are discussed.     

A proposed classification of environmental adaptation: the example of high altitude

Extreme environments are defined as the opposite of usual environments where the evoked physiological responses are unperceivable, repeatable and adjusted to the constraint. Adaptation strategies to a given environment show three levels: cultural or technological, where a buffer space is built to protect the organism from the hostile milieu, physiological, where temporary adaptive mechanisms are developed, and genetic, where full adaptation is possible with normal life and reproduction. The cost of adaptation increases from the genetic level (minimal cost) to the technological level. These concepts are illustrated by the example of adaptation to altitude hypoxia. The technological level is given by the use of oxygen bottles by high altitude climbers. The physiological level involves various physiological and biological systems (increase in heart rate, ventilation, erythropoiesis, expression of hypoxia-inducible factors, etc.). The genetic level has been reached by some animal species such as Yaks, Llamas, Pikas but has not yet been demonstrated in humans. Diseases developed during exposure to acute or chronic hypoxia may be considered as “adaptive crises” that mimic the transition to a lower energy level of adaptation.     

Modeling stochasticity and variability in gene regulatory networks

Modeling stochasticity in gene regulatory networks is an important and complex problem in molecular systems biology. To elucidate intrinsic noise, several modeling strategies such as the Gillespie algorithm have been used successfully. This article contributes an approach as an alternative to these classical settings. Within the discrete paradigm, where genes, proteins, and other molecular components of gene regulatory networks are modeled as discrete variables and are assigned as logical rules describing their regulation through interactions with other components. Stochasticity is modeled at the biological function level under the assumption that even if the expression levels of the input nodes of an update rule guarantee activation or degradation there is a probability that the process will not occur due to stochastic effects. This approach allows a finer analysis of discrete models and provides a natural setup for cell population simulations to study cell-to-cell variability. We applied our methods to two of the most studied regulatory networks, the outcome of lambda phage infection of bacteria and the p53-mdm2 complex.     

A stochastic model of evolutionary dynamics with deterministic large-population asymptotics

An evolutionary birth-death process is proposed as a model of evolutionary dynamics. Agents residing in a continuous spatial environment X, play a game G, with a continuous strategy set S, against other agents in the environment. The agents’ positions and strategies continuously change in response to other agents and to random effects. Agents spawn asexually at rates that depend on their current fitness, and agents die at rates that depend on their local population density. Agents’ individual evolutionary trajectories in X and S are governed by a system of stochastic ODEs. When the number of agents is large and distributed in a smooth density on (X,S), the collective dynamics of the entire population is governed by a certain (deterministic) PDE, which we call a fitness-diffusion equation.     

Characterization of two related exoantigens from the biodeteriogenic fungus Aspergillus versicolor

Aspergillus versicolor is one of the most common fungi in damp buildings in U. K., various European and Scandinavian countries as well as the United States and Canada. It is a proxy for species that occur at similar material water activities. Based on studies from Finland, Norway and Germany, it is among the common species resulting in an IgE reaction. Using pre-screened human sera with antibodies to various fungi, two related proteins were discovered with molecular weights 43 and 41 kDa based on SDS electrophoresis. Both proteins were excreted on the surfaces of spores and into culture media. The 41 kDa protein has a pI of 4.5. Based on a partial sequence, it is a serine protease. There are a number of Aspergillus proteases with overlapping sequences but these have different molecular weights and pI values. Polyclonal and monoclonal antibodies were developed that were specific compared to a diverse taxonomic array of related and unrelated fungi that commonly occur in the built environment. Initially this was done to ensure the specificity of the target protein. The measurement of other allergens and antigens associated with the built environment has a number of uses. Most importantly, these can be used to assess reliably biodeterioration and contribute to improved exposure assessments for population health studies.     

Plasmid Donor Affects Host Range of Promiscuous IncP-1β Plasmid pB10 in an Activated-Sludge Microbial Community

Horizontal transfer of multiresistance plasmids in the environment contributes to the growing problem of drug-resistant pathogens. Even though the plasmid host cell is the primary environment in which the plasmid functions, possible effects of the plasmid donor on the range of bacteria to which plasmids spread in microbial communities have not been investigated. In this study we show that the host range of a broad-host-range plasmid within an activated-sludge microbial community was influenced by the donor strain and that various mating conditions and isolation strategies increased the diversity of transconjugants detected. To detect transconjugants, the plasmid pB10 was marked with lacp-rfp, while rfp expression was repressed in the donors by chromosomal lacI^q. The phylogeny of 306 transconjugants obtained was determined by analysis of partial 16S rRNA gene sequences. The transconjugants belonged to 15 genera of the α- and γ-Proteobacteria. The phylogenetic diversity of transconjugants obtained in separate matings with donors Pseudomonas putida SM1443, Ralstonia eutropha JMP228, and Sinorhizobium meliloti RM1021 was significantly different. For example, the transconjugants obtained after matings in sludge with S. meliloti RM1021 included eight genera that were not represented among the transconjugants obtained with the other two donors. Our results indicate that the spectrum of hosts to which a promiscuous plasmid transfers in a microbial community can be strongly influenced by the donor from which it transfers.     

A Hierarchical Approach to Cooperativity in Macromolecular and Self-Assembling Binding Systems

The study of complex macromolecular binding systems reveals that a high number of states and processes are involved in their mechanism of action, as has become more apparent with the sophistication of the experimental techniques used. The resulting information is often difficult to interpret because of the complexity of the scheme (large size and profuse interactions, including cooperative and self-assembling interactions) and the lack of transparency that this complexity introduces into the interpretation of the indexes traditionally used to describe the binding properties. In particular, cooperative behaviour can be attributed to very different causes, such as direct chemical modification of the binding sites, conformational changes in the whole structure of the macromolecule, aggregation processes between different subunits, etc. In this paper, we propose a novel approach for the analysis of the binding properties of complex macromolecular and self-assembling systems. To quantify the binding behaviour, we use the global association quotient defined as K _c = [occupied sites]/([free sites] L), L being the free ligand concentration. K _c can be easily related to other measures of cooperativity (such as the Hill number or the Scatchard plot) and to the free energies involved in the binding processes at each ligand concentration. In a previous work, it was shown that K_c could be decomposed as an average of equilibrium constants in two ways: intrinsic constants for Adair binding systems and elementary constants for the general case. In this study, we show that these two decompositions are particular cases of a more general expression, where the average is over partial association quotients, associated with subsystems from which the system is composed. We also show that if the system is split into different subsystems according to a binding hierarchy that starts from the lower, microscopic level and ends at the higher, aggregation level, the global association quotient can be decomposed following the hierarchical levels of macromolecular organisation. In this process, the partial association quotients of one level are expressed, in a recursive way, as a function of the partial quotients of the level that is immediately below, until the microscopic level is reached. As a result, the binding properties of very complex macromolecular systems can be analysed in detail, making the mechanistic explanation of their behaviour transparent. In addition, our approach provides a model-independent interpretation of the intrinsic equilibrium constants in terms of the elementary ones.     

Biases in Visual,Auditory, and Audiovisual Perception of Space

Localization of objects and events in the environment is critical for survival, as many perceptual and motor tasks rely on estimation of spatial location. Therefore, it seems reasonable to assume that spatial localizations should generally be accurate. Curiously, some previous studies have reported biases in visual and auditory localizations, but these studies have used small sample sizes and the results have been mixed. Therefore, it is not clear (1) if the reported biases in localization responses are real (or due to outliers, sampling bias, or other factors), and (2) whether these putative biases reflect a bias in sensory representations of space or a priori expectations (which may be due to the experimental setup, instructions, or distribution of stimuli). Here, to address these questions, a dataset of unprecedented size (obtained from 384 observers) was analyzed to examine presence, direction, and magnitude of sensory biases, and quantitative computational modeling was used to probe the underlying mechanism(s) driving these effects. Data revealed that, on average, observers were biased towards the center when localizing visual stimuli, and biased towards the periphery when localizing auditory stimuli. Moreover, quantitative analysis using a Bayesian Causal Inference framework suggests that while pre-existing spatial biases for central locations exert some influence, biases in the sensory representations of both visual and auditory space are necessary to fully explain the behavioral data. How are these opposing visual and auditory biases reconciled in conditions in which both auditory and visual stimuli are produced by a single event? Potentially, the bias in one modality could dominate, or the biases could interact/cancel out. The data revealed that when integration occurred in these conditions, the visual bias dominated, but the magnitude of this bias was reduced compared to unisensory conditions. Therefore, multisensory integration not only improves the precision of perceptual estimates, but also the accuracy.     

Bisphenol A and Risk Management Ethics

It is widely recognized that endocrine disrupting compounds, such as Bisphenol A, pose challenges for traditional paradigms in toxicology, insofar as these substances appear to have a wider range of low‐dose effects than previously recognized. These compounds also pose challenges for ethics and policymaking. When a chemical does not have significant low‐dose effects, regulators can allow it to be introduced into commerce or the environment, provided that procedures and rules are in place to keep exposures below an acceptable level. This option allows society to maximize the benefits from the use of the chemical while minimizing risks to human health or the environment, and it represents a compromise between competing values. When it is not possible to establish acceptable exposure levels for chemicals that pose significant health or environmental risks, the most reasonable options for risk management may be to enact either partial or complete bans on their use. These options create greater moral conflict than other risk management strategies, leaving policymakers difficult choices between competing values.