WorldWideScience

Sample records for bacterial metapopulation adapts

  1. Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics.

    Science.gov (United States)

    Hand, Brian K; Muhlfeld, Clint C; Wade, Alisa A; Kovach, Ryan P; Whited, Diane C; Narum, Shawn R; Matala, Andrew P; Ackerman, Michael W; Garner, Brittany A; Kimball, John S; Stanford, Jack A; Luikart, Gordon

    2016-02-01

    Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population-specific and pairwise FST ) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate-related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and FST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin-wide to the metapopulation scale). Sensitivity analysis (leave-one-population-out) revealed consistent relationships between climate variables and FST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.

  2. Bacterial surface adaptation

    Science.gov (United States)

    Utada, Andrew

    2014-03-01

    Biofilms are structured multi-cellular communities that are fundamental to the biology and ecology of bacteria. Parasitic bacterial biofilms can cause lethal infections and biofouling, but commensal bacterial biofilms, such as those found in the gut, can break down otherwise indigestible plant polysaccharides and allow us to enjoy vegetables. The first step in biofilm formation, adaptation to life on a surface, requires a working knowledge of low Reynolds number fluid physics, and the coordination of biochemical signaling, polysaccharide production, and molecular motility motors. These crucial early stages of biofilm formation are at present poorly understood. By adapting methods from soft matter physics, we dissect bacterial social behavior at the single cell level for several prototypical bacterial species, including Pseudomonas aeruginosa and Vibrio cholerae.

  3. Adaptive Bacterial Foraging Optimization

    Directory of Open Access Journals (Sweden)

    Hanning Chen

    2011-01-01

    Full Text Available Bacterial Foraging Optimization (BFO is a recently developed nature-inspired optimization algorithm, which is based on the foraging behavior of E. coli bacteria. Up to now, BFO has been applied successfully to some engineering problems due to its simplicity and ease of implementation. However, BFO possesses a poor convergence behavior over complex optimization problems as compared to other nature-inspired optimization techniques. This paper first analyzes how the run-length unit parameter of BFO controls the exploration of the whole search space and the exploitation of the promising areas. Then it presents a variation on the original BFO, called the adaptive bacterial foraging optimization (ABFO, employing the adaptive foraging strategies to improve the performance of the original BFO. This improvement is achieved by enabling the bacterial foraging algorithm to adjust the run-length unit parameter dynamically during algorithm execution in order to balance the exploration/exploitation tradeoff. The experiments compare the performance of two versions of ABFO with the original BFO, the standard particle swarm optimization (PSO and a real-coded genetic algorithm (GA on four widely-used benchmark functions. The proposed ABFO shows a marked improvement in performance over the original BFO and appears to be comparable with the PSO and GA.

  4. High genetic variation in resting-stage production in a metapopulation: Is there evidence for local adaptation?

    Science.gov (United States)

    Roulin, Anne C; Mariadassou, Mahendra; Hall, Matthew D; Walser, Jean-Claude; Haag, Christoph; Ebert, Dieter

    2015-10-01

    Local adaptation is a key process for the maintenance of genetic diversity and population diversification. A better understanding of the mechanisms that allow (or prevent) local adaptation constitutes a key in apprehending how and at what spatial scale it occurs. The production of resting stages is found in many taxa and reflects an adaptation to outlast adverse environmental conditions. Daphnia magna (Crustacea) can alternate between asexual and sexual reproduction, the latter being linked to dormancy, as resting stages can only be produced sexually. In this species, on a continental scale, resting-stage production is locally adapted--that is, it is induced when the photoperiod indicates the imminence of habitat deterioration. Here, we aimed to explore whether selection is strong enough to maintain local adaptation at a scale of a few kilometers. We assessed life-history traits of 64 D. magna clones originating from 11 populations of a metapopulation with permanent and intermittent pool habitats. We found large within- and between-population variation for all dormancy-related traits, but no evidence for the hypothesized higher resting-stage production in animals from intermittent habitats. We discuss how gene flow, founder events, or other forms of selection might interfere with the process of local adaptation.

  5. Bacterial adaptation through loss of function.

    Directory of Open Access Journals (Sweden)

    Alison K Hottes

    Full Text Available The metabolic capabilities and regulatory networks of bacteria have been optimized by evolution in response to selective pressures present in each species' native ecological niche. In a new environment, however, the same bacteria may grow poorly due to regulatory constraints or biochemical deficiencies. Adaptation to such conditions can proceed through the acquisition of new cellular functionality due to gain of function mutations or via modulation of cellular networks. Using selection experiments on transposon-mutagenized libraries of bacteria, we illustrate that even under conditions of extreme nutrient limitation, substantial adaptation can be achieved solely through loss of function mutations, which rewire the metabolism of the cell without gain of enzymatic or sensory function. A systematic analysis of similar experiments under more than 100 conditions reveals that adaptive loss of function mutations exist for many environmental challenges. Drawing on a wealth of examples from published articles, we detail the range of mechanisms through which loss-of-function mutations can generate such beneficial regulatory changes, without the need for rare, specific mutations to fine-tune enzymatic activities or network connections. The high rate at which loss-of-function mutations occur suggests that null mutations play an underappreciated role in the early stages of adaption of bacterial populations to new environments.

  6. Bacterial adaptation to sublethal antibiotic gradients can change the ecological properties of multitrophic microbial communities.

    Science.gov (United States)

    Friman, Ville-Petri; Guzman, Laura Melissa; Reuman, Daniel C; Bell, Thomas

    2015-05-07

    Antibiotics leak constantly into environments due to widespread use in agriculture and human therapy. Although sublethal concentrations are well known to select for antibiotic-resistant bacteria, little is known about how bacterial evolution cascades through food webs, having indirect effect on species not directly affected by antibiotics (e.g. via population dynamics or pleiotropic effects). Here, we used an experimental evolution approach to test how temporal patterns of antibiotic stress, as well as migration within metapopulations, affect the evolution and ecology of microcosms containing one prey bacterium, one phage and two protist predators. We found that environmental variability, autocorrelation and migration had only subtle effects for population and evolutionary dynamics. However, unexpectedly, bacteria evolved greatest fitness increases to both antibiotics and enemies when the sublethal levels of antibiotics were highest, indicating positive pleiotropy. Crucially, bacterial adaptation cascaded through the food web leading to reduced predator-to-prey abundance ratio, lowered predator community diversity and increased instability of populations. Our results show that the presence of natural enemies can modify and even reverse the effects of antibiotics on bacteria, and that antibiotic selection can change the ecological properties of multitrophic microbial communities by having indirect effects on species not directly affected by antibiotics.

  7. Dispersal, environmental forcing, and parasites combine to affect metapopulation synehrony and stability.

    Science.gov (United States)

    Duncan, Alison B; Gonzalez, Andrew; Kaltz, Oliver

    2015-01-01

    Dispersal can have positive and negative effects on metapopulation stability and persistence. One prediction is that high levels of dispersal synchronize density fluctuations between subpopulations. However, little is still known about how biotic and abiotic factors combine to modify the effects of dispersal rate on synchrony and metapopulation dynamics. In a fully factorial experimental design, we investigated the combined effects of (1) dispersal, (2) parasite infection, and (3) synchrony in temperature fluctuations on subpopulation synchrony, metapopulation instability, and minimum population size, in laboratory metapopulations of the ciliate Paramecium caudatum. Metapopulations, comprising two subpopulations linked by high or low levels of dispersal, were exposed to daily fluctuations in temperature between permissive (23 degrees C) and restrictive (5 degrees C) conditions. Infected metapopulations started the experiment with one subpopulation uninfected, while the other was infected at a prevalence of 5% with the bacterial parasite Holospora undulata. The temperature synchrony treatment involved subpopulations within a metapopulation following the same (synchronous temperatures) or different (asynchronous temperatures) temporal sequences. Population size was tracked over the 56-day experiment. We found that subpopulation density fluctuations were synchronized by high dispersal in infected metapopulations, and by synchronous temperatures in all metapopulations. Subpopulation synchrony was positively correlated with metapopulation instability and minimum metapopulation size, highlighting the multiple consequences of our treatments for metapopulation dynamics. Our results illustrate how parasites can generate dispersal-driven synchrony in non-cycling, declining populations. This "biotic forcing" via a natural enemy added to the temperature-dependent environmental forcing. We therefore conclude that predictions of metapopulation persistence in natural populations

  8. Persistence and resistance as complementary bacterial adaptations to antibiotics

    OpenAIRE

    Vogwill, T.; Comfort, A. C.; Furió, V.; MacLean, R. C.

    2016-01-01

    Abstract Bacterial persistence represents a simple of phenotypic heterogeneity, whereby a proportion of cells in an isogenic bacterial population can survive exposure to lethal stresses such as antibiotics. In contrast, genetically based antibiotic resistance allows for continued growth in the presence of antibiotics. It is unclear, however, whether resistance and persistence are complementary or alternative evolutionary adaptations to antibiotics. Here, we investigate the co‐evolution of res...

  9. Bacterial adaptation to the gut environment favors successful colonization

    Science.gov (United States)

    Rezzonico, Enea; Mestdagh, Renaud; Delley, Michèle; Combremont, Séverine; Dumas, Marc-Emmanuel; Holmes, Elaine; Nicholson, Jeremy; Bibiloni, Rodrigo

    2011-01-01

    Rodent models harboring a simple yet functional human intestinal microbiota provide a valuable tool to study the relationships between mammals and their bacterial inhabitants. In this study, we aimed to develop a simplified gnotobiotic mouse model containing 10 easy-to-grow bacteria, readily available from culture repositories, and of known genome sequence, that overall reflect the dominant commensal bacterial makeup found in adult human feces. We observed that merely inoculating a mix of fresh bacterial cultures into ex-germ free mice did not guarantee a successful intestinal colonization of the entire bacterial set, as mice inoculated simultaneously with all strains only harbored 3 after 21 d. Therefore, several inoculation procedures were tested and levels of individual strains were quantified using molecular tools. Best results were obtained by inoculating single bacterial strains into individual animals followed by an interval of two weeks before allowing the animals to socialize to exchange their commensal microbes. Through this procedure, animals were colonized with almost the complete bacterial set (9/10). Differences in the intestinal composition were also reflected in the urine and plasma metabolic profiles, where changes in lipids, SCFA, and amino acids were observed. We conclude that adaptation of bacterial strains to the host’s gut environment (mono-colonization) may predict a successful establishment of a more complex microbiota in rodents. PMID:22157236

  10. Fenced and Fragmented: Conservation Value of Managed Metapopulations.

    Directory of Open Access Journals (Sweden)

    Susan M Miller

    Full Text Available Population fragmentation is threatening biodiversity worldwide. Species that once roamed vast areas are increasingly being conserved in small, isolated areas. Modern management approaches must adapt to ensure the continued survival and conservation value of these populations. In South Africa, a managed metapopulation approach has been adopted for several large carnivore species, all protected in isolated, relatively small, reserves that are fenced. As far as possible these approaches are based on natural metapopulation structures. In this network, over the past 25 years, African lions (Panthera leo were reintroduced into 44 fenced reserves with little attention given to maintaining genetic diversity. To examine the situation, we investigated the current genetic provenance and diversity of these lions. We found that overall genetic diversity was similar to that in a large national park, and included a mixture of four different southern African evolutionarily significant units (ESUs. This mixing of ESUs, while not ideal, provides a unique opportunity to study the impact of mixing ESUs over the long term. We propose a strategic managed metapopulation plan to ensure the maintenance of genetic diversity and improve the long-term conservation value of these lions. This managed metapopulation approach could be applied to other species under similar ecological constraints around the globe.

  11. Population proteomics: an emerging discipline to study metapopulation ecology.

    Science.gov (United States)

    Biron, David G; Loxdale, Hugh D; Ponton, Fleur; Moura, Hercules; Marché, Laurent; Brugidou, Christophe; Thomas, Frédéric

    2006-03-01

    Proteomics research has developed until recently in a relative isolation from other fast-moving disciplines such as ecology and evolution. This is unfortunate since applying proteomics to these disciplines has apparently the potential to open new perspectives. The huge majority of species indeed exhibit over their entire geographic range a metapopulation structure, occupying habitats that are fragmented and heterogeneous in space and/or through time. Traditionally, population genetics is the main tool used to studying metatopulations, as it describes the spatial structure of populations and the level of gene flow between them. In this Viewpoint, we present the reasons why we think that proteomics, because of the level of integration it promotes, has the potential to resolve interesting issues specific to metapopulation biology and adaptive processes.

  12. Dynamics of adaptive immunity against phage in bacterial populations

    CERN Document Server

    Bradde, Serena; Tesileanu, Tiberiu; Balasubramanian, Vijay

    2015-01-01

    The CRISPR (clustered regularly interspaced short palindromic repeats) mechanism allows bacteria to adaptively defend against phages by acquiring short genomic sequences (spacers) that target specific sequences in the viral genome. We propose a population dynamical model where immunity can be both acquired and lost. The model predicts regimes where bacterial and phage populations can co-exist, others where the populations oscillate, and still others where one population is driven to extinction. Our model considers two key parameters: (1) ease of acquisition and (2) spacer effectiveness in conferring immunity. Analytical calculations and numerical simulations show that if spacers differ mainly in ease of acquisition, or if the probability of acquiring them is sufficiently high, bacteria develop a diverse population of spacers. On the other hand, if spacers differ mainly in their effectiveness, their final distribution will be highly peaked, akin to a "winner-take-all" scenario, leading to a specialized spacer ...

  13. A model of excitation and adaptation in bacterial chemotaxis.

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    Spiro, P A; Parkinson, J S; Othmer, H G

    1997-07-08

    Bacterial chemotaxis is widely studied because of its accessibility and because it incorporates processes that are important in a number of sensory systems: signal transduction, excitation, adaptation, and a change in behavior, all in response to stimuli. Quantitative data on the change in behavior are available for this system, and the major biochemical steps in the signal transduction/processing pathway have been identified. We have incorporated recent biochemical data into a mathematical model that can reproduce many of the major features of the intracellular response, including the change in the level of chemotactic proteins to step and ramp stimuli such as those used in experimental protocols. The interaction of the chemotactic proteins with the motor is not modeled, but we can estimate the degree of cooperativity needed to produce the observed gain under the assumption that the chemotactic proteins interact directly with the motor proteins.

  14. Optimizing Hybrid Spreading in Metapopulations

    CERN Document Server

    Zhang, Changwang; Cox, Ingemar J; Chain, Benjamin M

    2014-01-01

    Epidemic spreading phenomena are ubiquitous in nature and society. Examples include the spreading of diseases, information, and computer viruses. Epidemics can spread by \\textit{local spreading}, where infected nodes can only infect a limited set of direct target nodes and \\textit{global spreading}, where an infected node can infect every other node. In reality, many epidemics spread using a hybrid mixture of both types of spreading. In this study we develop a theoretical framework for studying hybrid epidemics, and examine the optimum balance between spreading mechanisms in terms of achieving the maximum outbreak size. In a metapopulation, made up of many weakly connected subpopulations, we show that one can calculate an optimal tradeoff between local and global spreading which will maximise the extent of the epidemic. As an example we analyse the 2008 outbreak of the Internet worm Conficker, which uses hybrid spreading to propagate through the internet. Our results suggests that the worm would have been eve...

  15. Portfolio conservation of metapopulations under climate change.

    Science.gov (United States)

    Anderson, Sean C; Moore, Jonathan W; McClure, Michelle M; Dulvy, Nicholas K; Cooper, Andrew B

    2015-03-01

    Climate change is likely to lead to increasing population variability and extinction risk. Theoretically, greater population diversity should buffer against rising climate variability, and this theory is often invoked as a reason for greater conservation. However, this has rarely been quantified. Here we show how a portfolio approach to managing population diversity can inform metapopulation conservation priorities in a changing world. We develop a salmon metapopulation model in which productivity is driven by spatially distributed thermal tolerance and patterns of short- and long-term climate change. We then implement spatial conservation scenarios that control population carrying capacities and evaluate the metapopulation portfolios as a financial manager might: along axes of conservation risk and return. We show that preserving a diversity of thermal tolerances minimizes risk, given environmental stochasticity, and ensures persistence, given long-term environmental change. When the thermal tolerances of populations are unknown, doubling the number of populations conserved may nearly halve expected metapopulation variability. However, this reduction in variability can come at the expense of long-term persistence if climate change increasingly restricts available habitat, forcing ecological managers to balance society's desire for short-term stability and long-term viability. Our findings suggest the importance of conserving the processes that promote thermal-tolerance diversity, such as genetic diversity, habitat heterogeneity, and natural disturbance regimes, and demonstrate that diverse natural portfolios may be critical for metapopulation conservation in the face of increasing climate variability and change.

  16. Diversity Takes Shape: Understanding the Mechanistic and Adaptive Basis of Bacterial Morphology

    Science.gov (United States)

    2016-01-01

    The modern age of metagenomics has delivered unprecedented volumes of data describing the genetic and metabolic diversity of bacterial communities, but it has failed to provide information about coincident cellular morphologies. Much like metabolic and biosynthetic capabilities, morphology comprises a critical component of bacterial fitness, molded by natural selection into the many elaborate shapes observed across the bacterial domain. In this essay, we discuss the diversity of bacterial morphology and its implications for understanding both the mechanistic and the adaptive basis of morphogenesis. We consider how best to leverage genomic data and recent experimental developments in order to advance our understanding of bacterial shape and its functional importance. PMID:27695035

  17. From Environment to Man: Genome Evolution and Adaptation of Human Opportunistic Bacterial Pathogens

    OpenAIRE

    Estelle Jumas-Bilak; Hélène Marchandin; Brigitte Lamy; Anne Lotthé; Fabien Aujoulat; Frédéric Roger; Alice Bourdier

    2012-01-01

    Environment is recognized as a huge reservoir for bacterial species and a source of human pathogens. Some environmental bacteria have an extraordinary range of activities that include promotion of plant growth or disease, breakdown of pollutants, production of original biomolecules, but also multidrug resistance and human pathogenicity. The versatility of bacterial life-style involves adaptation to various niches. Adaptation to both open environment and human specific niches is a major challe...

  18. Seabird metapopulations: searching for alternative breeding habitats

    NARCIS (Netherlands)

    Schippers, P.; Snep, R.P.H.; Schotman, A.G.M.; Jochem, R.; Stienen, E.W.M.; Slim, P.A.

    2009-01-01

    Today, many seabird species nest in port areas, which are also necessary for human economic activity. In this paper, we evaluate, using a metapopulation model, the possibilities for creating alternative breeding sites for the Common Tern (Sterna hirundo) in the Rhine¿Meuse¿Scheldt estuary. We explor

  19. New insights into bacterial adaptation through in vivo and in silico experimental evolution.

    Science.gov (United States)

    Hindré, Thomas; Knibbe, Carole; Beslon, Guillaume; Schneider, Dominique

    2012-03-27

    Microbiology research has recently undergone major developments that have led to great progress towards obtaining an integrated view of microbial cell function. Microbial genetics, high-throughput technologies and systems biology have all provided an improved understanding of the structure and function of bacterial genomes and cellular networks. However, integrated evolutionary perspectives are needed to relate the dynamics of adaptive changes to the phenotypic and genotypic landscapes of living organisms. Here, we review evolution experiments, carried out both in vivo with microorganisms and in silico with artificial organisms, that have provided insights into bacterial adaptation and emphasize the potential of bacterial regulatory networks to evolve.

  20. Bacterial adaptation through distributed sensing of metabolic fluxes

    NARCIS (Netherlands)

    Kotte, Oliver; Zaugg, Judith B.; Heinemann, Matthias

    2010-01-01

    The recognition of carbon sources and the regulatory adjustments to recognized changes are of particular importance for bacterial survival in fluctuating environments. Despite a thorough knowledge base of Escherichia coli’s central metabolism and its regulation, fundamental aspects of the employed s

  1. Empirical determinants of measles metapopulation dynamics in England and Wales.

    OpenAIRE

    Finkenstädt, B; Grenfell, B.

    1998-01-01

    A key issue in metapopulation dynamics is the relative impact of internal patch dynamics and coupling between patches. This problem can be addressed by analysing large spatiotemporal data sets, recording the local and global dynamics of metapopulations. In this paper, we analyse the dynamics of measles meta-populations in a large spatiotemporal case notification data set, collected during the pre-vaccination era in England and Wales. Specifically, we use generalized linear statistical models ...

  2. Seasonal variance in P system models for metapopulations

    Institute of Scientific and Technical Information of China (English)

    Daniela Besozzi; Paolo Cazzaniga; Dario Pescini; Giancarlo Mauri

    2007-01-01

    Metapopulations are ecological models describing the interactions and the behavior of populations living in fragmented habitats. In this paper, metapopulations are modelled by means of dynamical probabilistic P systems, where additional structural features have been defined (e. g., a weighted graph associated with the membrane structure and the reduction of maximal parallelism). In particular, we investigate the influence of stochastic and periodic resource feeding processes, owing to seasonal variance, on emergent metapopulation dynamics.

  3. Adaptive capacity to bacterial diet modulates aging in C. elegans.

    Science.gov (United States)

    Pang, Shanshan; Curran, Sean P

    2014-02-04

    Diet has a substantial impact on cellular metabolism and physiology. Animals must sense different food sources and utilize distinct strategies to adapt to diverse diets. Here we show that Caenorhabditis elegans lifespan is regulated by their adaptive capacity to different diets, which is controlled by alh-6, a conserved proline metabolism gene. alh-6 mutants age prematurely when fed an Escherichia coli OP50 but not HT115 diet. Remarkably, this diet-dependent aging phenotype is determined by exposure to food during development. Mechanistically, the alh-6 mutation triggers diet-induced mitochondrial defects and increased generation of ROS, likely due to accumulation of its substrate 1-pyrroline-5-carboxylate. We also identify that neuromedin U receptor signaling is essential for diet-induced mitochondrial changes and premature aging. Moreover, dietary restriction requires alh-6 to induce longevity. Collectively, our data reveal a homeostatic mechanism that animals employ to cope with potential dietary insults and uncover an example of lifespan regulation by dietary adaptation.

  4. Antimicrobial effect against different bacterial strains and bacterial adaptation to essential oils used as feed additives

    OpenAIRE

    Melo, Antonio Diego Brandão; Amaral, Amanda Figueiredo; Schaefer, Gustavo; Luciano, Fernando Bittencourt; Andrade,Carla de; Costa, Leandro Batista; Rostagno, Marcos Horácio

    2015-01-01

    The aim of this study was to evaluate the antimicrobial activity and determine the minimum bactericidal concentration (MBC) of the essential oils derived from Origanum vulgare (oregano), Melaleuca alternifolia (tea tree), Cinnamomum cassia (cassia), and Thymus vulgaris (white thyme) against Salmonella Typhimurium, Salmonella Enteritidis, Escherichia coli, Staphylococcus aureus and Enterococcus faecalis. The study also investigated the ability of these different bacterial strains to develop ad...

  5. Dependence of bacterial chemotaxis on gradient shape and adaptation rate.

    Directory of Open Access Journals (Sweden)

    Nikita Vladimirov

    2008-12-01

    Full Text Available Simulation of cellular behavior on multiple scales requires models that are sufficiently detailed to capture central intracellular processes but at the same time enable the simulation of entire cell populations in a computationally cheap way. In this paper we present RapidCell, a hybrid model of chemotactic Escherichia coli that combines the Monod-Wyman-Changeux signal processing by mixed chemoreceptor clusters, the adaptation dynamics described by ordinary differential equations, and a detailed model of cell tumbling. Our model dramatically reduces computational costs and allows the highly efficient simulation of E. coli chemotaxis. We use the model to investigate chemotaxis in different gradients, and suggest a new, constant-activity type of gradient to systematically study chemotactic behavior of virtual bacteria. Using the unique properties of this gradient, we show that optimal chemotaxis is observed in a narrow range of CheA kinase activity, where concentration of the response regulator CheY-P falls into the operating range of flagellar motors. Our simulations also confirm that the CheB phosphorylation feedback improves chemotactic efficiency by shifting the average CheY-P concentration to fit the motor operating range. Our results suggest that in liquid media the variability in adaptation times among cells may be evolutionary favorable to ensure coexistence of subpopulations that will be optimally tactic in different gradients. However, in a porous medium (agar such variability appears to be less important, because agar structure poses mainly negative selection against subpopulations with low levels of adaptation enzymes. RapidCell is available from the authors upon request.

  6. Evolutionary remodeling of global regulatory networks during long-term bacterial adaptation to human hosts

    DEFF Research Database (Denmark)

    Pedersen, Søren Damkiær; Yang, Lei; Molin, Søren

    2013-01-01

    The genetic basis of bacterial adaptation to a natural environment has been investigated in a highly successful Pseudomonas aeruginosa lineage (DK2) that evolved within the airways of patients with cystic fibrosis (CF) for more than 35 y. During evolution in the CF airways, the DK2 lineage underw...

  7. Variability in primary productivity determines metapopulation dynamics.

    Science.gov (United States)

    Fernández, Néstor; Román, Jacinto; Delibes, Miguel

    2016-04-13

    Temporal variability in primary productivity can change habitat quality for consumer species by affecting the energy levels available as food resources. However, it remains unclear how habitat-quality fluctuations may determine the dynamics of spatially structured populations, where the effects of habitat size, quality and isolation have been customarily assessed assuming static habitats. We present the first empirical evaluation on the effects of stochastic fluctuations in primary productivity--a major outcome of ecosystem functions--on the metapopulation dynamics of a primary consumer. A unique 13-year dataset from an herbivore rodent was used to test the hypothesis that inter-annual variations in primary productivity determine spatiotemporal habitat occupancy patterns and colonization and extinction processes. Inter-annual variability in productivity and in the growing season phenology significantly influenced habitat colonization patterns and occupancy dynamics. These effects lead to changes in connectivity to other potentially occupied habitat patches, which then feed back into occupancy dynamics. According to the results, the dynamics of primary productivity accounted for more than 50% of the variation in occupancy probability, depending on patch size and landscape configuration. Evidence connecting primary productivity dynamics and spatiotemporal population processes has broad implications for metapopulation persistence in fluctuating and changing environments.

  8. Spatial and spatiotemporal variation in metapopulation structure affects population dynamics in a passively dispersing arthropod.

    Science.gov (United States)

    De Roissart, Annelies; Wang, Shaopeng; Bonte, Dries

    2015-11-01

    The spatial and temporal variation in the availability of suitable habitat within metapopulations determines colonization-extinction events, regulates local population sizes and eventually affects local population and metapopulation stability. Insights into the impact of such a spatiotemporal variation on the local population and metapopulation dynamics are principally derived from classical metapopulation theory and have not been experimentally validated. By manipulating spatial structure in artificial metapopulations of the spider mite Tetranychus urticae, we test to which degree spatial (mainland-island metapopulations) and spatiotemporal variation (classical metapopulations) in habitat availability affects the dynamics of the metapopulations relative to systems where habitat is constantly available in time and space (patchy metapopulations). Our experiment demonstrates that (i) spatial variation in habitat availability decreases variance in metapopulation size and decreases density-dependent dispersal at the metapopulation level, while (ii) spatiotemporal variation in habitat availability increases patch extinction rates, decreases local population and metapopulation sizes and decreases density dependence in population growth rates. We found dispersal to be negatively density dependent and overall low in the spatial variable mainland-island metapopulation. This demographic variation subsequently impacts local and regional population dynamics and determines patterns of metapopulation stability. Both local and metapopulation-level variabilities are minimized in mainland-island metapopulations relative to classical and patchy ones.

  9. From Environment to Man: Genome Evolution and Adaptation of Human Opportunistic Bacterial Pathogens

    Science.gov (United States)

    Aujoulat, Fabien; Roger, Frédéric; Bourdier, Alice; Lotthé, Anne; Lamy, Brigitte; Marchandin, Hélène; Jumas-Bilak, Estelle

    2012-01-01

    Environment is recognized as a huge reservoir for bacterial species and a source of human pathogens. Some environmental bacteria have an extraordinary range of activities that include promotion of plant growth or disease, breakdown of pollutants, production of original biomolecules, but also multidrug resistance and human pathogenicity. The versatility of bacterial life-style involves adaptation to various niches. Adaptation to both open environment and human specific niches is a major challenge that involves intermediate organisms allowing pre-adaptation to humans. The aim of this review is to analyze genomic features of environmental bacteria in order to explain their adaptation to human beings. The genera Pseudomonas, Aeromonas and Ochrobactrum provide valuable examples of opportunistic behavior associated to particular genomic structure and evolution. Particularly, we performed original genomic comparisons among aeromonads and between the strictly intracellular pathogens Brucella spp. and the mild opportunistic pathogens Ochrobactrum spp. We conclude that the adaptation to human could coincide with a speciation in action revealed by modifications in both genomic and population structures. This adaptation-driven speciation could be a major mechanism for the emergence of true pathogens besides the acquisition of specialized virulence factors. PMID:24704914

  10. Transcriptome-Level Signatures in Gene Expression and Gene Expression Variability during Bacterial Adaptive Evolution

    Science.gov (United States)

    Erickson, Keesha E.; Otoupal, Peter B.

    2017-01-01

    ABSTRACT Antibiotic-resistant bacteria are an increasingly serious public health concern, as strains emerge that demonstrate resistance to almost all available treatments. One factor that contributes to the crisis is the adaptive ability of bacteria, which exhibit remarkable phenotypic and gene expression heterogeneity in order to gain a survival advantage in damaging environments. This high degree of variability in gene expression across biological populations makes it a challenging task to identify key regulators of bacterial adaptation. Here, we research the regulation of adaptive resistance by investigating transcriptome profiles of Escherichia coli upon adaptation to disparate toxins, including antibiotics and biofuels. We locate potential target genes via conventional gene expression analysis as well as using a new analysis technique examining differential gene expression variability. By investigating trends across the diverse adaptation conditions, we identify a focused set of genes with conserved behavior, including those involved in cell motility, metabolism, membrane structure, and transport, and several genes of unknown function. To validate the biological relevance of the observed changes, we synthetically perturb gene expression using clustered regularly interspaced short palindromic repeat (CRISPR)-dCas9. Manipulation of select genes in combination with antibiotic treatment promotes adaptive resistance as demonstrated by an increased degree of antibiotic tolerance and heterogeneity in MICs. We study the mechanisms by which identified genes influence adaptation and find that select differentially variable genes have the potential to impact metabolic rates, mutation rates, and motility. Overall, this work provides evidence for a complex nongenetic response, encompassing shifts in gene expression and gene expression variability, which underlies adaptive resistance. IMPORTANCE Even initially sensitive bacteria can rapidly thwart antibiotic treatment

  11. Temperature adaptation of soil bacterial communities along an Antarctic climate gradient: predicting responses to climate warming

    DEFF Research Database (Denmark)

    Rinnan, Riikka; Rousk, Johannes; Yergeau, Etienne;

    2009-01-01

    the leucine incorporation technique, in order to predict future changes in temperature sensitivity of resident soil bacterial communities. Soil samples were collected along a climate gradient consisting of locations on the Antarctic Peninsula (Anchorage Island, 67 °34'S, 68 °08'W), Signy Island (60 °43'S, 45......Soil microorganisms, the central drivers of terrestrial Antarctic ecosystems, are being confronted with increasing temperatures as parts of the continent experience considerable warming. Here we determined short-term temperature dependencies of Antarctic soil bacterial community growth rates, using...... °38'W) and the Falkland Islands (51 °76'S 59 °03'W). At each location, experimental plots were subjected to warming by open top chambers (OTCs) and paired with control plots on vegetated and fell-field habitats. The bacterial communities were adapted to the mean annual temperature of their environment...

  12. Modeling vaccination in a heterogeneous metapopulation system

    Science.gov (United States)

    Lachiany, Menachem

    2016-09-01

    We present here a multicity SIS epidemic model with vaccination. The model describes the dynamics of heterogeneous metapopulations that contain imperfectly vaccinated individuals. The effect of vaccination on heterogeneous multicity models has not been previously studied. We show that under very generic conditions, the epidemic threshold does not depend on the diffusion coefficient of the vaccinated individuals, but it does depend on the diffusion coefficient of the infected population. We then show, using a novel methodology, that the reproduction number is determined by the homogeneous model parameters and by the maximal number of neighbors a city can have, when the diffusion coefficient of the infected population is low. Finally, we present numerical simulations to support the analytical results.

  13. Plague metapopulation dynamics in a natural reservoir

    DEFF Research Database (Denmark)

    Davis, S; Klassovskiy, N; Ageyev, V

    2007-01-01

    The ecology of plague (Yersinia pestis infection) in its ancient foci in Central Asia remains poorly understood. We present field data from two sites in Kazakhstan where the great gerbil (Rhombomys opimus) is the major natural host. Family groups inhabit and defend burrow systems spaced throughout...... the landscape, such that the host population may be considered a metapopulation, with each occupied burrow system a subpopulation. We examine plague transmission within and between family groups and its effect on survival. Transmission of plague occurred disproportionately within family groups although not all...... gerbils became infected once plague entered a burrow system. There were no spatial patterns to suggest that family groups in close proximity to infected burrow systems were more at risk of infection than those far away. At one site, infection increased the chances of burrow-system extinction. Overall...

  14. TIR Domain-Containing Adapter-Inducing Beta Interferon (TRIF) Mediates Immunological Memory against Bacterial Pathogens.

    Science.gov (United States)

    Kanagavelu, Saravana; Flores, Claudia; Termini, J M; Romero, Laura; Riveron, Reldy; Ruiz, Jose; Arditi, Moshe; Schesser, Kurt; Fukata, Masayuki

    2015-11-01

    Induction of adaptive immunity leads to the establishment of immunological memory; however, how innate immunity regulates memory T cell function remains obscure. Here we show a previously undefined mechanism in which innate and adaptive immunity are linked by TIR domain-containing adapter-inducing beta interferon (TRIF) during establishment and reactivation of memory T cells against Gram-negative enteropathogens. Absence of TRIF in macrophages (Mϕs) but not dendritic cells led to a predominant generation of CD4(+) central memory T cells that express IL-17 during enteric bacterial infection in mice. TRIF-dependent type I interferon (IFN) signaling in T cells was essential to Th1 lineage differentiation and reactivation of memory T cells. TRIF activated memory T cells to facilitate local neutrophil influx and enhance bacterial elimination. These results highlight the importance of TRIF as a mediator of the innate and adaptive immune interactions in achieving the protective properties of memory immunity against Gram-negative bacteria and suggest TRIF as a potential therapeutic target.

  15. Bacterial diversity and their adaptations in the shallow water hydrothermal vent at D. Joao de Castro Seamount (DJCS), Azores, Portugal

    Digital Repository Service at National Institute of Oceanography (India)

    Mohandass, C.; Rajasabapathy, R.; Ravindran, C.; Colaco, A.; Santos, R.S.; Meena, R.M.

    Bacterial diversity investigations were made from the shallow vent of D joao de castro, Azores, Portugal and their adaptations to a nutrient rich environment was investigated from 2004 and 2005 cruise samples. Assesment of the qualitative...

  16. Comparing large-scale computational approaches to epidemic modeling: Agent-based versus structured metapopulation models

    Directory of Open Access Journals (Sweden)

    Merler Stefano

    2010-06-01

    Full Text Available Abstract Background In recent years large-scale computational models for the realistic simulation of epidemic outbreaks have been used with increased frequency. Methodologies adapt to the scale of interest and range from very detailed agent-based models to spatially-structured metapopulation models. One major issue thus concerns to what extent the geotemporal spreading pattern found by different modeling approaches may differ and depend on the different approximations and assumptions used. Methods We provide for the first time a side-by-side comparison of the results obtained with a stochastic agent-based model and a structured metapopulation stochastic model for the progression of a baseline pandemic event in Italy, a large and geographically heterogeneous European country. The agent-based model is based on the explicit representation of the Italian population through highly detailed data on the socio-demographic structure. The metapopulation simulations use the GLobal Epidemic and Mobility (GLEaM model, based on high-resolution census data worldwide, and integrating airline travel flow data with short-range human mobility patterns at the global scale. The model also considers age structure data for Italy. GLEaM and the agent-based models are synchronized in their initial conditions by using the same disease parameterization, and by defining the same importation of infected cases from international travels. Results The results obtained show that both models provide epidemic patterns that are in very good agreement at the granularity levels accessible by both approaches, with differences in peak timing on the order of a few days. The relative difference of the epidemic size depends on the basic reproductive ratio, R0, and on the fact that the metapopulation model consistently yields a larger incidence than the agent-based model, as expected due to the differences in the structure in the intra-population contact pattern of the approaches. The age

  17. Community dynamics and glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass

    Energy Technology Data Exchange (ETDEWEB)

    Gladden, J.M.; Allgaier, M.; Miller, C.S.; Hazen, T.C.; VanderGheynst, J.S.; Hugenholtz, P.; Simmons, B.A.; Singer, S.W.

    2011-05-01

    Industrial-scale biofuel production requires robust enzymatic cocktails to produce fermentable sugars from lignocellulosic biomass. Thermophilic bacterial consortia are a potential source of cellulases and hemicellulases adapted to harsher reaction conditions than commercial fungal enzymes. Compost-derived microbial consortia were adapted to switchgrass at 60 C to develop thermophilic biomass-degrading consortia for detailed studies. Microbial community analysis using small-subunit rRNA gene amplicon pyrosequencing and short-read metagenomic sequencing demonstrated that thermophilic adaptation to switchgrass resulted in low-diversity bacterial consortia with a high abundance of bacteria related to thermophilic paenibacilli, Rhodothermus marinus, and Thermus thermophilus. At lower abundance, thermophilic Chloroflexi and an uncultivated lineage of the Gemmatimonadetes phylum were observed. Supernatants isolated from these consortia had high levels of xylanase and endoglucanase activities. Compared to commercial enzyme preparations, the endoglucanase enzymes had a higher thermotolerance and were more stable in the presence of 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), an ionic liquid used for biomass pretreatment. The supernatants were used to saccharify [C2mim][OAc]-pretreated switchgrass at elevated temperatures (up to 80 C), demonstrating that these consortia are an excellent source of enzymes for the development of enzymatic cocktails tailored to more extreme reaction conditions.

  18. Comparison of reintroduction and enhancement effects on metapopulation viability

    Science.gov (United States)

    Halsey, Samniqueka J; Bell, Timothy J.; McEachern, Kathryn; Pavlovic, Noel B.

    2015-01-01

    Metapopulation viability depends upon a balance of extinction and colonization of local habitats by a species. Mechanisms that can affect this balance include physical characteristics related to natural processes (e.g. succession) as well as anthropogenic actions. Plant restorations can help to produce favorable metapopulation dynamics and consequently increase viability; however, to date no studies confirm this is true. Population viability analysis (PVA) allows for the use of empirical data to generate theoretical future projections in the form of median time to extinction and probability of extinction. In turn, PVAs can inform and aid the development of conservation, recovery, and management plans. Pitcher's thistle (Cirsium pitcheri) is a dune endemic that exhibited metapopulation dynamics. We projected viability of three natural and two restored populations with demographic data spanning 15–23 years to determine the degree the addition of reintroduced population affects metapopulation viability. The models were validated by comparing observed and projected abundances and adjusting parameters associated with demographic and environmental stochasticity to improve model performance. Our chosen model correctly predicted yearly population abundance for 60% of the population-years. Using that model, 50-year projections showed that the addition of reintroductions increases metapopulation viability. The reintroduction that simulated population performance in early-successional habitats had the maximum benefit. In situ enhancements of existing populations proved to be equally effective. This study shows that restorations can facilitate and improve metapopulation viability of species dependent on metapopulation dynamics for survival with long-term persistence of C. pitcheri in Indiana likely to depend on continued active management.

  19. Investigating the adaptive immune response in influenza and secondary bacterial pneumonia and nanoparticle based therapeutic delivery

    Science.gov (United States)

    Chakravarthy, Krishnan V.

    In early 2000, influenza and its associated complications were the 7 th leading cause of death in the United States[1-4]. As of today, this major health problem has become even more of a concern, with the possibility of a potentially devastating avian flu (H5N1) or swine flu pandemic (H1N1). According to the Centers for Disease Control (CDC), over 10 countries have reported transmission of influenza A (H5N1) virus to humans as of June 2006 [5]. In response to this growing concern, the United States pledged over $334 million dollars in international aid for battling influenza[1-4]. The major flu pandemic of the early 1900's provided the first evidence that secondary bacterial pneumonia (not primary viral pneumonia) was the major cause of death in both community and hospital-based settings. Secondary bacterial infections currently account for 35-40% mortality following a primary influenza viral infection [1, 6]. The first component of this work addresses the immunological mechanisms that predispose patients to secondary bacterial infections following a primary influenza viral infection. By assessing host immune responses through various immune-modulatory tools, such as use of volatile anesthetics (i.e. halothane) and Apilimod/STA-5326 (an IL-12/Il-23 transcription blocker), we provide experimental evidence that demonstrates that the overactive adaptive Th1 immune response is critical in mediating increased susceptibility to secondary bacterial infections. We also present data that shows that suppressing the adaptive Th1 immune response enhances innate immunity, specifically in alveolar macrophages, by favoring a pro anti-bacterial phenotype. The second component of this work addresses the use of nanotechnology to deliver therapeutic modalities that affect the primary viral and associated secondary bacterial infections post influenza. First, we used surface functionalized quantum dots for selective targeting of lung alveolar macrophages both in vitro and in vivo

  20. Synchrony in Metapopulations with Sporadic Dispersal

    Science.gov (United States)

    Jeter, Russell; Belykh, Igor

    2015-06-01

    We study synchronization in ecological networks under the realistic assumption that the coupling among the patches is sporadic/stochastic and due to rare and short-term meteorological conditions. Each patch is described by a tritrophic food chain model, representing the producer, consumer, and predator. If all three species can migrate, we rigorously prove that the network can synchronize as long as the migration occurs frequently, i.e. fast compared to the period of the ecological cycle, even though the network is disconnected most of the time. In the case where only the top trophic level (i.e. the predator) can migrate, we reveal an unexpected range of intermediate switching frequencies where synchronization becomes stable in a network which switches between two nonsynchronous dynamics. As spatial synchrony increases the danger of extinction, this counterintuitive effect of synchrony emerging from slower switching dispersal can be destructive for overall metapopulation persistence, presumably expected from switching between two dynamics which are unfavorable to extinction.

  1. Are grazer-induced adaptations of bacterial abundance and morphology timedependent?

    Directory of Open Access Journals (Sweden)

    Gianluca CORNO

    2006-02-01

    predators belong to two voracious species: Spumella sp. and Ochromonas sp., strictly heterotrophic and mixotrophic, respectively. For all the treatments, it was impossible to find any clear evidence of a morphological adaptation stimulated by the mere presence of flagellates. On the other hand, for all bacterial strains the enrichment of the media due to the release of exudates, resulted in higher growth rates and higher abundances, confirming that grazers are fundamental actors involved in the inner recycling of the microbial loop.

  2. How Levins’ dynamics emerges from a Ricker metapopulation model

    KAUST Repository

    Elías-Wolff, F.

    2015-09-24

    Understanding the dynamics of metapopulations close to extinction is of vital importance for management. Levins-like models, in which local patches are treated as either occupied or empty, have been used extensively to explore the extinction dynamics of metapopulations, but they ignore the important role of local population dynamics. In this paper, we consider a stochastic metapopulation model where local populations follow a stochastic, density-dependent dynamics (the Ricker model), and use this framework to investigate the behaviour of the metapopulation on the brink of extinction. We determine under which circumstances the metapopulation follows a time evolution consistent with Levins’ dynamics. We derive analytical expressions for the colonisation and extinction rates (c and e) in Levins-type models in terms of reproduction, survival and dispersal parameters of the local populations, providing an avenue to parameterising Levins-like models from the type of information on local demography that is available for a number of species. To facilitate applying our results, we provide a numerical algorithm for computing c and e.

  3. ALTERNATIVE FOR PHENOL BIODEGRADATION IN OIL CONTAMINATED WASTEWATERS USING AN ADAPTED BACTERIAL BIOFILM LAYER

    Directory of Open Access Journals (Sweden)

    Maria Kopytko

    2008-12-01

    Full Text Available The project studied the biodegradation potential of phenols in an industrial wastewater from an oil field in the province of Santander, Colombia. An elevated potential was established, according to three important factors: the great abundance of microorganisms found in the wastewater and sludge samples collected, the bacterial adaptation to high phenol concentrations (10 mg/l and the elevated elimination efficiencies (up to 86% obtained in the laboratory tests. The laboratory scale treatment system, which consisted of fixed-bed bioreactors with adapted bacterial biofilm, was optimized using a 22 factorial experimental design. The selected variables, studied in their maximum and minimum level were: HRT (hydraulic retention time and the presence or absence of GAC (granular activated carbon layer. The response variable was phenol concentration. The optimum treatment conditions for low and high phenol concentrations (2.14 y 9.30 mg/l, were obtained with the presence of GAC and 18 hours of HRT. The best result for the intermediate phenol concentration (6.13 mg/l was obtained with a 24 hour HRT and the presence of GAC. Nevertheless, the presence of the GAC layer was not significantly important in terms of phenol removal. Moreover, the increase of HRT from 18 to 24 hours, showed no significant improvement in phenol removal.

  4. On optimal choices in increase of patch area and reduction of interpatch distance for metapopulation persistence

    NARCIS (Netherlands)

    Etienne, RS

    2004-01-01

    Metapopulation theory teaches that the viability of metapopulations may be enlarged by decreasing the probability of extinction of local populations, or by increasing the colonization probability of empty habitat patches. In a metapopulation model study it has recently been found that reducing the e

  5. CRISPR-Cas: From the Bacterial Adaptive Immune System to a Versatile Tool for Genome Engineering.

    Science.gov (United States)

    Kirchner, Marion; Schneider, Sabine

    2015-11-01

    The field of biology has been revolutionized by the recent advancement of an adaptive bacterial immune system as a universal genome engineering tool. Bacteria and archaea use repetitive genomic elements termed clustered regularly interspaced short palindromic repeats (CRISPR) in combination with an RNA-guided nuclease (CRISPR-associated nuclease: Cas) to target and destroy invading DNA. By choosing the appropriate sequence of the guide RNA, this two-component system can be used to efficiently modify, target, and edit genomic loci of interest in plants, insects, fungi, mammalian cells, and whole organisms. This has opened up new frontiers in genome engineering, including the potential to treat or cure human genetic disorders. Now the potential risks as well as the ethical, social, and legal implications of this powerful new technique move into the limelight.

  6. Detection of Bundle Branch Block using Adaptive Bacterial Foraging Optimization and Neural Network

    Directory of Open Access Journals (Sweden)

    Padmavthi Kora

    2017-03-01

    Full Text Available The medical practitioners analyze the electrical activity of the human heart so as to predict various ailments by studying the data collected from the Electrocardiogram (ECG. A Bundle Branch Block (BBB is a type of heart disease which occurs when there is an obstruction along the pathway of an electrical impulse. This abnormality makes the heart beat irregular as there is an obstruction in the branches of heart, this results in pulses to travel slower than the usual. Our current study involved is to diagnose this heart problem using Adaptive Bacterial Foraging Optimization (ABFO Algorithm. The Data collected from MIT/BIH arrhythmia BBB database applied to an ABFO Algorithm for obtaining best(important feature from each ECG beat. These features later fed to Levenberg Marquardt Neural Network (LMNN based classifier. The results show the proposed classification using ABFO is better than some recent algorithms reported in the literature.

  7. Abiotic and biotic interactions determine whether increased colonization is beneficial or detrimental to metapopulation management.

    Science.gov (United States)

    Southwell, Darren M; Rhodes, Jonathan R; McDonald-Madden, Eve; Nicol, Sam; Helmstedt, Kate J; McCarthy, Michael A

    2016-06-01

    Increasing the colonization rate of metapopulations can improve persistence, but can also increase exposure to threats. To make good decisions, managers must understand whether increased colonization is beneficial or detrimental to metapopulation persistence. While a number of studies have examined interactions between metapopulations, colonization, and threats, they have assumed that threat dynamics respond linearly to changes in colonization. Here, we determined when to increase colonization while explicitly accounting for non-linear dependencies between a metapopulation and its threats. We developed patch occupancy metapopulation models for species susceptible to abiotic, generalist, and specialist threats and modeled the total derivative of the equilibrium proportion of patches occupied by each metapopulation with respect to the colonization rate. By using the total derivative, we developed a rule for determining when to increase metapopulation colonization. This rule was applied to a simulated metapopulation where the dynamics of each threat responded to increased colonization following a power function. Before modifying colonization, we show that managers must understand: (1) whether a metapopulation is susceptible to a threat; (2) the type of threat acting on a metapopulation; (3) which component of threat dynamics might depend on colonization, and; (4) the likely response of a threat-dependent variable to changes in colonization. The sensitivity of management decisions to these interactions increases uncertainty in conservation planning decisions.

  8. Adaptive Remodeling of the Bacterial Proteome by Specific Ribosomal Modification Regulates Pseudomonas Infection and Niche Colonisation.

    Science.gov (United States)

    Little, Richard H; Grenga, Lucia; Saalbach, Gerhard; Howat, Alexandra M; Pfeilmeier, Sebastian; Trampari, Eleftheria; Malone, Jacob G

    2016-02-01

    Post-transcriptional control of protein abundance is a highly important, underexplored regulatory process by which organisms respond to their environments. Here we describe an important and previously unidentified regulatory pathway involving the ribosomal modification protein RimK, its regulator proteins RimA and RimB, and the widespread bacterial second messenger cyclic-di-GMP (cdG). Disruption of rimK affects motility and surface attachment in pathogenic and commensal Pseudomonas species, with rimK deletion significantly compromising rhizosphere colonisation by the commensal soil bacterium P. fluorescens, and plant infection by the pathogens P. syringae and P. aeruginosa. RimK functions as an ATP-dependent glutamyl ligase, adding glutamate residues to the C-terminus of ribosomal protein RpsF and inducing specific effects on both ribosome protein complement and function. Deletion of rimK in P. fluorescens leads to markedly reduced levels of multiple ribosomal proteins, and also of the key translational regulator Hfq. In turn, reduced Hfq levels induce specific downstream proteomic changes, with significant increases in multiple ABC transporters, stress response proteins and non-ribosomal peptide synthetases seen for both ΔrimK and Δhfq mutants. The activity of RimK is itself controlled by interactions with RimA, RimB and cdG. We propose that control of RimK activity represents a novel regulatory mechanism that dynamically influences interactions between bacteria and their hosts; translating environmental pressures into dynamic ribosomal changes, and consequently to an adaptive remodeling of the bacterial proteome.

  9. Adaptive Remodeling of the Bacterial Proteome by Specific Ribosomal Modification Regulates Pseudomonas Infection and Niche Colonisation.

    Directory of Open Access Journals (Sweden)

    Richard H Little

    2016-02-01

    Full Text Available Post-transcriptional control of protein abundance is a highly important, underexplored regulatory process by which organisms respond to their environments. Here we describe an important and previously unidentified regulatory pathway involving the ribosomal modification protein RimK, its regulator proteins RimA and RimB, and the widespread bacterial second messenger cyclic-di-GMP (cdG. Disruption of rimK affects motility and surface attachment in pathogenic and commensal Pseudomonas species, with rimK deletion significantly compromising rhizosphere colonisation by the commensal soil bacterium P. fluorescens, and plant infection by the pathogens P. syringae and P. aeruginosa. RimK functions as an ATP-dependent glutamyl ligase, adding glutamate residues to the C-terminus of ribosomal protein RpsF and inducing specific effects on both ribosome protein complement and function. Deletion of rimK in P. fluorescens leads to markedly reduced levels of multiple ribosomal proteins, and also of the key translational regulator Hfq. In turn, reduced Hfq levels induce specific downstream proteomic changes, with significant increases in multiple ABC transporters, stress response proteins and non-ribosomal peptide synthetases seen for both ΔrimK and Δhfq mutants. The activity of RimK is itself controlled by interactions with RimA, RimB and cdG. We propose that control of RimK activity represents a novel regulatory mechanism that dynamically influences interactions between bacteria and their hosts; translating environmental pressures into dynamic ribosomal changes, and consequently to an adaptive remodeling of the bacterial proteome.

  10. Metapopulation epidemic models with heterogeneous mixing and travel behaviour

    CERN Document Server

    Apolloni, Andrea; Ramasco, Jose' J; Jensen, Pablo; Colizza, Vittoria

    2014-01-01

    The complex interplay between population movements in space and non-homogeneous mixing patterns have so far hindered the fundamental understanding of the conditions for spatial invasion through a general theoretical framework. To address this issue, we present an analytical modelling approach taking into account such interplay under general conditions of mobility and interactions, in the simplifying assumption of two population classes. We describe a spatially structured population with non-homogeneous mixing and travel behaviour through a multi-host stochastic epidemic metapopulation model. Different population partitions, mixing patterns and mobility structures are considered, along with a specific application for the study of the role of age partition in the early spread of the 2009 H1N1 pandemic influenza. We provide a complete mathematical formulation of the model and derive a semi-analytical expression of the threshold condition for global invasion of an emerging infectious disease in the metapopulation...

  11. Emergence of metapopulations and echo chambers in mobile agents

    CERN Document Server

    Starnini, Michele; Baronchelli, Andrea

    2016-01-01

    Multi-agent models often describe populations segregated either in the physical space, i.e. subdivided in metapopulations, or in the ecology of opinions, i.e. partitioned in echo chambers. Here we show how the interplay between homophily and social influence controls the emergence of both kinds of segregation in a simple model of mobile agents, endowed with a continuous opinion variable. In the model, physical proximity determines a progressive convergence of opinions but differing opinions result in agents moving away from each others. This feedback between mobility and social dynamics determines to the onset of a stable dynamical metapopulation scenario where physically separated groups of like-minded individuals interact with each other through the exchange of agents. The further introduction of confirmation bias in social interactions, defined as the tendency of an individual to favor opinions that match his own, leads to the emergence of echo chambers where different opinions can coexist also within the ...

  12. Contagion dynamics in time-varying metapopulation networks

    CERN Document Server

    Liu, Suyu; Perra, Nicola

    2012-01-01

    The metapopulation framework is adopted in a wide array of disciplines to describe systems of well separated yet connected subpopulations. The subgroups/patches are often represented as nodes in a network whose links represent the migration routes among them. The connections are usually considered as static, an approximation that is appropriate for the description of many systems, such as cities connected by human mobility, but it is obviously inadequate in those real systems where links evolve in time on a faster timescale. In the case of farmed animals, for example, the connections between each farm/node vary in time according to the different stages of production. Here we address this case by investigating simple contagion processes on temporal metapopulation networks. We focus on the SIR process, and we determine the mobility threshold for the onset of an epidemic spreading in the framework of activity-driven network models. Remarkably, we find profound differences from the case of static networks, determ...

  13. Analysis of the spread of tuberculosis in heterogeneous complex metapopulations

    CERN Document Server

    Tsanou, Berge; Tewa, Jean Jules

    2011-01-01

    his paper describes and analyzes the spatial spread of tuberculosis (TB) on complex metapopulation, that is, networks of populations connected by migratory flows whose configurations are described in terms of connectivity distribution of nodes (patches) and the conditional probabilities of connections among classes of nodes sharing the same degree. The migration and transmission processes occur simultaneously. For uncorrelated networks under the assumption of standard incidence transmission, we compute the disease-free equilibrium and the basic reproduction number, and show that the disease-free equilibrium is locally asymptotically stable. Moreover, for uncorrelated networks and under assumption of simple mass action transmission, we give a necessary and sufficient conditions for the instability of the disease-free equilibrium. The existence of endemic equilibria is also discussed. Finally, the prevalence of the TB infection across the metapopulation as a function of the path connectivity is studied using nu...

  14. Connectivity dominates larval replenishment in a coastal reef fish metapopulation.

    Science.gov (United States)

    Saenz-Agudelo, Pablo; Jones, Geoffrey P; Thorrold, Simon R; Planes, Serge

    2011-10-07

    Direct estimates of larval retention and connectivity are essential to understand the structure and dynamics of marine metapopulations, and optimize the size and spacing of reserves within networks of marine-protected areas (MPAs). For coral reef fishes, while there are some empirical estimates of self-recruitment at isolated populations, exchange among sub-populations has been rarely quantified. Here, we used microsatellite DNA markers and a likelihood-based parentage analysis to assess the relative magnitude of self-recruitment and exchange among eight geographically distinct sub-populations of the panda clownfish Amphiprion polymnus along 30 km of coastline near Port Moresby, Papua New Guinea. In addition, we used an assignment/exclusion test to identify immigrants arriving from genetically distinct sources. Overall, 82 per cent of the juveniles were immigrants while 18 per cent were progeny of parents genotyped in our focal metapopulation. Of the immigrants, only 6 per cent were likely to be genetically distinct from the focal metapopulation, suggesting most of the connectivity is among sub-populations from a rather homogeneous genetic pool. Of the 18 per cent that were progeny of known adults, two-thirds dispersed among the eight sub-populations and only one-third settled back into natal sub-populations. Comparison of our data with previous studies suggested that variation in dispersal distances is likely to be influenced by the geographical setting and spacing of sub-populations.

  15. Empirical determinants of measles metapopulation dynamics in England and Wales.

    Science.gov (United States)

    Finkenstädt, B; Grenfell, B

    1998-02-07

    A key issue in metapopulation dynamics is the relative impact of internal patch dynamics and coupling between patches. This problem can be addressed by analysing large spatiotemporal data sets, recording the local and global dynamics of metapopulations. In this paper, we analyse the dynamics of measles meta-populations in a large spatiotemporal case notification data set, collected during the pre-vaccination era in England and Wales. Specifically, we use generalized linear statistical models to quantify the relative importance of local influences (birth rate and population size) and regional coupling on local epidemic dynamics. Apart from the proportional effect of local population size on case totals, the models indicate patterns of local and regional dynamic influences which depend on the current state of epidemics. Birth rate and geographic coupling are not associated with the size of major epidemics. By contrast, minor epidemics--and especially the incidence of local extinction of infection--are influenced both by birth rate and geographical coupling. Birth rate at a lag of four years provides the best fit, reflecting the delayed recruitment of susceptibles to school cohorts. A hierarchical index of spatial coupling to large centres provides the best spatial model. The model also indicates that minor epidemics and extinction patterns are more strongly influenced by this regional effect than the local impact of birth rate.

  16. Difference in metapopulation structure and dynamics of two species of coexistent melitaeine butterflies

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    According to investigation on two species of melitaeine butterflies in Yanjiaping Village, Chicheng County, Hebei Province, China, between 1998-2002, together with the use of 1:10000 contour map of the local area, some conclusions are shown by the SPSS and GIS analysis of data obained from GPS: (1) The two species of melitaeine butterflies have different metapopulation structures. M. phoebe is a source-sink metapopulation, while E. aurinia is a classical metapopulation, supporting the analytic result from our former genetic research. (2) The two species of melitaeine butterflies exhibit different trends of population dynamics. M. phoebe source-sink metapopulation is very unsteady, and is always small, thus has a tendency to go extinct gradually. But E. aurinia classical metapopulation is stable, and has maintained a larger population size. Therefore, it stands a better chance of long-term survival. (3) The two species of melitaeine butterflies are significantly related in both patch occupancy and local population size. (4) The effect of isolation is significant on the metapopulations of these two species of melitaeine butterflies, consistent with the classical theories, whereas the effect of patch area is not significant on the metapopulations of these two species of melitaeine butterflies, which is inconsistent with the classical theories. Therefore, other factors, such as habitat quality, should be considered for their influences on metapopulations.

  17. Spatial occupancy models for predicting metapopulation dynamics and viability following reintroduction

    Science.gov (United States)

    Chandler, Richard B.; Muths, Erin L.; Sigafus, Brent H.; Schwalbe, Cecil R.; Jarchow, Christopher J; Hossack, Blake R.

    2015-01-01

    The reintroduction of a species into its historic range is a critical component of conservation programmes designed to restore extirpated metapopulations. However, many reintroduction efforts fail, and the lack of rigorous monitoring programmes and statistical models have prevented a general understanding of the factors affecting metapopulation viability following reintroduction.

  18. Deadaption and Readaptation with Lactose, But No Cross-Adaptation to Lactulose: A Case of Occult Colonic Bacterial Adaptation

    Directory of Open Access Journals (Sweden)

    Andrew Szilagyi

    2004-01-01

    Full Text Available The standard 3 h breath hydrogen (3hBH2 test distinguishes lactose maldigesters from lactose digesters. However, multiple factors impact on BH2 and care is needed to exclude a priori variables. When these factors are controlled, a negative BH2 test implies lactase persistent status or lactase nonpersistent status with colonic adaptation. A case of a Sicilian man who tested negative (lactase persistent status confirmed on an initial 50 g lactose challenge is described. It was observed that he consumed 28.1 g lactose/day before testing. He subsequently underwent five additional challenge tests in the course of the next 10 months. In four tests the dose intake of lactose was varied upon instruction, and in the fifth test a 30 g lactulose challenge was carried out. It was demonstrated that on radically decreasing lactose intake, a full lactase nonpersistent status was unmasked. Output of 3hBH2 varied inversely with daily lactose intake. Finally, at a time when he was readapted to lactose, there was no discernible adaptation to lactulose challenge. It was concluded that 'occult' colonically adapted subjects may contribute to negative BH2 tests. There is a relationship between variation in lactose intake and the results of BH2 testing. Finally, there was no cross-adaptation to lactulose challenge when lactose was used as the adapting sugar.

  19. Connectivity, cycles, and persistence thresholds in metapopulation networks.

    Science.gov (United States)

    Artzy-Randrup, Yael; Stone, Lewi

    2010-08-05

    Synthesising the relationships between complexity, connectivity, and the stability of large biological systems has been a longstanding fundamental quest in theoretical biology and ecology. With the many exciting developments in modern network theory, interest in these issues has recently come to the forefront in a range of multidisciplinary areas. Here we outline a new theoretical analysis specifically relevant for the study of ecological metapopulations focusing primarily on marine systems, where subpopulations are generally connected via larval dispersal. Our work determines the qualitative and quantitative conditions by which dispersal and network structure control the persistence of a set of age-structured patch populations. Mathematical modelling combined with a graph theoretic analysis demonstrates that persistence depends crucially on the topology of cycles in the dispersal network which tend to enhance the effect of larvae "returning home." Our method clarifies the impact directly due to network structure, but this almost by definition can only be achieved by examining the simplified case in which patches are identical; an assumption that we later relax. The methodology identifies critical migration routes, whose presence are vital to overall stability, and therefore should have high conservation priority. In contrast, "lonely links," or links in the network that do not participate in a cyclical component, have no impact on persistence and thus have low conservation priority. A number of other intriguing criteria for persistence are derived. Our modelling framework reveals new insights regarding the determinants of persistence, stability, and thresholds in complex metapopulations. In particular, while theoretical arguments have, in the past, suggested that increasing connectivity is a destabilizing feature in complex systems, this is not evident in metapopulation networks where connectivity, cycles, coherency, and heterogeneity all tend to enhance

  20. Connectivity, cycles, and persistence thresholds in metapopulation networks.

    Directory of Open Access Journals (Sweden)

    Yael Artzy-Randrup

    Full Text Available Synthesising the relationships between complexity, connectivity, and the stability of large biological systems has been a longstanding fundamental quest in theoretical biology and ecology. With the many exciting developments in modern network theory, interest in these issues has recently come to the forefront in a range of multidisciplinary areas. Here we outline a new theoretical analysis specifically relevant for the study of ecological metapopulations focusing primarily on marine systems, where subpopulations are generally connected via larval dispersal. Our work determines the qualitative and quantitative conditions by which dispersal and network structure control the persistence of a set of age-structured patch populations. Mathematical modelling combined with a graph theoretic analysis demonstrates that persistence depends crucially on the topology of cycles in the dispersal network which tend to enhance the effect of larvae "returning home." Our method clarifies the impact directly due to network structure, but this almost by definition can only be achieved by examining the simplified case in which patches are identical; an assumption that we later relax. The methodology identifies critical migration routes, whose presence are vital to overall stability, and therefore should have high conservation priority. In contrast, "lonely links," or links in the network that do not participate in a cyclical component, have no impact on persistence and thus have low conservation priority. A number of other intriguing criteria for persistence are derived. Our modelling framework reveals new insights regarding the determinants of persistence, stability, and thresholds in complex metapopulations. In particular, while theoretical arguments have, in the past, suggested that increasing connectivity is a destabilizing feature in complex systems, this is not evident in metapopulation networks where connectivity, cycles, coherency, and heterogeneity all tend

  1. Metapopulation Structure and Dynamics of an Endangered Butterfly

    Science.gov (United States)

    2010-01-01

    patterns in the population dynamic, and tested for density-dependent growth and weather factors as potential explanatory factors of the yearly variation ...Steuergrößen für die jährliche Variation . Wir fanden nicht-abnehmende bzw. stabile Populationen des Karner-Bläulings auf allen elf Arealen auf Fort McCoy...classic metapopulation model, specifying minimum population size, spatial area and fire-based renewal rates (Givnish et al. 1988). The phenology of L

  2. Motion-induced synchronization in metapopulations of mobile agents

    CERN Document Server

    Gómez-Gardeñes, Jesús; Sinatra, Roberta; Latora, Vito

    2012-01-01

    We study the influence of motion on the emergence of synchronization in a metapopulation of random walkers moving on a heterogeneous network and subject to Kuramoto interactions at the network nodes. We discover a novel mechanism of transition to macroscopic dynamical order induced by the walkers' motion. Furthermore, we observe two different microscopic paths to synchronization: depending on the rules of the motion, either low-degree nodes or the hubs drive the whole system towards synchronization. We provide analytical arguments to understand these results.

  3. The colitis-associated transcriptional profile of commensal Bacteroides thetaiotaomicron enhances adaptive immune responses to a bacterial antigen.

    Directory of Open Access Journals (Sweden)

    Jonathan J Hansen

    Full Text Available BACKGROUND: Inflammatory bowel diseases (IBD may be caused in part by aberrant immune responses to commensal intestinal microbes including the well-characterized anaerobic gut commensal Bacteroides thetaiotaomicron (B. theta. Healthy, germ-free HLA-B27 transgenic (Tg rats develop chronic colitis when colonized with complex gut commensal bacteria whereas non-transgenic (nTg rats remain disease-free. However, the role of B. theta in causing disease in Tg rats is unknown nor is much known about how gut microbes respond to host inflammation. METHODS: Tg and nTg rats were monoassociated with a human isolate of B. theta. Colonic inflammation was assessed by histologic scoring and tissue pro-inflammatory cytokine measurement. Whole genome transcriptional profiling of B. theta recovered from ceca was performed using custom GeneChips and data analyzed using dChip, Significance Analysis of Microarrays, and Gene Set Enrichment Analysis (GSEA software. Western Blots were used to determine adaptive immune responses to a differentially expressed B. theta gene. RESULTS: B. theta monoassociated Tg rats, but not nTg or germ-free controls, developed chronic colitis. Transcriptional profiles of cecal B. theta were significantly different in Tg vs. nTg rats. GSEA revealed that genes in KEGG canonical pathways involved in bacterial growth and metabolism were downregulated in B. theta from Tg rats with colitis though luminal bacterial concentrations were unaffected. Bacterial genes in the Gene Ontology molecular function "receptor activity", most of which encode nutrient binding proteins, were significantly upregulated in B. theta from Tg rats and include a SusC homolog that induces adaptive immune responses in Tg rats. CONCLUSIONS: B. theta induces colitis in HLA-B27 Tg rats, which is associated with regulation of bacterial genes in metabolic and nutrient binding pathways that may affect host immune responses. These studies of the host-microbial dialogue may lead to

  4. Contagion dynamics in time-varying metapopulation networks

    Science.gov (United States)

    Perra, Nicola; Liu, Suyu; Baronchelli, Andrea

    2014-03-01

    The metapopulation framework is adopted in a wide array of disciplines to describe systems of well separated yet connected subpopulations. The subgroups/patches are often represented as nodes in a network whose links represent the migration routes among them. The connections has been so far mostly considered as static, but in general evolve in time. Here we address this case by investigating simple contagion processes on time-varying metapopulation networks. We focus on the SIR process, and determine analytically the mobility threshold for the onset of an epidemic spreading in the framework of activity-driven network models. We find profound differences from the case of static networks. The threshold is entirely described by the dynamical parameters defining the average number of instantaneously migrating individuals, and does not depend on the properties of the static network representation. Remarkably, the diffusion and contagion processes are slower in time-varying graphs than in their aggregated static counterparts, the mobility threshold been even two orders of magnitude larger in the first case. The presented results confirm the importance of considering the time-varying nature of complex networks.

  5. Emergence of metapopulations and echo chambers in mobile agents

    Science.gov (United States)

    Starnini, Michele; Frasca, Mattia; Baronchelli, Andrea

    2016-08-01

    Multi-agent models often describe populations segregated either in the physical space, i.e. subdivided in metapopulations, or in the ecology of opinions, i.e. partitioned in echo chambers. Here we show how both kinds of segregation can emerge from the interplay between homophily and social influence in a simple model of mobile agents endowed with a continuous opinion variable. In the model, physical proximity determines a progressive convergence of opinions but differing opinions result in agents moving away from each others. This feedback between mobility and social dynamics determines the onset of a stable dynamical metapopulation scenario where physically separated groups of like-minded individuals interact with each other through the exchange of agents. The further introduction of confirmation bias in social interactions, defined as the tendency of an individual to favor opinions that match his own, leads to the emergence of echo chambers where different opinions coexist also within the same group. We believe that the model may be of interest to researchers investigating the origin of segregation in the offline and online world.

  6. Pre-adapting parasitic phages to a pathogen leads to increased pathogen clearance and lowered resistance evolution with Pseudomonas aeruginosacystic fibrosis bacterial isolates

    DEFF Research Database (Denmark)

    Friman, Ville-Petri; Soanes-Brown, Daniel; Sierocinski, Pawel

    2016-01-01

    Recent years have seen renewed interest in phage therapy - the use of viruses to specifically kill disease-causing bacteria – because of the alarming rise in antibiotic resistance. However, a major limitation of phage therapy is the ease at with bacteria can evolve resistance to phages. Here we...... determined if in vitro experimental coevolution can increase the efficiency of phage therapy by limiting the resistance evolution of intermittent and chronic cystic fibrosis Pseudomonas aeruginosa lung isolates to four different phages. We first pre-adapted all phage strains against all bacterial strains...... and then compared the efficacy of pre-adapted and non-adapted phages against ancestral bacterial strains. We found that evolved phages were more efficient in reducing bacterial densities than ancestral phages. This was primarily because only 50% of bacterial strains were able to evolve resistance to evolved phages...

  7. Comparative proteome analysis of psychrophilic versus mesophilic bacterial species: Insights into the molecular basis of cold adaptation of proteins

    Directory of Open Access Journals (Sweden)

    Reddy Boojala

    2009-01-01

    Full Text Available Abstract Background Cold adapted or psychrophilic organisms grow at low temperatures, where most of other organisms cannot grow. This adaptation requires a vast array of sequence, structural and physiological adjustments. To understand the molecular basis of cold adaptation of proteins, we analyzed proteomes of psychrophilic and mesophilic bacterial species and compared the differences in amino acid composition and substitution patterns to investigate their likely association with growth temperatures. Results In psychrophilic bacteria, serine, aspartic acid, threonine and alanine are overrepresented in the coil regions of secondary structures, whilst glutamic acid and leucine are underrepresented in the helical regions. Compared to mesophiles, psychrophiles comprise a significantly higher proportion of amino acids that contribute to higher protein flexibility in the coil regions of proteins, such as those with tiny/small or neutral side chains. Amino acids with aliphatic, basic, aromatic and hydrophilic side chains are underrepresented in the helical regions of proteins of psychrophiles. The patterns of amino acid substitutions between the orthologous proteins of psychrophiles versus mesophiles are significantly different for several amino acids when compared to their substitutions in orthologous proteins of within the mesophiles or psychrophiles. Conclusion Current results provide quantitative substitution preferences (or avoidance of amino acids that lead to the adaptation of proteins to cold temperatures. These finding would help future efforts in selecting mutations for rational design of proteins with enhanced psychrophilic properties.

  8. Amoeba host-Legionella synchronization of amino acid auxotrophy and its role in bacterial adaptation and pathogenic evolution.

    Science.gov (United States)

    Price, Christopher T D; Richards, Ashley M; Von Dwingelo, Juanita E; Samara, Hala A; Abu Kwaik, Yousef

    2014-02-01

    Legionella pneumophila, the causative agent of Legionnaires' disease, invades and proliferates within a diverse range of free-living amoeba in the environment, but upon transmission to humans, the bacteria hijack alveolar macrophages. Intracellular proliferation of L. pneumophila in two evolutionarily distant hosts is facilitated by bacterial exploitation of conserved host processes that are targeted by bacterial protein effectors injected into the host cell. A key aspect of microbe-host interaction is microbial extraction of nutrients from the host, but understanding of this is still limited. AnkB functions as a nutritional virulence factor and promotes host proteasomal degradation of polyubiquitinated proteins generating gratuitous levels of limiting host cellular amino acids. Legionella pneumophila is auxotrophic for several amino acids including cysteine, which is a metabolically preferred source of carbon and energy during intracellular proliferation, but is limiting in both amoebae and humans. We propose that synchronization of bacterial amino acids auxotrophy with the host is a driving force in pathogenic evolution and nutritional adaptation of L. pneumophila and other intracellular bacteria to life within the host cell. Understanding microbial strategies of nutrient generation and acquisition in the host will provide novel antimicrobial strategies to disrupt pathogen access to essential sources of carbon and energy.

  9. The adaptive response of bacterial food-borne pathogens in the environment, host and food: Implications for food safety.

    Science.gov (United States)

    Alvarez-Ordóñez, Avelino; Broussolle, Véronique; Colin, Pierre; Nguyen-The, Christophe; Prieto, Miguel

    2015-11-20

    Bacteria are constantly faced to stress situations in their ecological niches, the food and the host gastrointestinal tract. The capacity to detect and respond to surrounding changes is crucial for bacterial pathogens to survive or grow in changing environments. To this purpose, cells have evolved various sophisticated networks designed to protect against stressors or repair damage caused by them. Challenges can occur during production of foods when subjected to processing, and after food ingestion when confronted with host defensive barriers. Some pathogenic bacteria have shown the capacity to develop stable resistance against extreme conditions within a defined genomic context and a limited number of generations. On the other hand, bacteria can also respond to adverse conditions in a transient manner, through the so-called stress tolerance responses. Bacterial stress tolerance responses include both structural and physiological modifications in the cell and are mediated by complex genetic regulatory machinery. Major aspects in the adaptive response are the sensing mechanisms, the characterization of cell defensive systems, such as the operation of regulatory proteins (e.g. RpoS), the induction of homeostatic and repair systems, the synthesis of shock response proteins, and the modifications of cell membranes, particularly in their fatty acid composition and physical properties. This article reviews certain strategies used by food-borne bacteria to respond to particular stresses (acid, cold stress, extreme pressure) in a permanent or transient manner and discusses the implications that such adaptive responses pose for food safety.

  10. Effects of Demographic Noise on the Synchronization of a Metapopulation in a Fluctuating Environment

    KAUST Repository

    Lai, Yi Ming

    2011-09-08

    We use the theory of noise-induced phase synchronization to analyze the effects of demographic noise on the synchronization of a metapopulation of predator-prey systems within a fluctuating environment (Moran effect). Treating each local predator-prey population as a stochastic urn model, we derive a Langevin equation for the stochastic dynamics of the metapopulation. Assuming each local population acts as a limit cycle oscillator in the deterministic limit, we use phase reduction and averaging methods to derive the steady-state probability density for pairwise phase differences between oscillators, which is then used to determine the degree of synchronization of the metapopulation. © 2011 American Physical Society.

  11. Sufficient conditions of endemic threshold on metapopulation networks

    CERN Document Server

    Takaguchi, Taro

    2014-01-01

    In the present paper, we focus on susceptible-infected-susceptible dynamics on metapopulation networks in which nodes represent subpopulations. Recent studies suggest that heterogeneous network structure between elements plays an important role in determining the threshold of infection rate at the onset of epidemics, one of fundamental quantities governing epidemic dynamics. We consider the general case in which the infection rate at each node depends on its population size, as shown in recent empirical observations. We prove that the sufficient condition for the endemic threshold (i.e., its upper bound), which was previously derived based on a mean-field approximation of network structure, also holds true for arbitrary networks. We also derive an improved condition which implies that networks with the rich-club property (that is, high connectivity between nodes with large number of links) are more favorable to disease spreading. The dependency of infection rate on population size introduces remarkable differ...

  12. Stationary solutions for metapopulation Moran models with mutation and selection

    Science.gov (United States)

    Constable, George W. A.; McKane, Alan J.

    2015-03-01

    We construct an individual-based metapopulation model of population genetics featuring migration, mutation, selection, and genetic drift. In the case of a single "island," the model reduces to the Moran model. Using the diffusion approximation and time-scale separation arguments, an effective one-variable description of the model is developed. The effective description bears similarities to the well-mixed Moran model with effective parameters that depend on the network structure and island sizes, and it is amenable to analysis. Predictions from the reduced theory match the results from stochastic simulations across a range of parameters. The nature of the fast-variable elimination technique we adopt is further studied by applying it to a linear system, where it provides a precise description of the slow dynamics in the limit of large time-scale separation.

  13. Bacterial adaptation to sublethal antibiotic gradients can change the ecological properties of multitrophic microbial communities

    OpenAIRE

    Friman, Ville-Petri; Guzman, Laura Melissa; Reuman, Daniel C.; Bell, Thomas

    2015-01-01

    Antibiotics leak constantly into environments due to widespread use in agriculture and human therapy. Although sublethal concentrations are well known to select for antibiotic-resistant bacteria, little is known about how bacterial evolution cascades through food webs, having indirect effect on species not directly affected by antibiotics (e.g. via population dynamics or pleiotropic effects). Here, we used an experimental evolution approach to test how temporal patterns of antibiotic stress, ...

  14. Bubonic plague: a metapopulation model of a zoonosis.

    Science.gov (United States)

    Keeling, M J; Gilligan, C A

    2000-01-01

    Bubonic plague (Yersinia pestis) is generally thought of as a historical disease; however, it is still responsible for around 1000-3000 deaths each year worldwide. This paper expands the analysis of a model for bubonic plague that encompasses the disease dynamics in rat, flea and human populations. Some key variables of the deterministic model, including the force of infection to humans, are shown to be robust to changes in the basic parameters, although variation in the flea searching efficiency, and the movement rates of rats and fleas will be considered throughout the paper. The stochastic behaviour of the corresponding metapopulation model is discussed, with attention focused on the dynamics of rats and the force of infection at the local spatial scale. Short-lived local epidemics in rats govern the invasion of the disease and produce an irregular pattern of human cases similar to those observed. However, the endemic behaviour in a few rat subpopulations allows the disease to persist for many years. This spatial stochastic model is also used to identify the criteria for the spread to human populations in terms of the rat density. Finally, the full stochastic model is reduced to the form of a probabilistic cellular automaton, which allows the analysis of a large number of replicated epidemics in large populations. This simplified model enables us to analyse the spatial properties of rat epidemics and the effects of movement rates, and also to test whether the emergent metapopulation behaviour is a property of the local dynamics rather than the precise details of the model. PMID:11413636

  15. An Analysis on the Influence of Network Topologies on Local and Global Dynamics of Metapopulation Systems

    Directory of Open Access Journals (Sweden)

    Daniela Besozzi

    2010-08-01

    Full Text Available Metapopulations are models of ecological systems, describing the interactions and the behavior of populations that live in fragmented habitats. In this paper, we present a model of metapopulations based on the multivolume simulation algorithm tau-DPP, a stochastic class of membrane systems, that we utilize to investigate the influence that different habitat topologies can have on the local and global dynamics of metapopulations. In particular, we focus our analysis on the migration rate of individuals among adjacent patches, and on their capability of colonizing the empty patches in the habitat. We compare the simulation results obtained for each habitat topology, and conclude the paper with some proposals for other research issues concerning metapopulations.

  16. Epidemic modeling in metapopulation systems with heterogeneous coupling pattern: theory and simulations

    CERN Document Server

    Colizza, Vittoria

    2007-01-01

    The spatial structure of populations is a key element in the understanding of the large scale spreading of epidemics. Motivated by the recent empirical evidence on the heterogeneous properties of transportation and commuting patterns among urban areas, we present a thorough analysis of the behavior of infectious diseases in metapopulation models characterized by heterogeneous connectivity and mobility patterns. We derive the basic reaction-diffusion equation describing the metapopulation system at the mechanistic level and derive an early stage dynamics approximation for the subpopulation invasion dynamics. The analytical description uses degree block variables that allows us to take into account arbitrary degree distribution of the metapopulation network. We show that along with the usual single population epidemic threshold the metapopulation network exhibits a global threshold for the subpopulation invasion. We find an explicit analytic expression for the invasion threshold that determines the minimum numb...

  17. Human-facilitated metapopulation dynamics in an emerging pest species, Cimex lectularius

    OpenAIRE

    Fountain, T; Duvaux, L; Horsburgh, G.; Reinhardt, K.; Butlin, R. K.

    2014-01-01

    The number and demographic history of colonists can have dramatic consequences for the way in which genetic diversity is distributed and maintained in a metapopulation. The bed bug (Cimex lectularius) is a re-emerging pest species whose close association with humans has led to frequent local extinction and colonization, that is, to metapopulation dynamics. Pest control limits the lifespan of subpopulations, causing frequent local extinctions, and human-facilitated dispersal allows the coloniz...

  18. Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity

    NARCIS (Netherlands)

    Charpentier, Emmanuelle; Richter, Hagen; Oost, van der John; White, Malcolm F.

    2015-01-01

    CRISPR-Cas is an RNA-mediated adaptive immune system that defends bacteria and archaea against mobile genetic elements. Short mature CRISPR RNAs (crRNAs) are key elements in the interference step of the immune pathway. A CRISPR array composed of a series of repeats interspaced by spacer sequences

  19. Measuring bacterial adaptation dynamics at the single-cell level using a microfluidic chemostat and time-lapse fluorescence microscopy.

    Science.gov (United States)

    Long, Zhicheng; Olliver, Anne; Brambilla, Elisa; Sclavi, Bianca; Lagomarsino, Marco Cosentino; Dorfman, Kevin D

    2014-10-21

    We monitored the dynamics of cell dimensions and reporter GFP expression in individual E. coli cells growing in a microfluidic chemostat using time-lapse fluorescence microscopy. This combination of techniques allows us to study the dynamical responses of single bacterial cells to nutritional shift-down or shift-up for longer times and with more precision over the chemical environment than similar experiments performed on conventional agar pads. We observed two E. coli strains containing different promoter-reporter gene constructs and measured how both their cell dimensions and the GFP expression change after nutritional upshift and downshift. As expected, both strains have similar adaptation dynamics for cell size rearrangement. However, the strain with a ribosomal RNA promoter dependent reporter has a faster GFP production rate than the strain with a constitutive promoter reporter. As a result, the mean GFP concentration in the former strain changes rapidly with the nutritional shift, while that in the latter strain remains relatively stable. These findings characterize the present microfluidic chemostat as a versatile platform for measuring single-cell bacterial dynamics and physiological transitions.

  20. Application of Dynamic adaptive bacterial foraging algorithm for optimum economic dispatch with valve-point effects and wind power

    Directory of Open Access Journals (Sweden)

    mahmood Joorabian

    2013-02-01

    Full Text Available This study presents a dynamically adapted bacterial foraging algorithm (BFA to solve the economic dispatch (ED problem considering valve-point effects and power losses. In addition, wind power is included in the problem formulation. Renewable sources and wind energy in particular have recently been getting more interest because of various environmental and economical considerations. The original BFA is a recently developed evolutionary optimisation technique inspired by the foraging behaviour of the Escherichia coli bacteria. The basic BFA has been successfully implemented to solve small optimisation problems; however, it shows poor convergence characteristics for larger constrained problems. To deal with the complexity and highdimensioned search space of the ED problem, essential modifications are introduced to enhance the performance of the algorithm. The basic chemotactic step is adjusted to have a dynamic non-linear behavior in order to improve balancing the global and local search. The stopping criterion of the original BFA is also modified to be adaptive depending on the solution improvement instead of the preset maximum number of iterations. The proposed algorithm is validated using several test systems. The results are compared with those obtained by other algorithms previously applied to solve the problem considering valve-point effects and power losses in addition to wind power.

  1. Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts

    KAUST Repository

    Neave, Matthew J.

    2017-01-17

    Endozoicomonas bacteria are globally distributed and often abundantly associated with diverse marine hosts including reef-building corals, yet their function remains unknown. In this study we generated novel Endozoicomonas genomes from single cells and metagenomes obtained directly from the corals Stylophora pistillata, Pocillopora verrucosa, and Acropora humilis. We then compared these culture-independent genomes to existing genomes of bacterial isolates acquired from a sponge, sea slug, and coral to examine the functional landscape of this enigmatic genus. Sequencing and analysis of single cells and metagenomes resulted in four novel genomes with 60–76% and 81–90% genome completeness, respectively. These data also confirmed that Endozoicomonas genomes are large and are not streamlined for an obligate endosymbiotic lifestyle, implying that they have free-living stages. All genomes show an enrichment of genes associated with carbon sugar transport and utilization and protein secretion, potentially indicating that Endozoicomonas contribute to the cycling of carbohydrates and the provision of proteins to their respective hosts. Importantly, besides these commonalities, the genomes showed evidence for differential functional specificity and diversification, including genes for the production of amino acids. Given this metabolic diversity of Endozoicomonas we propose that different genotypes play disparate roles and have diversified in concert with their hosts.

  2. Reptile Toll-like receptor 5 unveils adaptive evolution of bacterial flagellin recognition.

    Science.gov (United States)

    Voogdt, Carlos G P; Bouwman, Lieneke I; Kik, Marja J L; Wagenaar, Jaap A; van Putten, Jos P M

    2016-01-07

    Toll-like receptors (TLR) are ancient innate immune receptors crucial for immune homeostasis and protection against infection. TLRs are present in mammals, birds, amphibians and fish but have not been functionally characterized in reptiles despite the central position of this animal class in vertebrate evolution. Here we report the cloning, characterization, and function of TLR5 of the reptile Anolis carolinensis (Green Anole lizard). The receptor (acTLR5) displays the typical TLR protein architecture with 22 extracellular leucine rich repeats flanked by a N- and C-terminal leucine rich repeat domain, a membrane-spanning region, and an intracellular TIR domain. The receptor is phylogenetically most similar to TLR5 of birds and most distant to fish TLR5. Transcript analysis revealed acTLR5 expression in multiple lizard tissues. Stimulation of acTLR5 with TLR ligands demonstrated unique responsiveness towards bacterial flagellin in both reptile and human cells. Comparison of acTLR5 and human TLR5 using purified flagellins revealed differential sensitivity to Pseudomonas but not Salmonella flagellin, indicating development of species-specific flagellin recognition during the divergent evolution of mammals and reptiles. Our discovery of reptile TLR5 fills the evolutionary gap regarding TLR conservation across vertebrates and provides novel insights in functional evolution of host-microbe interactions.

  3. Past, growth and persistence of source-sink metapopulations

    CERN Document Server

    Bansaye, Vincent

    2011-01-01

    Source-sink systems are metapopulations of patches that can be of variable habitat quality. They can be seen as graphs, where vertices represent the patches, and the weighted oriented edges give the probability of dispersal from one patch to another. We consider either finite or source-transitive graphs, i.e., graphs that are identical when viewed from a(ny) source. We assume stochastic, individual-based, density-independent reproduction and dispersal. By studying the path of a single random disperser, we are able to display simple criteria for persistence, either necessary and sufficient, or just sufficient. In case of persistence, we characterize the growth rate of the population as well as the asymptotic occupancy frequencies of the line of ascent of a random survivor. Our method allows to decouple the roles of reproduction and dispersal. Finally, we extend our results to the case of periodic or random environments, where some habitats can have variable growth rates, autocorrelated in space and possibly in...

  4. Effects of Lead Exposure, Environmental Conditions, and Metapopulation Processes on Population Dynamics of Spectacled Eiders.

    Science.gov (United States)

    Flint, Paul L.; Grand, James B.; Petersen, Margaret; Robert Rockwell,

    2016-01-01

    Spectacled eider Somateria fischeri numbers have declined and they are considered threatened in accordance with the US Endangered Species Act throughout their range. We synthesized the available information for spectacled eiders to construct deterministic, stochastic, and metapopulation models for this species that incorporated current estimates of vital rates such as nest success, adult survival, and the impact of lead poisoning on survival. Elasticities of our deterministic models suggested that the populations would respond most dramatically to changes in adult female survival and that the reductions in adult female survival related to lead poisoning were locally important. We also examined the sensitivity of the population to changes in lead exposure rates. With the knowledge that some vital rates vary with environmental conditions, we cast stochastic models that mimicked observed variation in productivity. We also used the stochastic model to examine the probability that a specific population will persist for periods of up to 50 y. Elasticity analysis of these models was consistent with that for the deterministic models, with perturbations to adult female survival having the greatest effect on population projections. When used in single population models, demographic data for some localities predicted rapid declines that were inconsistent with our observations in the field. Thus, we constructed a metapopulation model and examined the predictions for local subpopulations and the metapopulation over a wide range of dispersal rates. Using the metapopulation model, we were able to simulate the observed stability of local subpopulations as well as that of the metapopulation. Finally, we developed a global metapopulation model that simulates periodic winter habitat limitation, similar to that which might be experienced in years of heavy sea ice in the core wintering area of spectacled eiders in the central Bering Sea. Our metapopulation analyses suggested that no

  5. Adaptation in Toxic Environments: Arsenic Genomic Islands in the Bacterial Genus Thiomonas.

    Directory of Open Access Journals (Sweden)

    Kelle C Freel

    Full Text Available Acid mine drainage (AMD is a highly toxic environment for most living organisms due to the presence of many lethal elements including arsenic (As. Thiomonas (Tm. bacteria are found ubiquitously in AMD and can withstand these extreme conditions, in part because they are able to oxidize arsenite. In order to further improve our knowledge concerning the adaptive capacities of these bacteria, we sequenced and assembled the genome of six isolates derived from the Carnoulès AMD, and compared them to the genomes of Tm. arsenitoxydans 3As (isolated from the same site and Tm. intermedia K12 (isolated from a sewage pipe. A detailed analysis of the Tm. sp. CB2 genome revealed various rearrangements had occurred in comparison to what was observed in 3As and K12 and over 20 genomic islands (GEIs were found in each of these three genomes. We performed a detailed comparison of the two arsenic-related islands found in CB2, carrying the genes required for arsenite oxidation and As resistance, with those found in K12, 3As, and five other Thiomonas strains also isolated from Carnoulès (CB1, CB3, CB6, ACO3 and ACO7. Our results suggest that these arsenic-related islands have evolved differentially in these closely related Thiomonas strains, leading to divergent capacities to survive in As rich environments.

  6. Demographic stochasticity reduces the synchronizing effect of dispersal in predator-prey metapopulations.

    Science.gov (United States)

    Simonis, Joseph L

    2012-07-01

    Dispersal may affect predator-prey metapopulations by rescuing local sink populations from extinction or by synchronizing population dynamics across the metapopulation, increasing the risk of regional extinction. Dispersal is likely influenced by demographic stochasticity, however, particularly because dispersal rates are often very low in metapopulations. Yet the effects of demographic stochasticity on predator-prey metapopulations are not well known. To that end, I constructed three models of a two-patch predator-prey system. The models constitute a hierarchy of complexity, allowing direct comparisons. Two models included demographic stochasticity (pure jump process [PJP] and stochastic differential equations [SDE]), and the third was deterministic (ordinary differential equations [ODE]). One stochastic model (PJP) treated population sizes as discrete, while the other (SDE) allowed population sizes to change continuously. Both stochastic models only produced synchronized predator-prey dynamics when dispersal was high for both trophic levels. Frequent dispersal by only predators or prey in the PJP and SDE spatially decoupled the trophic interaction, reducing synchrony of the non-dispersive species. Conversely, the ODE generated synchronized predator-prey dynamics across all dispersal rates, except when initial conditions produced anti-phase transients. These results indicate that demographic stochasticity strongly reduces the synchronizing effect of dispersal, which is ironic because demographic stochasticity is often invoked post hoc as a driver of extinctions in synchronized metapopulations.

  7. Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses.

    Science.gov (United States)

    Pride, David T; Salzman, Julia; Relman, David A

    2012-09-01

    Explorations of human microbiota have provided substantial insight into microbial community composition; however, little is known about interactions between various microbial components in human ecosystems. In response to the powerful impact of viral predation, bacteria have acquired potent defences, including an adaptive immune response based on the clustered regularly interspaced short palindromic repeats (CRISPRs)/Cas system. To improve our understanding of the interactions between bacteria and their viruses in humans, we analysed 13 977 streptococcal CRISPR sequences and compared them with 2 588 172 virome reads in the saliva of four human subjects over 17 months. We found a diverse array of viruses and CRISPR spacers, many of which were specific to each subject and time point. There were numerous viral sequences matching CRISPR spacers; these matches were highly specific for salivary viruses. We determined that spacers and viruses coexist at the same time, which suggests that streptococcal CRISPR/Cas systems are under constant pressure from salivary viruses. CRISPRs in some subjects were just as likely to match viral sequences from other subjects as they were to match viruses from the same subject. Because interactions between bacteria and viruses help to determine the structure of bacterial communities, CRISPR-virus analyses are likely to provide insight into the forces shaping the human microbiome.

  8. Biogas production from coumarin-rich plants--inhibition by coumarin and recovery by adaptation of the bacterial community.

    Science.gov (United States)

    Popp, Denny; Schrader, Steffi; Kleinsteuber, Sabine; Harms, Hauke; Sträuber, Heike

    2015-09-01

    Plants like sweet clover (Melilotus spp.) are not suitable as fodder for cattle because of harmful effects of the plant secondary metabolite coumarin. As an alternative usage, the applicability of coumarin-rich plants as substrates for biogas production was investigated. When coumarin was added to continuous fermentation processes codigesting grass silage and cow manure, it caused a strong inhibition noticeable as decrease of biogas production by 19% and increase of metabolite concentrations to an organic acids/alkalinity ratio higher than 0.3(gorganic acids) gCaCO3 (-1). Microbial communities of methanogenic archaea were dominated by the genera Methanosarcina (77%) and Methanoculleus (11%). This community composition was not influenced by coumarin addition. The bacterial community analysis unraveled a divergence caused by coumarin addition correlating with the anaerobic degradation of coumarin and the recovery of the biogas process. As a consequence, biogas production resumed similar to the coumarin-free control with a biogas yield of 0.34 LN g(volatile solids) (-1) and at initial metabolite concentrations (∼ 0.2 g(organic acids) gCaCO3 (-1)). Coumarin acts as inhibitor and as substrate during anaerobic digestion. Hence, coumarin-rich plants might be suitable for biogas production, but should only be used after adaptation of the microbial community to coumarin.

  9. Predicting Metapopulation Responses To Conservation In Human-Dominated Landscapes

    Directory of Open Access Journals (Sweden)

    Zachary S. Ladin

    2016-10-01

    Full Text Available Loss of habitat to urbanization is a primary cause of population declines as human-dominated landscapes expand at increasing rates. Understanding how the relative effects of different conservation strategies is important to slow population declines for species in urban landscapes. We studied the wood thrush Hylocichla mustelina, a declining forest-breeding Neotropical migratory species, and umbrella species for forest-breeding songbirds, within the urbanized mid-Atlantic United States. We integrated 40 years of demographic data with contemporary metapopulation model simulations of breeding wood thrushes to predict population responses to differing conservation scenarios. We compared four conservation scenarios over a 30-year time period (2014–2044 representing A current observed state (Null, B replacing impervious surface with forest (Reforest, C reducing brown-headed cowbird Molothrus ater parasitism pressure (Cowbird removal, and D simultaneous reforesting and cowbird removal. Compared to the Null scenario, the Reforest scenario increased mean annual population trends by 54 % , the Remove cowbirds scenario increased mean annual population trends by 38 %, and the scenario combining reforestation and cowbird removal increased mean annual population trends by 98 %. Mean annual growth rates (λ per site were greater in the Reforest (λ = 0.94 and Remove cowbirds (λ = 0.92 compared to the Null (λ = 0.88 model scenarios. However, only by combining the positive effects of reforestation and cowbird removal did wood thrush populations stop declining (λ = 1.00. Our results suggest that independently replacing impervious surface with forest habitat around forest patches and removing cowbirds may slow current negative population trends. Furthermore, conservation efforts that combine reforestation and cowbird removal may potentially benefit populations of wood thrushes and other similarly forest-breeding songbird species within urbanized fragmented

  10. Persistence in epidemic metapopulations: quantifying the rescue effects for measles, mumps, rubella and whooping cough.

    Directory of Open Access Journals (Sweden)

    C Jessica E Metcalf

    Full Text Available Metapopulation rescue effects are thought to be key to the persistence of many acute immunizing infections. Yet the enhancement of persistence through spatial coupling has not been previously quantified. Here we estimate the metapopulation rescue effects for four childhood infections using global WHO reported incidence data by comparing persistence on island countries vs all other countries, while controlling for key variables such as vaccine cover, birth rates and economic development. The relative risk of extinction on islands is significantly higher, and approximately double the risk of extinction in mainland countries. Furthermore, as may be expected, infections with longer infectious periods tend to have the strongest metapopulation rescue effects. Our results quantitate the notion that demography and local community size controls disease persistence.

  11. Persistence in epidemic metapopulations: quantifying the rescue effects for measles, mumps, rubella and whooping cough.

    Science.gov (United States)

    Metcalf, C Jessica E; Hampson, Katie; Tatem, Andrew J; Grenfell, Bryan T; Bjørnstad, Ottar N

    2013-01-01

    Metapopulation rescue effects are thought to be key to the persistence of many acute immunizing infections. Yet the enhancement of persistence through spatial coupling has not been previously quantified. Here we estimate the metapopulation rescue effects for four childhood infections using global WHO reported incidence data by comparing persistence on island countries vs all other countries, while controlling for key variables such as vaccine cover, birth rates and economic development. The relative risk of extinction on islands is significantly higher, and approximately double the risk of extinction in mainland countries. Furthermore, as may be expected, infections with longer infectious periods tend to have the strongest metapopulation rescue effects. Our results quantitate the notion that demography and local community size controls disease persistence.

  12. Lumpers or splitters? Evaluating recovering and management plans for metapopulations of herring

    NARCIS (Netherlands)

    Kell, L.T.; Dickey-Collas, M.; Hintzen, N.T.; Nash, R.D.M.; Pilling, G.M.

    2009-01-01

    The long-term management of a stock representing a metapopulation has been simulated in a case study loosely based upon herring to the west of the British isles, where stocks are currently assessed and managed by management area, although there is evidence of mixing between stocks (in terms of conne

  13. Metapopulations in agricultural landscapes: a spatially explicit trade-off analysis

    NARCIS (Netherlands)

    Groeneveld, R.A.; Grashof-Bokdam, C.J.; Ierland, van E.C.

    2005-01-01

    This paper presents a spatially explicit trade-off analysis of species conservation in agricultural areas. A spatially explicit model is presented that integrates an applied metapopulation model with a farm management model. The model is used to calculate production possibilities frontiers of net mo

  14. Extinction, reintroduction, and restoration of a lizard meta-population equilibrium in the Missouri Ozarks.

    Science.gov (United States)

    Sites, Jack W

    2013-07-01

    In this issue of Molecular Ecology, Neuwald & Templeton (2013) report on a 22-year study of natural populations of Collared Lizards (Crotaphytus collaris) that evolved on isolated on rock outcrops (‘glades’) in the Ozark Mountains in eastern Missouri. This ecosystem was originally maintained by frequent fires that kept the forest understory open, but fire-suppression was adopted as official policy in about 1945, which led to a loss of native biodiversity, including local extinctions of some lizard populations. Policies aimed at restoring biodiversity included controlled burns and re-introductions of lizards to some glades, which began in 1984. Populations were monitored from 1984–2006, and demographic and genetic data collected from 1 679 lizards were used to documents shifts in meta-population dynamics over four distinct phases of lizard recovery: 1–an initial translocation of lizards drawn from the same source populations onto three glades that were likely part of one metapopulation; 2–a period of isolation and genetic drift associated with the absence of fires; 3–a period of rapid colonization and population increase following restoration of fire; and 4–stabilization of the meta-population under regular prescribed burning. This study system thus provides a rare opportunity to characterize the dynamics of a landscape-scale management strategy on the restoration of the meta-population of a reintroduced species; long-term case studies of the extinction, founding, increase, and stabilization of a well-defined meta-population, based on both demographic and population genetic data, are rare in the conservation, ecological, and evolutionary literature.

  15. Biodecolorization and Bioremediation of Denim Industrial Wastewater by Adapted Bacterial Consortium Immobilized on Inert Polyurethane Foam (PUF) Matrix: A First Approach with Biobarrier Model.

    Science.gov (United States)

    Rajendran, R; Prabhavathi, P; Karthiksundaram, S; Pattab, S; Kumar, S Dinesh; Santhanam, P

    2015-01-01

    The present experiments were studied on bioremediation of denim industry wastewater by using polyurethane foam (PU foam) immobilized bacterial cells. About 30 indigenous adapted bacterial strains were isolated from denim textile effluent out of which only four isolates were found to be efficient against crude indigo carmine degradation using broth decolorization method. The selected bacterial strains were identified as Actinomyces sp., (PK07), Pseudomonas sp., (PK18), Stenotrophomonas sp., (PK23) and Staphylococcus sp., (PK28) based on microscopic and biochemical characteristics. The bacterial immobilized cells have the highest number of viable cells (PK07, PK18, PK23 and PK28 appeared to be 1 x 10(8), 1 x 10(9), 1 x 10(6) and 1 x 10(7) CFU/ml respectively) and maximum attachment efficiency of 92% on PU foam. The complete degradation using a consortium of PU foam immobilized cells was achieved at pH 6, 27 degrees C, 100% of substrate concentration and allowed to develop biofilm for one day (1.5% W/V). In SEM analysis, it was found that immobilization of bacterial cells using PUF stably maintained the production of various extracellular enzymes at levels higher than achieved with suspended forms. Finally, isatin and anthranilic acid were found to be degradation products by NMR and TLC. The decolorized dye was not toxic to monkey kidney cell (HBL 100) at a concentration of 50 μl and 95% of cell viability was retained. A mathematical model that describes bacterial transport with biodegradation involves a set of coupled reaction equations with non-standard numerical approach based on the time step scheme.

  16. Intermediate fragmentation per se provides stable predator-prey metapopulation dynamics.

    Science.gov (United States)

    Cooper, Jennifer K; Li, Jiqiu; Montagnes, David J S

    2012-08-01

    The extent to which a landscape is fragmented affects persistence of predator-prey dynamics. Increasing fragmentation concomitantly imposes conditions that stabilise and destabilise metapopulations. For the first time, we explicitly assessed the hypothesis that intermediate levels provide optimal conditions for stability. We examine four structural changes arising from increased fragmentation: increased fragment number; decreased fragment size; increased connectedness (corridors scaled to fragment); increased fragment heterogeneity (based on connectedness). Using the model predator-prey system (Didinium-Paramecium) we support our hypothesis, by examining replicated metapopulations dynamics at five fragmentation levels. Although both species became extinct without fragmentation, prey survived at low and high levels, and both survived at intermediate levels. By examining time to extinction, maximum abundances, and population asynchrony we conclude that fragmentation produces structural heterogeneity (independent of environmental heterogeneity), which influences stability. Our analysis suggests why some theoretical, field and microcosm studies present conflicting views of fragmentation effects on population persistence.

  17. Dispersal-induced destabilization of metapopulations and oscillatory Turing patterns in ecological networks

    Science.gov (United States)

    Hata, Shigefumi; Nakao, Hiroya; Mikhailov, Alexander S.

    2014-01-01

    As shown by Alan Turing in 1952, differential diffusion may destabilize uniform distributions of reacting species and lead to emergence of patterns. While stationary Turing patterns are broadly known, the oscillatory instability, leading to traveling waves in continuous media and sometimes called the wave bifurcation, remains less investigated. Here, we extend the original analysis by Turing to networks and apply it to ecological metapopulations with dispersal connections between habitats. Remarkably, the oscillatory Turing instability does not lead to wave patterns in networks, but to spontaneous development of heterogeneous oscillations and possible extinction of species. We find such oscillatory instabilities for all possible food webs with three predator or prey species, under various assumptions about the mobility of individual species and nonlinear interactions between them. Hence, the oscillatory Turing instability should be generic and must play a fundamental role in metapopulation dynamics, providing a common mechanism for dispersal-induced destabilization of ecosystems.

  18. Rising relative fluctuation as a warning indicator of discontinuous transitions in symbiotic metapopulations

    Science.gov (United States)

    Lumi, Neeme; Laas, Katrin; Mankin, Romi

    2015-11-01

    The long-time limit behavior of the stochastic Lotka-Volterra model of a symbiotic metapopulation subjected to generalized Verhulst self-regulation is considered. The influence of a time-variable environment on the carrying capacities of subpopulations is modeled as a periodic deterministic part and a symmetric dichotomous noise. Relying on the mean-field approach it is established that at certain parameter regimes the mean field (average subpopulations size) exhibits hysteresis in respect to the noise correlation time, manifested in the appearance of colored-noise-induced discontinuous transitions. Especially, it is shown that the relative fluctuation of the subpopulation sizes exhibits accelerated increase prior to abrupt transitions of the metapopulation state. Moreover, in certain cases the autocorrelation function of the population sizes demonstrates anticorrelation at some values of the lag time.

  19. Human-facilitated metapopulation dynamics in an emerging pest species, Cimex lectularius.

    Science.gov (United States)

    Fountain, Toby; Duvaux, Ludovic; Horsburgh, Gavin; Reinhardt, Klaus; Butlin, Roger K

    2014-03-01

    The number and demographic history of colonists can have dramatic consequences for the way in which genetic diversity is distributed and maintained in a metapopulation. The bed bug (Cimex lectularius) is a re-emerging pest species whose close association with humans has led to frequent local extinction and colonization, that is, to metapopulation dynamics. Pest control limits the lifespan of subpopulations, causing frequent local extinctions, and human-facilitated dispersal allows the colonization of empty patches. Founder events often result in drastic reductions in diversity and an increased influence of genetic drift. Coupled with restricted migration, this can lead to rapid population differentiation. We therefore predicted strong population structuring. Here, using 21 newly characterized microsatellite markers and approximate Bayesian computation (ABC), we investigate simplified versions of two classical models of metapopulation dynamics, in a coalescent framework, to estimate the number and genetic composition of founders in the common bed bug. We found very limited diversity within infestations but high degrees of structuring across the city of London, with extreme levels of genetic differentiation between infestations (FST  = 0.59). ABC results suggest a common origin of all founders of a given subpopulation and that the numbers of colonists were low, implying that even a single mated female is enough to found a new infestation successfully. These patterns of colonization are close to the predictions of the propagule pool model, where all founders originate from the same parental infestation. These results show that aspects of metapopulation dynamics can be captured in simple models and provide insights that are valuable for the future targeted control of bed bug infestations.

  20. Multi-state models: metapopulation and life history analyses

    Directory of Open Access Journals (Sweden)

    Arnason, A. N.

    2004-06-01

    state ambiguity (dormant or dead? and can permit assessing the influence of environmental covariates on this proportion. The presentation by Christophe Barbraud (Barbraud & Weimerskirk, 2004, included in these proceedings as an extended abstract, takes the life–history trade–off application of MSMR models a step further by taking into account environmental and individual covariates on survival. The trade–off considered is between survival and transitions among several states describing breeding experience of long–lived petrels and how it is affected by harsh climate conditions. The study is a showcase for the powers of the new software (U–Care and M–Surge. The paper by Senar and Conroy (Senar & Conroy, 2004 is a novel application of MSMR models to animal epidemiology. States included age, sex and infected state and the model permits estimation of survival, infection, and recovery rates for birds during an outbreak of Serin avian pox. The use of a MSMR model permits estimation of the prevalence rate unconfounded by differences in capture rates of infected and non–infected birds. Here too there is a potential for ambiguous states in that the uninfected state might include both immune post–infection animals and susceptible pre–infection animals and these groups would likely have different survival rates. The authors are able to deal with this because of the length of the study and the availability of data outside the main outbreak. Finally, this session includes a paper by Jamieson and Brooks (Jamieson & Brooks, 2004 that appears to lie outside the MSMR theme of this session but which was included because of its relevanceto metapopulation analyses. Our call for papers for this session also invited papers illustrating multi– population meta–analysis and use of Bayesian methods. By these criteria, their paper is no outlier. It addresses the longstanding question of density dependence in game bird survival; a question of great interest to theoretical

  1. Structural complexity, movement bias, and metapopulation extinction risk in dendritic ecological networks

    Science.gov (United States)

    Campbell Grant, Evan H.

    2011-01-01

    Spatial complexity in metacommunities can be separated into 3 main components: size (i.e., number of habitat patches), spatial arrangement of habitat patches (network topology), and diversity of habitat patch types. Much attention has been paid to lattice-type networks, such as patch-based metapopulations, but interest in understanding ecological networks of alternative geometries is building. Dendritic ecological networks (DENs) include some increasingly threatened ecological systems, such as caves and streams. The restrictive architecture of dendritic ecological networks might have overriding implications for species persistence. I used a modeling approach to investigate how number and spatial arrangement of habitat patches influence metapopulation extinction risk in 2 DENs of different size and topology. Metapopulation persistence was higher in larger networks, but this relationship was mediated by network topology and the dispersal pathways used to navigate the network. Larger networks, especially those with greater topological complexity, generally had lower extinction risk than smaller and less-complex networks, but dispersal bias and magnitude affected the shape of this relationship. Applying these general results to real systems will require empirical data on the movement behavior of organisms and will improve our understanding of the implications of network complexity on population and community patterns and processes.

  2. Applications of Rapid Evaluation of Metapopulation Persistence (REMP) in Conservation Planning for Vulnerable Fauna Species

    Science.gov (United States)

    Taylor, Subhashni; Drielsma, Michael; Taylor, Robert; Kumar, Lalit

    2016-06-01

    In many regions species are declining due to fragmentation and loss of habitat. If species persistence is to be achieved, ecologically informed, effective conservation action is required. Yet it remains a challenge to identify optimal places in a landscape to direct habitat reconstruction and management. Rather than relying on individual landscape metrics, process-based regional scale assessment methodology is needed that focuses primarily on species persistence. This means integrating, according to species' ecology, habitat extent, suitability, quality and spatial configuration. The rapid evaluation of metapopulation persistence (REMP) methodology has been developed for this purpose. However, till now no practical conservation planning application of REMP has been described. By integration of expert ecological knowledge, we extended REMP's capabilities to prioritize conservation action for a highly modified agricultural region of central NSW, Australia based on the metapopulation ecology of 34 fauna species. The region's current capacity to support the species was evaluated in relation to the pre-European state for which there was known viability. Six of the species were found to currently have insufficient habitat to support viable populations. Seeking locations to maximize overall improvement in viability for these species, we prioritized conservation action to locations near the threshold of metapopulation persistence.

  3. Hiding in Plain Sight: A Case for Cryptic Metapopulations in Brook Trout (Salvelinus fontinalis.

    Directory of Open Access Journals (Sweden)

    David C Kazyak

    Full Text Available A fundamental issue in the management and conservation of biodiversity is how to define a population. Spatially contiguous fish occupying a stream network have often been considered to represent a single, homogenous population. However, they may also represent multiple discrete populations, a single population with genetic isolation-by-distance, or a metapopulation. We used microsatellite DNA and a large-scale mark-recapture study to assess population structure in a spatially contiguous sample of Brook Trout (Salvelinus fontinalis, a species of conservation concern. We found evidence for limited genetic exchange across small spatial scales and in the absence of barriers to physical movement. Mark-recapture and stationary passive integrated transponder antenna records demonstrated that fish from two tributaries very seldom moved into the opposite tributary, but movements between the tributaries and mainstem were more common. Using Bayesian genetic clustering, we identified two genetic groups that exhibited significantly different growth rates over three years of study, yet survival rates were very similar. Our study highlights the importance of considering the possibility of multiple genetically distinct populations occurring within spatially contiguous habitats, and suggests the existence of a cryptic metapopulation: a spatially continuous distribution of organisms exhibiting metapopulation-like behaviors.

  4. Forest corridors maintain historical gene flow in a tiger metapopulation in the highlands of central India.

    Science.gov (United States)

    Sharma, Sandeep; Dutta, Trishna; Maldonado, Jesús E; Wood, Thomas C; Panwar, Hemendra Singh; Seidensticker, John

    2013-09-22

    Understanding the patterns of gene flow of an endangered species metapopulation occupying a fragmented habitat is crucial for landscape-level conservation planning and devising effective conservation strategies. Tigers (Panthera tigris) are globally endangered and their populations are highly fragmented and exist in a few isolated metapopulations across their range. We used multi-locus genotypic data from 273 individual tigers (Panthera tigris tigris) from four tiger populations of the Satpura-Maikal landscape of central India to determine whether the corridors in this landscape are functional. This 45 000 km(2) landscape contains 17% of India's tiger population and 12% of its tiger habitat. We applied Bayesian and coalescent-based analyses to estimate contemporary and historical gene flow among these populations and to infer their evolutionary history. We found that the tiger metapopulation in central India has high rates of historical and contemporary gene flow. The tests for population history reveal that tigers populated central India about 10 000 years ago. Their population subdivision began about 1000 years ago and accelerated about 200 years ago owing to habitat fragmentation, leading to four spatially separated populations. These four populations have been in migration-drift equilibrium maintained by high gene flow. We found the highest rates of contemporary gene flow in populations that are connected by forest corridors. This information is highly relevant to conservation practitioners and policy makers, because deforestation, road widening and mining are imminent threats to these corridors.

  5. Insights into the strategies used by related group II introns to adapt successfully for the colonisation of a bacterial genome.

    Science.gov (United States)

    Martínez-Rodríguez, Laura; García-Rodríguez, Fernando M; Molina-Sánchez, María Dolores; Toro, Nicolás; Martínez-Abarca, Francisco

    2014-01-01

    Group II introns are self-splicing RNAs and site-specific mobile retroelements found in bacterial and organellar genomes. The group II intron RmInt1 is present at high copy number in Sinorhizobium meliloti species, and has a multifunctional intron-encoded protein (IEP) with reverse transcriptase/maturase activities, but lacking the DNA-binding and endonuclease domains. We characterized two RmInt1-related group II introns RmInt2 from S. meliloti strain GR4 and Sr.md.I1 from S. medicae strain WSM419 in terms of splicing and mobility activities. We used both wild-type and engineered intron-donor constructs based on ribozyme ΔORF-coding sequence derivatives, and we determined the DNA target requirements for RmInt2, the element most distantly related to RmInt1. The excision and mobility patterns of intron-donor constructs expressing different combinations of IEP and intron RNA provided experimental evidence for the co-operation of IEPs and intron RNAs from related elements in intron splicing and, in some cases, in intron homing. We were also able to identify the DNA target regions recognized by these IEPs lacking the DNA endonuclease domain. Our results provide new insight into the versatility of related group II introns and the possible co-operation between these elements to facilitate the colonization of bacterial genomes.

  6. Adaptation of the neutral bacterial comet assay to assess antimicrobial-mediated DNA double-strand breaks in Escherichia coli

    Science.gov (United States)

    SOLANKY, DIPESH; HAYDEL, SHELLEY E.

    2012-01-01

    This study aimed to determine the mechanism of action of a natural antibacterial clay mineral mixture, designated CB, by investigating the induction of DNA double-strand breaks (DSBs) in Escherichia coli. To quantify DNA damage upon exposure to soluble antimicrobial compounds, we modified a bacterial neutral comet assay, which primarily associates the general length of an electrophoresed chromosome, or comet, with the degree of DSB-associated DNA damage. To appropriately account for antimicrobial-mediated strand fragmentation, suitable control reactions consisting of exposures to water, ethanol, kanamycin, and bleomycin were developed and optimized for the assay. Bacterial exposure to the CB clay resulted in significantly longer comet lengths, compared to water and kanamycin exposures, suggesting that the induction of DNA DSBs contributes to the killing activity of this antibacterial clay mineral mixture. The comet assay protocol described herein provides a general technique for evaluating soluble antimicrobial-derived DNA damage and for comparing DNA fragmentation between experimental and control assays. PMID:22940101

  7. The post-transcriptional regulator CsrA plays a central role in the adaptation of bacterial pathogens to different stages of infection in animal hosts.

    Science.gov (United States)

    Lucchetti-Miganeh, Céline; Burrowes, Elizabeth; Baysse, Christine; Ermel, Gwennola

    2008-01-01

    The importance of Csr post-transcriptional systems is gradually emerging; these systems control a variety of virulence-linked physiological traits in many pathogenic bacteria. This review focuses on the central role that Csr systems play in the pathogenesis of certain bacteria and in the establishment of successful infections in animal hosts. Csr systems appear to control the 'switch' between different physiological states in the infection process; for example switching pathogens from a colonization state to a persistence state. Csr systems are controlled by two-component sensor/regulator systems and by non-coding RNAs. In addition, recent findings suggest that the RNA chaperone Hfq may play an integral role in Csr-mediated bacterial adaptation to the host environment.

  8. Short- and long-term biomarkers for bacterial robustness: a framework for quantifying correlations between cellular indicators and adaptive behavior.

    Directory of Open Access Journals (Sweden)

    Heidy M W den Besten

    Full Text Available The ability of microorganisms to adapt to changing environments challenges the prediction of their history-dependent behavior. Cellular biomarkers that are quantitatively correlated to stress adaptive behavior will facilitate our ability to predict the impact of these adaptive traits. Here, we present a framework for identifying cellular biomarkers for mild stress induced enhanced microbial robustness towards lethal stresses. Several candidate-biomarkers were selected by comparing the genome-wide transcriptome profiles of our model-organism Bacillus cereus upon exposure to four mild stress conditions (mild heat, acid, salt and oxidative stress. These candidate-biomarkers--a transcriptional regulator (activating general stress responses, enzymes (removing reactive oxygen species, and chaperones and proteases (maintaining protein quality--were quantitatively determined at transcript, protein and/or activity level upon exposure to mild heat, acid, salt and oxidative stress for various time intervals. Both unstressed and mild stress treated cells were also exposed to lethal stress conditions (severe heat, acid and oxidative stress to quantify the robustness advantage provided by mild stress pretreatment. To evaluate whether the candidate-biomarkers could predict the robustness enhancement towards lethal stress elicited by mild stress pretreatment, the biomarker responses upon mild stress treatment were correlated to mild stress induced robustness towards lethal stress. Both short- and long-term biomarkers could be identified of which their induction levels were correlated to mild stress induced enhanced robustness towards lethal heat, acid and/or oxidative stress, respectively, and are therefore predictive cellular indicators for mild stress induced enhanced robustness. The identified biomarkers are among the most consistently induced cellular components in stress responses and ubiquitous in biology, supporting extrapolation to other microorganisms

  9. Effects of city-size heterogeneity on epidemic spreading in a metapopulation: A reaction-diffusion approach

    CERN Document Server

    Lund, Halvor; Simonsen, Ingve

    2012-01-01

    We review and introduce a generalized reaction-diffusion approach to epidemic spreading in a metapopulation modeled as a complex network. The metapopulation consists of susceptible and infected individuals that are grouped in subpopulations symbolising cities and villages that are coupled by human travel in a transportation network. By analytic methods and numerical simulations we calculate the fraction of infected people in the metaopoluation in the long time limit, as well as the relevant parameters characterising the epidemic threshold that separates an epidemic from a non-epidemic phase. Within this model, we investigate the effect of a heterogeneous network topology and a heterogeneous subpopulation size distribution. Such a system is suited for epidemic modeling where small villages and big cities exist simultaneously in the metapopulation. We find that the heterogeneous conditions cause the epidemic threshold to be a non-trivial function of the reaction rates (local parameters), the network's topology ...

  10. Advances in studies on metapopulation dynamics%复合种群动态研究进展

    Institute of Scientific and Technical Information of China (English)

    黄世能; 王伯荪

    2001-01-01

    复合种群动态研究是当今保护生物学和生态学中最热门的课题之一。在此较为详细地介绍了复合种群动态的有关概念和术语、经验研究和理论探索的最新进展以及相关的预测模型,对我国开展相关研究有参考价值。%Study of metapopulation dynamics is one of the most important subjects in modern conservation biology and ecology. In this paper, the key metapopulation terms, advances in empirical and theoretical approaches and predictive models in relation to metapopulation dynamics as well as their implications for biological conser vation practices were outlined.

  11. Linking local retention, self-recruitment, and persistence in marine metapopulations

    KAUST Repository

    Lett, Christophe

    2015-08-01

    Three indices of larval retention have been used in the literature to assess the tendency for self-maintenance of local marine populations: local retention (LR), self-recruitment (SR), and relative local retention (RLR). Only one of these, LR, defined as the ratio of locally produced settlement to local egg production, has a clear relationship to self-persistence of individual sites. However, SR, the ratio of locally produced settlement to settlement of all origins at a site, is generally easier to measure experimentally. We use theoretical, simulation, and empirical approaches to bridge the gap between these different indices, and demonstrate that there is a proportional relationship between SR and LR for metapopulations close to a stable state and with lifetime egg production (LEP) approximately uniform over space. Similarly, for systems where larval mortality rates are a relatively uniform function of release site, RLR (defined as the ratio of locally produced settlement to all settlement of local origin) and LR will also be proportional. Therefore, SR and RLR provide information on relative rates of LR for systems satisfying these conditions. Furthermore, the ratio between LR and SR can be used to evaluate global persistence of metapopulations, and therefore provides valuable information not necessarily available if only LR is considered.

  12. The maintenance of genetic variation due to asymmetric gene flow in dendritic metapopulations.

    Science.gov (United States)

    Morrissey, Michael B; de Kerckhove, Derrick T

    2009-12-01

    Dendritic landscapes can have ecological properties that differ importantly from simpler spatial arrangements of habitats. Most dendritic landscapes are structured by elevation, and therefore, migration is likely to be directionally biased. While the population-genetic consequences of both dendritic landscape arrangements and asymmetric migration have begun to be studied, these processes have not been considered together. Simple conceptual models predict that if migration into branch (headwater) populations is limited, such populations can act as reservoirs for potentially unique alleles. As a consequence of the fact that dendritic landscapes have, by definition, more branches than internal habitat patches, this process may lead to the maintenance of higher overall genetic diversities in metapopulations inhabiting dendritic networks where migration is directionally biased. Here we begin to address the generality of these simple predictions using genetic models and a review of empirical literature. We show, for a range of demographic parameters, that dendritic systems with asymmetric migration can maintain levels of genetic variation that are very different, sometimes very elevated, compared with more classical models of geographical population structure. Furthermore, predicted patterns of genetic variation within metapopulations--that is, stepwise increases in genetic diversity at nodes--do occur in some empirical data.

  13. Hierarchical modeling and inference in ecology: The analysis of data from populations, metapopulations and communities

    Science.gov (United States)

    Royle, J. Andrew; Dorazio, Robert M.

    2008-01-01

    A guide to data collection, modeling and inference strategies for biological survey data using Bayesian and classical statistical methods. This book describes a general and flexible framework for modeling and inference in ecological systems based on hierarchical models, with a strict focus on the use of probability models and parametric inference. Hierarchical models represent a paradigm shift in the application of statistics to ecological inference problems because they combine explicit models of ecological system structure or dynamics with models of how ecological systems are observed. The principles of hierarchical modeling are developed and applied to problems in population, metapopulation, community, and metacommunity systems. The book provides the first synthetic treatment of many recent methodological advances in ecological modeling and unifies disparate methods and procedures. The authors apply principles of hierarchical modeling to ecological problems, including * occurrence or occupancy models for estimating species distribution * abundance models based on many sampling protocols, including distance sampling * capture-recapture models with individual effects * spatial capture-recapture models based on camera trapping and related methods * population and metapopulation dynamic models * models of biodiversity, community structure and dynamics.

  14. Comprehensive analysis of an Antarctic bacterial community with the adaptability of growth at higher temperatures than those in Antarctica.

    Science.gov (United States)

    Hosoi-Tanabe, Shoko; Zhang, Hongyan; Zhu, Daochen; Nagata, Shinichi; Ban, Syuhei; Imura, Satoshi

    2010-06-01

    To investigate the adaptability to higher temperatures of Antarctic microorganisms persisting in low temperature conditions for a long time, Antarctic lake samples were incubated in several selection media at 25 degrees C and 30 degrees C. The microorganisms did not grow at 30 degrees C; however, some of them grew at 25 degrees C, indicating that the bacteria in Antarctic have the ability to grow at a wide range of temperatures. Total DNA was extracted from these microorganisms and amplified using the bacteria-universal primers. The amplified fragments were cloned, and randomly selected 48 clones were sequenced. The sequenced clones showed high similarity to the alpha-subdivision of the Proteobacteria with specific affinity to the genus Agrobacterium, Caulobacter and Brevundimonas, the ss-subdivision of Proteobacteria with specific affinity to the genus Cupriavidus, and Bacillus of the phylum Firmicutes. These results showed the presence of universal genera, suggesting that the bacteria in the Antarctic lake were not specific to this environment.

  15. Geographical patterns of dominant bivalves and a polychaete in Europe: no metapopulations in the marine coastal zone?

    NARCIS (Netherlands)

    Hummel, H.

    2003-01-01

    The genetic diversity, differentiation and performance of some dominant invertebrates in the marine coastal zone of Europe are reviewed in order to discuss the use of the metapopulation concept in the marine coastal realm. A consistently high genetic diversity of the species studied (mussels of the

  16. The emergence of the rescue effect from explicit within and between-patch dynamics in a metapopulation

    KAUST Repository

    Eriksson, Anders

    2014-02-12

    Immigration can rescue local populations from extinction, helping to stabilize a metapopulation. Local population dynamics is important for determining the strength of this rescue effect, but the mechanistic link between local demographic parameters and the rescue effect at the metapopulation level has received very little attention by modellers. We develop an analytical framework that allows us to describe the emergence of the rescue effect from interacting local stochastic dynamics. We show this framework to be applicable to a wide range of spatial scales, providing a powerful and convenient alternative to individual-based models for making predictions concerning the fate of metapopulations. We show that the rescue effect plays an important role in minimizing the increase in local extinction probability associated with high demographic stochasticity, but its role is more limited in the case of high local environmental stochasticity of recruitment or survival. While most models postulate the rescue effect, our framework provides an explicit mechanistic link between local dynamics and the emergence of the rescue effect, and more generally the stability of the whole metapopulation. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  17. A portrait of a sucker using landscape genetics: how colonization and life history undermine the idealized dendritic metapopulation.

    Science.gov (United States)

    Salisbury, Sarah J; McCracken, Gregory R; Keefe, Donald; Perry, Robert; Ruzzante, Daniel E

    2016-09-01

    Dendritic metapopulations have been attributed unique properties by in silico studies, including an elevated genetic diversity relative to a panmictic population of equal total size. These predictions have not been rigorously tested in nature, nor has there been full consideration of the interacting effects among contemporary landscape features, colonization history and life history traits of the target species. We tested for the effects of dendritic structure as well as the relative importance of life history, environmental barriers and historical colonization on the neutral genetic structure of a longnose sucker (Catostomus catostomus) metapopulation in the Kogaluk watershed of northern Labrador, Canada. Samples were collected from eight lakes, genotyped with 17 microsatellites, and aged using opercula. Lakes varied in differentiation, historical and contemporary connectivity, and life history traits. Isolation by distance was detected only by removing two highly genetically differentiated lakes, suggesting a lack of migration-drift equilibrium and the lingering influence of historical factors on genetic structure. Bayesian analyses supported colonization via the Kogaluk's headwaters. The historical concentration of genetic diversity in headwaters inferred by this result was supported by high historical and contemporary effective sizes of the headwater lake, T-Bone. Alternatively, reduced allelic richness in headwaters confirmed the dendritic structure's influence on gene flow, but this did not translate to an elevated metapopulation effective size. A lack of equilibrium and upstream migration may have dampened the effects of dendritic structure. We suggest that interacting historical and contemporary factors prevent the achievement of the idealized traits of a dendritic metapopulation in nature.

  18. Matrix matters: differences of grand skink metapopulation parameters in native tussock grasslands and exotic pasture grasslands.

    Directory of Open Access Journals (Sweden)

    Konstanze Gebauer

    Full Text Available Modelling metapopulation dynamics is a potentially very powerful tool for conservation biologists. In recent years, scientists have broadened the range of variables incorporated into metapopulation modelling from using almost exclusively habitat patch size and isolation, to the inclusion of attributes of the matrix and habitat patch quality. We investigated the influence of habitat patch and matrix characteristics on the metapopulation parameters of a highly endangered lizard species, the New Zealand endemic grand skink (Oligosoma grande taking into account incomplete detectability. The predictive ability of the developed zxmetapopulation model was assessed through cross-validation of the data and with an independent data-set. Grand skinks occur on scattered rock-outcrops surrounded by indigenous tussock (bunch and pasture grasslands therefore implying a metapopulation structure. We found that the type of matrix surrounding the habitat patch was equally as important as the size of habitat patch for estimating occupancy, colonisation and extinction probabilities. Additionally, the type of matrix was more important than the physical distance between habitat patches for colonisation probabilities. Detection probability differed between habitat patches in the two matrix types and between habitat patches with different attributes such as habitat patch composition and abundance of vegetation on the outcrop. The developed metapopulation models can now be used for management decisions on area protection, monitoring, and the selection of translocation sites for the grand skink. Our study showed that it is important to incorporate not only habitat patch size and distance between habitat patches, but also those matrix type and habitat patch attributes which are vital in the ecology of the target species.

  19. Matrix matters: differences of grand skink metapopulation parameters in native tussock grasslands and exotic pasture grasslands.

    Science.gov (United States)

    Gebauer, Konstanze; Dickinson, Katharine J M; Whigham, Peter A; Seddon, Philip J

    2013-01-01

    Modelling metapopulation dynamics is a potentially very powerful tool for conservation biologists. In recent years, scientists have broadened the range of variables incorporated into metapopulation modelling from using almost exclusively habitat patch size and isolation, to the inclusion of attributes of the matrix and habitat patch quality. We investigated the influence of habitat patch and matrix characteristics on the metapopulation parameters of a highly endangered lizard species, the New Zealand endemic grand skink (Oligosoma grande) taking into account incomplete detectability. The predictive ability of the developed zxmetapopulation model was assessed through cross-validation of the data and with an independent data-set. Grand skinks occur on scattered rock-outcrops surrounded by indigenous tussock (bunch) and pasture grasslands therefore implying a metapopulation structure. We found that the type of matrix surrounding the habitat patch was equally as important as the size of habitat patch for estimating occupancy, colonisation and extinction probabilities. Additionally, the type of matrix was more important than the physical distance between habitat patches for colonisation probabilities. Detection probability differed between habitat patches in the two matrix types and between habitat patches with different attributes such as habitat patch composition and abundance of vegetation on the outcrop. The developed metapopulation models can now be used for management decisions on area protection, monitoring, and the selection of translocation sites for the grand skink. Our study showed that it is important to incorporate not only habitat patch size and distance between habitat patches, but also those matrix type and habitat patch attributes which are vital in the ecology of the target species.

  20. The Bartonella quintana Extracytoplasmic Function Sigma Factor RpoE Has a Role in Bacterial Adaptation to the Arthropod Vector Environment

    Science.gov (United States)

    Abromaitis, Stephanie

    2013-01-01

    Bartonella quintana is a vector-borne bacterial pathogen that causes fatal disease in humans. During the infectious cycle, B. quintana transitions from the hemin-restricted human bloodstream to the hemin-rich body louse vector. Because extracytoplasmic function (ECF) sigma factors often regulate adaptation to environmental changes, we hypothesized that a previously unstudied B. quintana ECF sigma factor, RpoE, is involved in the transition from the human host to the body louse vector. The genomic context of B. quintana rpoE identified it as a member of the ECF15 family of sigma factors found only in alphaproteobacteria. ECF15 sigma factors are believed to be the master regulators of the general stress response in alphaproteobacteria. In this study, we examined the B. quintana RpoE response to two stressors that are encountered in the body louse vector environment, a decreased temperature and an increased hemin concentration. We determined that the expression of rpoE is significantly upregulated at the body louse (28°C) versus the human host (37°C) temperature. rpoE expression also was upregulated when B. quintana was exposed to high hemin concentrations. In vitro and in vivo analyses demonstrated that RpoE function is regulated by a mechanism involving the anti-sigma factor NepR and the response regulator PhyR. The ΔrpoE ΔnepR mutant strain of B. quintana established that RpoE-mediated transcription is important in mediating the tolerance of B. quintana to high hemin concentrations. We present the first analysis of an ECF15 sigma factor in a vector-borne human pathogen and conclude that RpoE has a role in the adaptation of B. quintana to the hemin-rich arthropod vector environment. PMID:23564167

  1. The RpfB-Dependent Quorum Sensing Signal Turnover System Is Required for Adaptation and Virulence in Rice Bacterial Blight Pathogen Xanthomonas oryzae pv. oryzae.

    Science.gov (United States)

    Wang, Xing-Yu; Zhou, Lian; Yang, Jun; Ji, Guang-Hai; He, Ya-Wen

    2016-03-01

    Xanthomonas oryzae pv. oryzae, the bacterial blight pathogen of rice, produces diffusible signal factor (DSF) family quorum sensing signals to regulate virulence. The biosynthesis and perception of DSF family signals require components of the rpf (regulation of pathogenicity factors) cluster. In this study, we report that RpfB plays an essential role in DSF family signal turnover in X. oryzae pv. oryzae PXO99A. The production of DSF family signals was boosted by deletion of the rpfB gene and was abolished by its overexpression. The RpfC/RpfG-mediated DSF signaling system negatively regulates rpfB expression via the global transcription regulator Clp, whose activity is reversible in the presence of cyclic diguanylate monophosphate. These findings indicate that the DSF family signal turnover system in PXO99A is generally consistent with that in Xanthomonas campestris pv. campestris. Moreover, this study has revealed several specific roles of RpfB in PXO99A. First, the rpfB deletion mutant produced high levels of DSF family signals but reduced extracellular polysaccharide production, extracellular amylase activity, and attenuated pathogenicity. Second, the rpfB/rpfC double-deletion mutant was partially deficient in xanthomonadin production. Taken together, the RpfB-dependent DSF family signal turnover system is a conserved and naturally presenting signal turnover system in Xanthomonas spp., which plays unique roles in X. oryzae pv. oryzae adaptation and pathogenesis.

  2. Local enrichment and its nonlocal consequences for victim-exploiter metapopulations

    CERN Document Server

    Yaari, Gur; Schiffer, Marcelo; Shnerb, Nadav M

    2008-01-01

    The stabilizing effects of local enrichment are revisited. Diffusively coupled host-parasitoid and predator-prey metapopulations are shown to admit a stable fixed point, limit cycle or stable torus with a rich bifurcation structure. A linear toy model that yields many of the basic qualitative features of this system is presented. The further nonlinear complications are analyzed in the framework of the marginally stable Lotka-Volterra model, and the continuous time analog of the unstable, host-parasitoid Nicholson-Bailey model. The dependence of the results on the migration rate and level of spatial variations is examined, and the possibility of "nonlocal" effect of enrichment, where local enrichment induces stable oscillations at a distance, is studied. A simple method for basic estimation of the relative importance of this effect in experimental systems is presented and exemplified.

  3. Metapopulation dynamics enable persistence of influenza A, including A/H5N1, in poultry.

    Science.gov (United States)

    Hosseini, Parviez Rana; Fuller, Trevon; Harrigan, Ryan; Zhao, Delong; Arriola, Carmen Sofia; Gonzalez, Armandoe; Miller, Matthew Joshua; Xiao, Xiangming; Smith, Tom B; Jones, Jamie Holland; Daszak, Peter

    2013-01-01

    Highly pathogenic influenza A/H5N1 has persistently but sporadically caused human illness and death since 1997. Yet it is still unclear how this pathogen is able to persist globally. While wild birds seem to be a genetic reservoir for influenza A, they do not seem to be the main source of human illness. Here, we highlight the role that domestic poultry may play in maintaining A/H5N1 globally, using theoretical models of spatial population structure in poultry populations. We find that a metapopulation of moderately sized poultry flocks can sustain the pathogen in a finite poultry population for over two years. Our results suggest that it is possible that moderately intensive backyard farms could sustain the pathogen indefinitely in real systems. This fits a pattern that has been observed from many empirical systems. Rather than just employing standard culling procedures to control the disease, our model suggests ways that poultry production systems may be modified.

  4. Exact solution for a metapopulation version of Schelling’s model

    Science.gov (United States)

    Durrett, Richard; Zhang, Yuan

    2014-01-01

    In 1971, Schelling introduced a model in which families move if they have too many neighbors of the opposite type. In this paper, we will consider a metapopulation version of the model in which a city is divided into N neighborhoods, each of which has L houses. There are ρNL red families and ρNL blue families for some ρ ρb, a new segregated equilibrium appears; for ρb < ρ < ρd, there is bistability, but when ρ increases past ρd the random state is no longer stable. When ρc is small enough, the random state will again be the stationary distribution when ρ is close to 1/2. If so, this is preceded by a region of bistability. PMID:25225367

  5. Node discovery in meta-population network behind infectious disease outbreak

    CERN Document Server

    Maeno, Yoshiharu

    2010-01-01

    Stochasticity and spatial heterogeneity are of great interest recently in studying the spread of an infectious disease. Populations in a combination of epidemiological compartment models and a meta-population network model are described by stochastic differential equations. The presented method solves a node discovery problem to identify the nodes within a given dataset which are directly influenced by an unknown neighboring node during the spread. The dataset is either the time sequence data on the number of infectious persons or new cases in the early growth phase of an infectious disease outbreak. The network topology and transmission parameters are revealed by the maximal likelihood estimation. The degree of influence on individual nodes from an unknown origin is calculated with the technique of the extreme sequence detection given the revealed topology and parameters. The method is tested with computationally synthesized datasets and the WHO dataset on SARS outbreak.

  6. Find the weakest link. A comparison between demographic, genetic and demo-genetic metapopulation extinction times

    Directory of Open Access Journals (Sweden)

    Robert Alexandre

    2011-09-01

    Full Text Available Abstract Background While the ultimate causes of most species extinctions are environmental, environmental constraints have various secondary consequences on evolutionary and ecological processes. The roles of demographic, genetic mechanisms and their interactions in limiting the viabilities of species or populations have stirred much debate and remain difficult to evaluate in the absence of demography-genetics conceptual and technical framework. Here, I computed projected times to metapopulation extinction using (1 a model focusing on the effects of species properties, habitat quality, quantity and temporal variability on the time to demographic extinction; (2 a genetic model focusing on the dynamics of the drift and inbreeding loads under the same species and habitat constraints; (3 a demo-genetic model accounting for demographic-genetic processes and feedbacks. Results Results indicate that a given population may have a high demographic, but low genetic viability or vice versa; and whether genetic or demographic aspects will be the most limiting to overall viability depends on the constraints faced by the species (e.g., reduction of habitat quantity or quality. As a consequence, depending on metapopulation or species characteristics, incorporating genetic considerations to demographically-based viability assessments may either moderately or severely reduce the persistence time. On the other hand, purely genetically-based estimates of species viability may either underestimate (by neglecting demo-genetic interactions or overestimate (by neglecting the demographic resilience true viability. Conclusion Unbiased assessments of the viabilities of species may only be obtained by identifying and considering the most limiting processes (i.e., demography or genetics, or, preferentially, by integrating them.

  7. Initial genetic diversity enhances population establishment and alters genetic structuring of a newly established Daphnia metapopulation.

    Science.gov (United States)

    Holmes, Christopher J; Pantel, Jelena H; Schulz, Kimberly L; Cáceres, Carla E

    2016-07-01

    When newly created habitats are initially colonized by genotypes with rapid population growth rates, later arriving colonists may be prevented from establishing. Although these priority effects have been documented in multiple systems, their duration may be influenced by the diversity of the founding population. We conducted a large-scale field manipulation to investigate how initial clonal diversity influences temporal and landscape patterns of genetic structure in a developing metapopulation. Six genotypes of obligately asexual Daphnia pulex were stocked alone (no clonal diversity) or in combination ('high' clonal diversity) into newly created experimental woodland ponds. We also measured the population growth rate of all clones in the laboratory when raised on higher-quality and lower-quality resources. Our predictions were that in the 3 years following stocking, clonally diverse populations would be more likely to persist than nonclonally diverse populations and exhibit evidence for persistent founder effects. We expected that faster growing clones would be found in more pools and comprise a greater proportion of individuals genotyped from the landscape. Genetic composition, both locally and regionally, changed significantly following stocking. Six of 27 populations exhibited evidence for persistent founder effects, and populations stocked with 'high' clonal diversity were more likely to exhibit these effects than nonclonally diverse populations. Performance in the laboratory was not predictive of clonal persistence or overall dominance in the field. Hence, we conclude that although laboratory estimates of fitness did not fully explain metapopulation genetic structure, initial clonal diversity did enhance D. pulex population establishment and persistence in this system.

  8. Local competition and metapopulation processes drive long-term seagrass-epiphyte population dynamics.

    Science.gov (United States)

    Lobelle, Delphine; Kenyon, Emma J; Cook, Kevan J; Bull, James C

    2013-01-01

    It is well known that ecological processes such as population regulation and natural enemy interactions potentially occur over a range of spatial scales, and there is a substantial body of literature developing theoretical understanding of the interplay between these processes. However, there are comparatively few studies quantifying the long-term effects of spatial scaling in natural ecosystems. A key challenge is that trophic complexity in real-world biological communities quickly obscures the signal from a focal process. Seagrass meadows provide an excellent opportunity in this respect: in many instances, seagrasses effectively form extensive natural monocultures, in which hypotheses about endogenous dynamics can be formulated and tested. We present amongst the longest unbroken, spatially explict time series of seagrass abundance published to date. Data include annual measures of shoot density, total above-ground abundance, and associated epiphyte cover from five Zostera marina meadows distributed around the Isles of Scilly, UK, from 1996 to 2011. We explore empirical patterns at the local and metapopulation scale using standard time series analysis and develop a simple population dynamic model, testing the hypothesis that both local and metapopulation scale feedback processes are important. We find little evidence of an interaction between scales in seagrass dynamics but that both scales contribute approximately equally to observed local epiphyte abundance. By quantifying the long-term dynamics of seagrass-epiphyte interactions we show how measures of density and extent are both important in establishing baseline information relevant to predicting responses to environmental change and developing management plans. We hope that this study complements existing mechanistic studies of physiology, genetics and productivity in seagrass, whilst highlighting the potential of seagrass as a model ecosystem. More generally, this study provides a rare opportunity to test

  9. The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems.

    Directory of Open Access Journals (Sweden)

    Sophie S Abby

    2012-09-01

    Full Text Available Type 3 secretion systems (T3SSs are essential components of two complex bacterial machineries: the flagellum, which drives cell motility, and the non-flagellar T3SS (NF-T3SS, which delivers effectors into eukaryotic cells. Yet the origin, specialization, and diversification of these machineries remained unclear. We developed computational tools to identify homologous components of the two systems and to discriminate between them. Our analysis of >1,000 genomes identified 921 T3SSs, including 222 NF-T3SSs. Phylogenomic and comparative analyses of these systems argue that the NF-T3SS arose from an exaptation of the flagellum, i.e. the recruitment of part of the flagellum structure for the evolution of the new protein delivery function. This reconstructed chronology of the exaptation process proceeded in at least two steps. An intermediate ancestral form of NF-T3SS, whose descendants still exist in Myxococcales, lacked elements that are essential for motility and included a subset of NF-T3SS features. We argue that this ancestral version was involved in protein translocation. A second major step in the evolution of NF-T3SSs occurred via recruitment of secretins to the NF-T3SS, an event that occurred at least three times from different systems. In rhizobiales, a partial homologous gene replacement of the secretin resulted in two genes of complementary function. Acquisition of a secretin was followed by the rapid adaptation of the resulting NF-T3SSs to multiple, distinct eukaryotic cell envelopes where they became key in parasitic and mutualistic associations between prokaryotes and eukaryotes. Our work elucidates major steps of the evolutionary scenario leading to extant NF-T3SSs. It demonstrates how molecular evolution can convert one complex molecular machine into a second, equally complex machine by successive deletions, innovations, and recruitment from other molecular systems.

  10. The different sources of variation in inbreeding depression, heterosis and outbreeding depression in a metapopulation of Physa acuta.

    Science.gov (United States)

    Escobar, Juan Sebastián; Nicot, Antoine; David, Patrice

    2008-11-01

    Understanding how parental distance affects offspring fitness, i.e., the effects of inbreeding and outbreeding in natural populations, is a major goal in evolutionary biology. While inbreeding is often associated with fitness reduction (inbreeding depression), interpopulation outcrossing may have either positive (heterosis) or negative (outbreeding depression) effects. Within a metapopulation, all phenomena may occur with various intensities depending on the focal population (especially its effective size) and the trait studied. However, little is known about interpopulation variation at this scale. We here examine variation in inbreeding depression, heterosis, and outbreeding depression on life-history traits across a full-life cycle, within a metapopulation of the hermaphroditic snail Physa acuta. We show that all three phenomena can co-occur at this scale, although they are not always expressed on the same traits. A large variation in inbreeding depression, heterosis, and outbreeding depression is observed among local populations. We provide evidence that, as expected from theory, small and isolated populations enjoy higher heterosis upon outcrossing than do large, open populations. These results emphasize the need for an integrated theory accounting for the effects of both deleterious mutations and genetic incompatibilities within metapopulations and to take into account the variability of the focal population to understand the genetic consequences of inbreeding and outbreeding at this scale.

  11. 基于菌群自适应觅食的公交调度建模仿真与优化%Adaptive Bacterial Foraging Optimization and Its Application for Bus Scheduling

    Institute of Scientific and Technical Information of China (English)

    高政威; 庞哈利; 汪定伟

    2011-01-01

    提出了一种新型群体智能优化方法—菌群自适应搜索算法(Adaptive Bacterial Foraging Optimization,ABFO)。ABFO算法在细菌觅食算法(Bacterial Foraging Optimization,BFO)研究工作的基础上,将细菌的趋化行为,群体感应机制和自适应搜索策略相集成,体现细菌个体通过信息交流与合作在群体层面表现出更高智能行为的特性。此外,ABFO算法的自适应策略动态地控制人工细菌的趋化步长,从而能够在运行时有效地平衡算法的探索和开发能力。然后,基于ABFO%A variation on the original BFO algorithm,called the Adaptive Bacterial Foraging Optimization(ABFO) was proposed,which employed chemotactic behavior,quorum sensing,and adaptive foraging strategy to significantly improve the performance of the original algorithm.This improvement was achieved by enabling the bacterial foraging algorithm to adjust the run-length unit parameter dynamically during algorithm execution in order to balance the exploration/exploitation tradeoff.ABFO was then applied to schedule the bus departing interval by minimizing the average of passengers' waiting time and public transportation company's total running times in one day.Simulation results demonstrate that the ABFO algorithm is more feasible and efficient.

  12. Quantifying the importance of patch-specific changes in habitat to metapopulation viability of an endangered songbird.

    Science.gov (United States)

    Horne, Jon S; Strickler, Katherine M; Alldredge, Mathew

    2011-10-01

    A growing number of programs seek to facilitate species conservation using incentive-based mechanisms. Recently, a market-based incentive program for the federally endangered Golden-cheeked Warbler (Dendroica chrysoparia) was implemented on a trial basis at Fort Hood, an Army training post in Texas, USA. Under this program, recovery credits accumulated by Fort Hood through contracts with private landowners are used to offset unintentional loss of breeding habitat of Golden-cheeked Warblers within the installation. Critical to successful implementation of such programs is the ability to value, in terms of changes to overall species viability, both habitat loss and habitat restoration or protection. In this study, we sought to answer two fundamental questions: Given the same amount of change in breeding habitat, does the change in some patches have a greater effect on metapopulation persistence than others? And if so, can characteristics of a patch (e.g., size or spatial location) be used to predict how the metapopulation will respond to these changes? To answer these questions, we describe an approach for using sensitivity analysis of a metapopulation projection model to predict how changes to specific habitat patches would affect species viability. We used a stochastic, discrete-time projection model based on stage-specific estimates of survival and fecundity, as well as various assumptions about dispersal among populations. To assess a particular patch's leverage, we quantified how much metapopulation viability was expected to change in response to changing the size of that patch. We then related original patch size and distance from the largest patch to each patch's leverage to determine if general patch characteristics could be used to develop guidelines for valuing changes to patches within a metapopulation. We found that both the characteristic that best predicted patch leverage and the magnitude of the relationship changed under different model scenarios

  13. Metapopulation dynamics enable persistence of influenza A, including A/H5N1, in poultry.

    Directory of Open Access Journals (Sweden)

    Parviez Rana Hosseini

    Full Text Available Highly pathogenic influenza A/H5N1 has persistently but sporadically caused human illness and death since 1997. Yet it is still unclear how this pathogen is able to persist globally. While wild birds seem to be a genetic reservoir for influenza A, they do not seem to be the main source of human illness. Here, we highlight the role that domestic poultry may play in maintaining A/H5N1 globally, using theoretical models of spatial population structure in poultry populations. We find that a metapopulation of moderately sized poultry flocks can sustain the pathogen in a finite poultry population for over two years. Our results suggest that it is possible that moderately intensive backyard farms could sustain the pathogen indefinitely in real systems. This fits a pattern that has been observed from many empirical systems. Rather than just employing standard culling procedures to control the disease, our model suggests ways that poultry production systems may be modified.

  14. Sulfolobus islandicus meta-populations in Yellowstone National Park hot springs.

    Science.gov (United States)

    Campbell, Kate M; Kouris, Angela; England, Whitney; Anderson, Rika E; McCleskey, R Blaine; Nordstrom, D Kirk; Whitaker, Rachel J

    2017-03-09

    Abiotic and biotic forces shape the structure and evolution of microbial populations. We investigated forces that shape the spatial and temporal population structure of Sulfolobus islandicus by comparing geochemical and molecular analysis from seven hot springs in five regions sampled over three years in Yellowstone National Park. Through deep amplicon sequencing, we uncovered 148 unique alleles at two loci whose relative frequency provides clear evidence for independent populations in different hot springs. Although geography controls regional geochemical composition and population differentiation, temporal changes in population were not explained by corresponding variation in geochemistry. The data suggest that the influence of extinction, bottleneck events, and/or selective sweeps within a spring and low migration between springs shape these populations. We suggest that hydrologic events such as storm events and surface snowmelt runoff destabilize smaller hot spring environments with smaller populations and result in high variation in the S. islandicus population over time. Therefore, physical abiotic features such as hot spring size and position in the landscape are important factors shaping the stability and diversity of the S. islandicus meta-population within Yellowstone National Park. This article is protected by copyright. All rights reserved.

  15. Patterns and persistence of larval retention and connectivity in a marine fish metapopulation

    KAUST Repository

    Saenz Agudelo, Pablo

    2012-08-14

    Connectivity, the demographic linking of local populations through the dispersal of individuals, is one of the most poorly understood processes in population dynamics, yet has profound implications for conservation and harvest strategies. For marine species with pelagic larvae, direct estimation of connectivity remains logistically challenging and has mostly been limited to single snapshots in time. Here, we document seasonal and interannual patterns of larval dispersal in a metapopulation of the coral reef fish Amphiprion polymnus. A 3-year record of larval trajectories within and among nine discrete local populations from an area of approximately 35 km was established by determining the natal origin of settled juveniles through DNA parentage analysis. We found that spatial patterns of both self-recruitment and connectivity were remarkably consistent over time, with a low level of self-recruitment at the scale of individual sites. Connectivity among sites was common and multidirectional in all years and was not significantly influenced by seasonal variability of predominant surface current directions. However, approximately 75% of the sampled juveniles could not be assigned to parents within the study area, indicating high levels of immigrations from sources outside the study area. The data support predictions that the magnitude and temporal stability of larval connectivity decreases significantly with increasing distance between subpopulations, but increases with the size of subpopulations. Given the considerable effort needed to directly measure larval exchange, the consistent patterns suggest snapshot parentage analyses can provide useful dispersal estimates to inform spatial management decisions. © 2012 Blackwell Publishing Ltd.

  16. Metapopulation structure in the lagoon cockle Cerastoderma lamarcki in the northern Wadden Sea

    Science.gov (United States)

    Reise, Karsten

    2003-01-01

    Benthic invertebrates in discontinuous inshore habitats and with short or no pelagic larval dispersal are likely to exhibit regional metapopulation dynamics with partially isolated local populations. Near the island of Sylt, the bivalve Cerastoderma (Cardium) lamarcki (Reeve, 1844, syn. in part with C. glaucum Bruguiére, 1789) was widespread in intertidal seagrass beds, coexisting with the sibling species C. edule (Linné, 1758). However, the last C. lamarcki in this habitat was found in 1980. At present the lagoon cockle is restricted to disjunct ditches, creeks and ponds within island salt marshes. There it differs in year-class structure between localities. Successful recruitment events did not coincide. At one locality, a period with regular recruitment was followed by 5 years of recruitment failure, resulting in an overaged population probably at the rim of extinction. In a nearby brackish pond, extinction was followed by recolonization 3 years later. Other lagoonal habitats which seem to be suitable are without cockles. It is speculated that small and isolated habitats occasionally receive colonizers by eggs and juveniles adhering to avian vectors.

  17. On biodiversity in river networks: A trade-off metapopulation model and comparative analysis

    Science.gov (United States)

    Muneepeerakul, R.; Levin, S. A.; Rinaldo, A.; Rodriguez-Iturbe, I.

    2007-07-01

    A discrete, structured metapopulation model is coupled with the strictly hierarchical competition-colonization trade-off model, in which competitively superior species have lower fecundity rates and thus lower colonizing ability, to study the resulting biodiversity patterns in river networks. These patterns are then compared with those resulting from the neutral dynamics, in which every species has the same fecundity rate and is competitively equivalent at a per capita level. Significant differences exist between riparian biodiversity patterns and those predicted by theories developed for two-dimensional landscapes. We find that dispersal directionality and network structure promote species that produce a large number of propagules at a species level; such species are considered competitively superior in the neutral model and inferior in the trade-off model. As a result, the two key characteristics of riparian systems, dispersal directionality and network structure, lead to lower and higher overall γ diversity in the former and the latter models, respectively. The network structure, through the containment effect due to limited cross-basin dispersal, always leads to higher between-community, β diversity. The spatial distribution of local, α diversity becomes heterogeneous and thus important under directional dispersal and network structure. A higher degree of dividedness results in higher γ diversity for communities obeying both neutral and trade-off models, but the increase is more dramatic in the latter.

  18. Host discrimination in modular mutualisms: a theoretical framework for meta-populations of mutualists and exploiters.

    Science.gov (United States)

    Steidinger, Brian S; Bever, James D

    2016-01-13

    Plants in multiple symbioses are exploited by symbionts that consume their resources without providing services. Discriminating hosts are thought to stabilize mutualism by preferentially allocating resources into anatomical structures (modules) where services are generated, with examples of modules including the entire inflorescences of figs and the root nodules of legumes. Modules are often colonized by multiple symbiotic partners, such that exploiters that co-occur with mutualists within mixed modules can share rewards generated by their mutualist competitors. We developed a meta-population model to answer how the population dynamics of mutualists and exploiters change when they interact with hosts with different module occupancies (number of colonists per module) and functionally different patterns of allocation into mixed modules. We find that as module occupancy increases, hosts must increase the magnitude of preferentially allocated resources in order to sustain comparable populations of mutualists. Further, we find that mixed colonization can result in the coexistence of mutualist and exploiter partners, but only when preferential allocation follows a saturating function of the number of mutualists in a module. Finally, using published data from the fig-wasp mutualism as an illustrative example, we derive model predictions that approximate the proportion of exploiter, non-pollinating wasps observed in the field.

  19. Anthropogenic impacts on an oyster metapopulation: Pathogen introduction, climate change and responses to natural selection

    Directory of Open Access Journals (Sweden)

    David Bushek

    2016-08-01

    Full Text Available Abstract Humans rely on marine ecosystems for a variety of services but often impact these ecosystems directly or indirectly limiting their capacity to provide such services. One growing impact is the emergence of marine disease. We present results from a unique case study examining how oysters, a dominant organism in many coastal bays and estuaries that is often harvested for food, have responded to pathogens influenced by human activities, namely the introduction of novel pathogens. Climate change has enabled a northward spread and establishment of Dermo disease in oysters along the eastern seaboard of North America and human activities inadvertently introduced MSX disease along this same coast. Oysters in Delaware Bay have responded differently to each pathogen, and uniquely to MSX disease by developing a highly resistant baywide population not documented in any other bay. Offspring were produced using parents collected from low or high disease (MSX and Dermo regions of Delaware Bay and exposed in a common garden experiment along with a naïve population from Maine. Results indicated widespread resistance to MSX disease, but not to Dermo disease, across Delaware Bay. One striking result was the demonstration of resilience in the population through its capacity to spread, presumably through larval transport, resistance to MSX disease into portions of the population that have experienced little to no MSX disease pressure themselves. Related studies indicated that larval transport mechanisms allowed widespread dispersal such that the entire metapopulation could acquire a high level of resistance over time if disease resistance is sufficiently heritable. The findings have implications for restoration, management and recovery of diseased populations. Namely, that if left to their own devices, natural selection may find a solution that enables populations to recover from introduced pathogens.

  20. A metapopulation of the lizard Anguis fragilis (Squamata: Anguidae on a local scale in Dorset, Great Britain, as indicated by spatial distribution and movement

    Directory of Open Access Journals (Sweden)

    Thomas Haley

    2014-12-01

    Full Text Available A metapopulation is a group of spatially structured populations, consisting of distinct units (subpopulations that are separated by space or barriers, and connected by dispersal movements. Evidence derived from Gaussian finite-mixture models and dispersal events suggests that slow-worms may exist in a metapopulation. The Gaussian finite-mixture models showed that slow-worms are aggregated into individual subpopulations; the movement data revealed that males are more likely to migrate than females and that they have the ability to travel sufficiently far to bridge subpopulations. Therefore, the evidence supports the metapopulation theory and that slow-worms exist in multiple small subpopulations instead of one large homogenous population.

  1. The transition from isolated patches to a metapopulation in the eastern collared lizard in response to prescribed fires.

    Science.gov (United States)

    Templeton, Alan R; Brazeal, Hilary; Neuwald, Jennifer L

    2011-09-01

    Habitat fragmentation often arises from human-induced alterations to the matrix that reduce or eliminate dispersal between habitat patches. Elimination of dispersal increases local extinction and decreases recolonization. These phenomena were observed in the eastern collared lizard (Crotaphytus collaris collaris), which lives in the mid-continental highland region of the Ozarks (Missouri, USA) on glades: habitats of exposed bedrock that form desert-like habitats imbedded in a woodland matrix. With the onset of woodland fire suppression, glade habitats degenerated and the woodland matrix was altered to create a strong barrier to dispersal. By 1980, lizard populations in the Ozarks were rapidly going extinct. In response to this decline, some glades were restored by clearing and burning. Starting in 1984, collared lizard populations were translocated onto these restored habitats. The translocated populations persisted but did not colonize nearby glades or disperse among one another. In 1994 prescribed woodland fires were initiated, which unleashed much dispersal and colonizing behavior. Dispersal was highly nonrandom by both intrinsic variables (age, gender) and extrinsic variables (overall demography, glade population sizes, glade areas, landscape features), resulting in different classes of lizards being dominant in creating demographic cohesiveness among glades, colonizing new glades on a mountain, and colonizing new mountain systems. A dramatic transition was documented from isolated fragments, to a nonequilibrium colonizing metapopulation, and finally to a stable metapopulation. This transition is characterized by the convergence of rates of extinction and recolonization and a major alteration of dispersal probabilities and pattern in going from the nonequilibrium to stable metapopulation states.

  2. Zoos through the lens of the IUCN Red List: a global metapopulation approach to support conservation breeding programs.

    Science.gov (United States)

    Conde, Dalia A; Colchero, Fernando; Gusset, Markus; Pearce-Kelly, Paul; Byers, Onnie; Flesness, Nate; Browne, Robert K; Jones, Owen R

    2013-01-01

    Given current extinction trends, the number of species requiring conservation breeding programs (CBPs) is likely to increase dramatically. To inform CBP policies for threatened terrestrial vertebrates, we evaluated the number and representation of threatened vertebrate species on the IUCN Red List held in the ISIS zoo network and estimated the complexity of their management as metapopulations. Our results show that 695 of the 3,955 (23%) terrestrial vertebrate species in ISIS zoos are threatened. Only two of the 59 taxonomic orders show a higher proportion of threatened species in ISIS zoos than would be expected if species were selected at random. In addition, for most taxa, the management of a zoo metapopulation of more than 250 individuals will require the coordination of a cluster of 11 to 24 ISIS zoos within a radius of 2,000 km. Thus, in the zoo network, the representation of species that may require CBPs is currently low and the spatial distribution of these zoo populations makes management difficult. Although the zoo community may have the will and the logistical potential to contribute to conservation actions, including CBPs, to do so will require greater collaboration between zoos and other institutions, alongside the development of international agreements that facilitate cross-border movement of zoo animals. To maximize the effectiveness of integrated conservation actions that include CBPs, it is fundamental that the non-zoo conservation community acknowledges and integrates the expertise and facilities of zoos where it can be helpful.

  3. Zoos through the lens of the IUCN Red List: a global metapopulation approach to support conservation breeding programs.

    Directory of Open Access Journals (Sweden)

    Dalia A Conde

    Full Text Available Given current extinction trends, the number of species requiring conservation breeding programs (CBPs is likely to increase dramatically. To inform CBP policies for threatened terrestrial vertebrates, we evaluated the number and representation of threatened vertebrate species on the IUCN Red List held in the ISIS zoo network and estimated the complexity of their management as metapopulations. Our results show that 695 of the 3,955 (23% terrestrial vertebrate species in ISIS zoos are threatened. Only two of the 59 taxonomic orders show a higher proportion of threatened species in ISIS zoos than would be expected if species were selected at random. In addition, for most taxa, the management of a zoo metapopulation of more than 250 individuals will require the coordination of a cluster of 11 to 24 ISIS zoos within a radius of 2,000 km. Thus, in the zoo network, the representation of species that may require CBPs is currently low and the spatial distribution of these zoo populations makes management difficult. Although the zoo community may have the will and the logistical potential to contribute to conservation actions, including CBPs, to do so will require greater collaboration between zoos and other institutions, alongside the development of international agreements that facilitate cross-border movement of zoo animals. To maximize the effectiveness of integrated conservation actions that include CBPs, it is fundamental that the non-zoo conservation community acknowledges and integrates the expertise and facilities of zoos where it can be helpful.

  4. Bacterial Vaginosis

    Science.gov (United States)

    ... Issues > Conditions > Sexually Transmitted > Bacterial Vaginosis Health Issues Listen Español Text Size Email Print Share Bacterial Vaginosis Page Content Bacterial vaginosis (BV) is the most common vaginal infection in sexually active teenaged girls . It appears to be caused by ...

  5. Genetic Variation, Structure, and Gene Flow in a Sloth Bear (Melursus ursinus Meta-Population in the Satpura-Maikal Landscape of Central India.

    Directory of Open Access Journals (Sweden)

    Trishna Dutta

    Full Text Available Sloth bears (Melursus ursinus are endemic to the Indian subcontinent. As a result of continued habitat loss and degradation over the past century, sloth bear populations have been in steady decline and now exist only in isolated or fragmented habitat across the entire range. We investigated the genetic connectivity of the sloth bear meta-population in five tiger reserves in the Satpura-Maikal landscape of central India. We used noninvasively collected fecal and hair samples to obtain genotypic information using a panel of seven polymorphic loci. Out of 194 field collected samples, we identified 55 individuals in this meta-population. We found that this meta-population has moderate genetic variation, and is subdivided into two genetic clusters. Further, we identified five first-generation migrants and signatures of contemporary gene flow. We found evidence of sloth bears in the corridor between the Kanha and Pench Tiger Reserves, and our results suggest that habitat connectivity and corridors play an important role in maintaining gene flow in this meta-population. These corridors face several anthropogenic and infrastructure development threats that have the potential to sever ongoing gene flow, if policies to protect them are not put into action immediately.

  6. Genetic Variation, Structure, and Gene Flow in a Sloth Bear (Melursus ursinus) Meta-Population in the Satpura-Maikal Landscape of Central India.

    Science.gov (United States)

    Dutta, Trishna; Sharma, Sandeep; Maldonado, Jesús E; Panwar, Hemendra Singh; Seidensticker, John

    2015-01-01

    Sloth bears (Melursus ursinus) are endemic to the Indian subcontinent. As a result of continued habitat loss and degradation over the past century, sloth bear populations have been in steady decline and now exist only in isolated or fragmented habitat across the entire range. We investigated the genetic connectivity of the sloth bear meta-population in five tiger reserves in the Satpura-Maikal landscape of central India. We used noninvasively collected fecal and hair samples to obtain genotypic information using a panel of seven polymorphic loci. Out of 194 field collected samples, we identified 55 individuals in this meta-population. We found that this meta-population has moderate genetic variation, and is subdivided into two genetic clusters. Further, we identified five first-generation migrants and signatures of contemporary gene flow. We found evidence of sloth bears in the corridor between the Kanha and Pench Tiger Reserves, and our results suggest that habitat connectivity and corridors play an important role in maintaining gene flow in this meta-population. These corridors face several anthropogenic and infrastructure development threats that have the potential to sever ongoing gene flow, if policies to protect them are not put into action immediately.

  7. Critical paths in a metapopulation model of H1N1: Efficiently delaying influenza spreading through flight cancellation

    CERN Document Server

    Marcelino, Jose; 10.1371/4f8c9a2e1fca8

    2012-01-01

    Disease spreading through human travel networks has been a topic of great interest in recent years, as witnessed during outbreaks of influenza A (H1N1) or SARS pandemics. One way to stop spreading over the airline network are travel restrictions for major airports or network hubs based on the total number of passengers of an airport. Here, we test alternative strategies using edge removal, cancelling targeted flight connections rather than restricting traffic for network hubs, for controlling spreading over the airline network. We employ a SEIR metapopulation model that takes into account the population of cities, simulates infection within cities and across the network of the top 500 airports, and tests different flight cancellation methods for limiting the course of infection. The time required to spread an infection globally, as simulated by a stochastic global spreading model was used to rank the candidate control strategies. The model includes both local spreading dynamics at the level of populations and...

  8. A metapopulation model to assess the capacity of spread of meticillin-resistant Staphylococcus aureus ST398 in humans.

    Directory of Open Access Journals (Sweden)

    Thibaud Porphyre

    Full Text Available The emergence of the livestock-associated clone of meticillin-resistant Staphylococcus aureus (MRSA ST398 is a serious public health issue throughout Europe. In The Netherlands a stringent 'search-and-destroy' policy has been adopted, keeping low the level of MRSA prevalence. However, reports have recently emerged of transmission events between humans showing no links to livestock, contradicting belief that MRSA ST398 is poorly transmissible in humans. The question regarding the transmissibility of MRSA ST398 in humans therefore remains of great interest. Here, we investigated the capacity of MRSA ST398 to spread into an entirely susceptible human population subject to the effect of a single MRSA-positive commercial pig farm. Using a stochastic, discrete-time metapopulation model, we explored the effect of varying both the probability of persistent carriage and that of acquiring MRSA due to contact with pigs on the transmission dynamics of MRSA ST398 in humans. In particular, we assessed the value and key determinants of the basic reproduction ratio (R(0 for MRSA ST398. Simulations showed that the presence of recurrent exposures with pigs in risky populations allows MRSA ST398 to persist in the metapopulation and transmission events to occur beyond the farming community, even when the probability of persistent carriage is low. We further showed that persistent carriage should occur in less than 10% of the time for MRSA ST398 to conserve epidemiological characteristics similar to what has been previously reported. These results indicate that implementing control policy that only targets human carriers may not be sufficient to control MRSA ST398 in the community if it remains in pigs. We argue that farm-level control measures should be implemented if an eradication programme is to be considered.

  9. Climate change winners: receding ice fields facilitate colony expansion and altered dynamics in an Adelie penguin metapopulation.

    Directory of Open Access Journals (Sweden)

    Michelle A LaRue

    Full Text Available There will be winners and losers as climate change alters the habitats of polar organisms. For an Adélie penguin (Pygoscelis adeliae colony on Beaufort Island (Beaufort, part of a cluster of colonies in the southern Ross Sea, we report a recent population increase in response to increased nesting habitat as glaciers have receded. Emigration rates of birds banded as chicks on Beaufort to colonies on nearby Ross Island decreased after 2005 as available habitat on Beaufort increased, leading to altered dynamics of the metapopulation. Using aerial photography beginning in 1958 and modern satellite imagery, we measured change in area of available nesting habitat and population size of the Beaufort colony. Population size varied with available habitat, and both increased rapidly since the 1990s. In accord with glacial retreat, summer temperatures at nearby McMurdo Station increased by ~0.50 °C per decade since the mid-1980s. Although the Ross Sea is likely to be the last ocean with an intact ecosystem, the recent retreat of ice fields at Beaufort that resulted in increased breeding habitat exemplifies a process that has been underway in the Ross Sea during the entire Holocene. Furthermore, our results are in line with predictions that major ice shelves and glaciers will retreat rapidly elsewhere in the Antarctic, potentially leading to increased breeding habitat for Adélie penguins. Results further indicated that satellite imagery may be used to estimate large changes in Adélie penguin populations, facilitating our understanding of metapopulation dynamics and environmental factors that influence regional populations.

  10. A modeling framework for integrated harvest and habitat management of North American waterfowl: Case-study of northern pintail metapopulation dynamics

    Science.gov (United States)

    Mattsson, Brady J.; Runge, M.C.; Devries, J.H.; Boomer, G.S.; Eadie, J.M.; Haukos, D.A.; Fleskes, J.P.; Koons, D.N.; Thogmartin, W.E.; Clark, R.G.

    2012-01-01

    We developed and evaluated the performance of a metapopulation model enabling managers to examine, for the first time, the consequences of alternative management strategies involving habitat conditions and hunting on both harvest opportunity and carrying capacity (i.e., equilibrium population size in the absence of harvest) for migratory waterfowl at a continental scale. Our focus is on the northern pintail (Anas acuta; hereafter, pintail), which serves as a useful model species to examine the potential for integrating waterfowl harvest and habitat management in North America. We developed submodel structure capturing important processes for pintail populations during breeding, fall migration, winter, and spring migration while encompassing spatial structure representing three core breeding areas and two core nonbreeding areas. A number of continental-scale predictions from our baseline parameterization (e.g., carrying capacity of 5.5 million, equilibrium population size of 2.9 million and harvest rate of 12% at maximum sustained yield [MSY]) were within 10% of those from the pintail harvest strategy under current use by the U.S. Fish and Wildlife Service. To begin investigating the interaction of harvest and habitat management, we examined equilibrium population conditions for pintail at the continental scale across a range of harvest rates while perturbing model parameters to represent: (1) a 10% increase in breeding habitat quality in the Prairie Pothole population (PR); and (2) a 10% increase in nonbreeding habitat quantity along in the Gulf Coast (GC). Based on our model and analysis, a greater increase in carrying capacity and sustainable harvest was seen when increasing a proxy for habitat quality in the Prairie Pothole population. This finding and underlying assumptions must be critically evaluated, however, before specific management recommendations can be made. To make such recommendations, we require (1) extended, refined submodels with additional

  11. Pseudomonas aeruginosa SoxR does not conform to the archetypal paradigm for SoxR-dependent regulation of the bacterial oxidative stress adaptive response.

    Science.gov (United States)

    Palma, Marco; Zurita, Juan; Ferreras, Julian A; Worgall, Stefan; Larone, Davise H; Shi, Lei; Campagne, Fabien; Quadri, Luis E N

    2005-05-01

    SoxR is a transcriptional regulator that controls an oxidative stress response in Escherichia coli. The regulator is primarily activated by superoxide anion-dependent oxidation. Activated SoxR turns on transcription of a single gene, soxS, which encodes a transcriptional regulator that activates a regulon that includes dozens of oxidative stress response genes. SoxR homologues have been identified in many bacterial species, including the opportunistic pathogen Pseudomonas aeruginosa. However, the expected SoxR partner, SoxS, has not been found in P. aeruginosa. Thus, the primary gene target(s) of P. aeruginosa SoxR is unknown and the involvement of this regulator in the oxidative stress response of the bacterium remains unclear. We utilized transcriptome profiling to identify the P. aeruginosa SoxR regulon and constructed and characterized an unmarked P. aeruginosa DeltasoxR mutant. We provide evidence indicating that P. aeruginosa SoxR activates a six-gene regulon in response to O(2)(.-)-induced stress. The regulon includes three transcriptional units: (i) the recently identified mexGHI-ompD four-gene operon, which encodes a multidrug efflux pump system involved in quorum-sensing signal homeostasis; (ii) gene PA3718, encoding a probable efflux pump; and (iii) gene PA2274, encoding a probable monooxygenase. We also demonstrate that P. aeruginosa SoxR is not a key regulatory player in the oxidative stress response. Finally, we show that P. aeruginosa SoxR is required for virulence in a mouse model of intrapulmonary infection. These results demonstrate that the E. coli-based SoxRS paradigm does not hold in P. aeruginosa and foster new hypotheses for the possible physiological role of P. aeruginosa SoxR.

  12. Bacterial gastroenteritis

    Science.gov (United States)

    Bacterial gastroenteritis is present when bacteria cause an infection of the stomach and intestines ... has not been treated Many different types of bacteria can cause ... Campylobacter jejuni E coli Salmonella Shigella Staphylococcus ...

  13. Temporal and spatial variation in prevalence of the parasite Syngamus trachea in a metapopulation of house sparrows (Passer domesticus).

    Science.gov (United States)

    Holand, Håkon; Jensen, Henrik; Tufto, Jarle; Sæther, Bernt-Erik; Ringsby, Thor Harald

    2013-09-01

    When investigating parasite-host dynamics in wild populations, a fundamental parameter to investigate is prevalence. This quantifies the percentage of individuals infected in the population. Investigating how prevalence changes over time and space can reveal interesting aspects in the parasite-host relationship in natural populations. We investigated the dynamic between a common avian parasite (Syngamus trachea) in a host metapopulation of house sparrows (Passer domesticus) on the coast of Helgeland in northern Norway. We found that parasite prevalence varied in both time and space. In addition, the parasite prevalence was found to be different between demographic groups in the local populations. Our results reveal just how complex the dynamic between a host and its parasite may become in a fragmented landscape. Although temperature may be an important factor, the specific mechanisms causing this complexity are not fully understood, but need to be further examined to understand how parasite-host interactions may affect the ecological and evolutionary dynamics and viability of host populations.

  14. Paternal transmission of mitochondrial DNA as an integral part of mitochondrial inheritance in metapopulations of Drosophila simulans.

    Science.gov (United States)

    Wolff, J N; Nafisinia, M; Sutovsky, P; Ballard, J W O

    2013-01-01

    Maternal inheritance is one of the hallmarks of animal mitochondrial DNA (mtDNA) and central to its success as a molecular marker. This mode of inheritance and subsequent lack of heterologous recombination allows us to retrace evolutionary relationships unambiguously down the matriline and without the confounding effects of recombinant genetic information. Accumulating evidence of biparental inheritance of mtDNA (paternal leakage), however, challenges our current understanding of how this molecule is inherited. Here, using Drosophila simulans collected from an East African metapopulation exhibiting recurring mitochondrial heteroplasmy, we conducted single fly matings and screened F1 offspring for the presence of paternal mtDNA using allele-specific PCR assays (AS-PCR). In all, 27 out of 4092 offspring were identified as harboring paternal mtDNA, suggesting a frequency of 0.66% paternal leakage in this species. Our findings strongly suggest that recurring mtDNA heteroplasmy as observed in natural populations of Drosophila simulans is most likely caused by repeated paternal leakage. Our findings further suggest that this phenomenon to potentially be an integral part of mtDNA inheritance in these populations and consequently of significance for mtDNA as a molecular marker.

  15. Bacterial Adhesion & Blocking Bacterial Adhesion

    DEFF Research Database (Denmark)

    Vejborg, Rebecca Munk

    2008-01-01

    tract to the microbial flocs in waste water treatment facilities. Microbial biofilms may however also cause a wide range of industrial and medical problems, and have been implicated in a wide range of persistent infectious diseases, including implantassociated microbial infections. Bacterial adhesion...... is the first committing step in biofilm formation, and has therefore been intensely scrutinized. Much however, still remains elusive. Bacterial adhesion is a highly complex process, which is influenced by a variety of factors. In this thesis, a range of physico-chemical, molecular and environmental parameters......, which influence the transition from a planktonic lifestyle to a sessile lifestyle, have been studied. Protein conditioning film formation was found to influence bacterial adhesion and subsequent biofilm formation considerable, and an aqueous extract of fish muscle tissue was shown to significantly...

  16. Bacterial lipases

    NARCIS (Netherlands)

    Jaeger, Karl-Erich; Ransac, Stéphane; Dijkstra, Bauke W.; Colson, Charles; Heuvel, Margreet van; Misset, Onno

    1994-01-01

    Many different bacterial species produce lipases which hydrolyze esters of glycerol with preferably long-chain fatty acids. They act at the interface generated by a hydrophobic lipid substrate in a hydrophilic aqueous medium. A characteristic property of lipases is called interfacial activation, mea

  17. Bacterial Ecology

    DEFF Research Database (Denmark)

    Fenchel, Tom

    2011-01-01

    Bacterial ecology is concerned with the interactions between bacteria and their biological and nonbiological environments and with the role of bacteria in biogeochemical element cycling. Many fundamental properties of bacteria are consequences of their small size. Thus, they can efficiently exploit...

  18. Metapopulation structure of a seed-predator weevil and its host plant in arms race coevolution.

    Science.gov (United States)

    Toju, Hirokazu; Ueno, Saneyoshi; Taniguchi, Fumiya; Sota, Teiji

    2011-06-01

    Although the importance of gene flow in the geographic structuring of host-parasite interactions has been well discussed, little is known about how dispersal drives the spatial dynamics of other types of coevolutionary interactions in nature. We evaluated the roles of gene flow in the geographically structured processes of a predator-prey arms race involving a seed-predatory weevil with a long mouthpart and its host camellia plant with a thick fruit coat. Molecular genetic analyses showed that both weevil and camellia populations were structured at a spatial scale of several kilometers. Importantly, the spatial pattern of the migration of weevils, but not that of camellias, imposed significant effects on the geographic configuration of the levels of coevolutionary escalation. This result suggests that even if migration is limited in one species (camellia), local coevolution with the other species that migrates between neighboring localities (weevil) can reduce the interpopulation difference in the local adaptive optima of the former species. Thus, gene flow of a species potentially homogenizes the local biological environments provided by the species and thereby promotes the evolutionary convergence of its coevolving counterparts. Consequently, by focusing on coevolutionary interactions in natural communities, "indirect" effects of gene flow on the adaptive divergence of organisms could be identified.

  19. [Bacterial vaginosis].

    Science.gov (United States)

    Romero Herrero, Daniel; Andreu Domingo, Antonia

    2016-07-01

    Bacterial vaginosis (BV) is the main cause of vaginal dysbacteriosis in the women during the reproductive age. It is an entity in which many studies have focused for years and which is still open for discussion topics. This is due to the diversity of microorganisms that cause it and therefore, its difficult treatment. Bacterial vaginosis is probably the result of vaginal colonization by complex bacterial communities, many of them non-cultivable and with interdependent metabolism where anaerobic populations most likely play an important role in its pathogenesis. The main symptoms are an increase of vaginal discharge and the unpleasant smell of it. It can lead to serious consequences for women, such as an increased risk of contracting sexually transmitted infections including human immunodeficiency virus and upper genital tract and pregnancy complications. Gram stain is the gold standard for microbiological diagnosis of BV, but can also be diagnosed using the Amsel clinical criteria. It should not be considered a sexually transmitted disease but it is highly related to sex. Recurrence is the main problem of medical treatment. Apart from BV, there are other dysbacteriosis less characterized like aerobic vaginitis of which further studies are coming slowly but are achieving more attention and consensus among specialists.

  20. Decomposed pairwise regression analysis of genetic and geographic distances reveals a metapopulation structure of stream-dwelling Dolly Varden charr.

    Science.gov (United States)

    Koizumi, Itsuro; Yamamoto, Shoichiro; Maekawa, Koji

    2006-10-01

    Isolation by distance is usually tested by the correlation of genetic and geographic distances separating all pairwise populations' combinations. However, this method can be significantly biased by only a few highly diverged populations and lose the information of individual population. To detect outlier populations and investigate the relative strengths of gene flow and genetic drift for each population, we propose a decomposed pairwise regression analysis. This analysis was applied to the well-described one-dimensional stepping-stone system of stream-dwelling Dolly Varden charr (Salvelinus malma). When genetic and geographic distances were plotted for all pairs of 17 tributary populations, the correlation was significant but weak (r(2) = 0.184). Seven outlier populations were determined based on the systematic bias of the regression residuals, followed by Akaike's information criteria. The best model, 10 populations included, showed a strong pattern of isolation by distance (r(2) = 0.758), suggesting equilibrium between gene flow and genetic drift in these populations. Each outlier population was also analysed by plotting pairwise genetic and geographic distances against the 10 nonoutlier populations, and categorized into one of the three patterns: strong genetic drift, genetic drift with a limited gene flow and a high level of gene flow. These classifications were generally consistent with a priori predictions for each population (physical barrier, population size, anthropogenic impacts). Combined the genetic analysis with field observations, Dolly Varden in this river appeared to form a mainland-island or source-sink metapopulation structure. The generality of the method will merit many types of spatial genetic analyses.

  1. Mechanism of bacterial adaptation to low temperature

    Indian Academy of Sciences (India)

    M K Chattopadhyay

    2006-03-01

    Survival of bacteria at low temperatures provokes scientific interest because of several reasons. Investigations in this area promise insight into one of the mysteries of life science – namely, how the machinery of life operates at extreme environments. Knowledge obtained from these studies is likely to be useful in controlling pathogenic bacteria, which survive and thrive in cold-stored food materials. The outcome of these studies may also help us to explore the possibilities of existence of life in distant frozen planets and their satellites.

  2. Síndrome de intestino corto: definición, causas, adaptación intestinal y sobrecrecimiento bacteriano Short bowel syndrome: definition, causes, intestinal adaptation and bacterial overgrowth

    Directory of Open Access Journals (Sweden)

    M. D. Ballesteros Pomar

    2007-05-01

    ón parenteral.The short bowel syndrome (SBS is a complex entity due to anatomical or functional loss of part of the small bowel originating a clinical picture with severe metabolic and nutritional impairments due to reduction of the effective absorptive surface area of the gut. SBS is one of the causes of a larger entity known as "intestinal failure". Currently, mesenteric vascular accidents are the main cause in adults, followed by inflammatory bowel disease, and radiation enteritis, whereas in children, the main causes are congenital and perinatal diseases. The clinical picture associated with SBS varies according to the length and location of affected small bowel, the presence of underlying disease, the presence or absence of the large bowel and ileocecal valve, and the nature of the underlying disease. Intestinal adaptation is the process by which, throughout 1-2 years, intestinal absorption is reestablished to the situation prior to intestinal resection, and is a key factor determining whether a patient with SBS will progress to intestinal failure and depend on DPN. Intestinal adaptation may take place if the patient does oral intake higher than the usual one (hyperphagia; besides, the bowel may also adapt to secure a more effective absorption per surface area unit, either by increasing the absorptive surface area (structural adaptation and/or slowing intestinal transit (functional adaptation. These changes are not still clearly established in humans, but there are so in animal models. The presence of nutrients within the intestinal lumen and certain gastrointestinal hormones, particularly GLP-2, have an influence on a successful adaptation process. Patients with SBS are prone to the occurrence of bacterial overgrowth that makes adaptation difficult and worsens the symptoms, besides being a factor for dependence on parenteral nutrition.

  3. Bacterial hydrodynamics

    CERN Document Server

    Lauga, Eric

    2015-01-01

    Bacteria predate plants and animals by billions of years. Today, they are the world's smallest cells yet they represent the bulk of the world's biomass, and the main reservoir of nutrients for higher organisms. Most bacteria can move on their own, and the majority of motile bacteria are able to swim in viscous fluids using slender helical appendages called flagella. Low-Reynolds-number hydrodynamics is at the heart of the ability of flagella to generate propulsion at the micron scale. In fact, fluid dynamic forces impact many aspects of bacteriology, ranging from the ability of cells to reorient and search their surroundings to their interactions within mechanically and chemically-complex environments. Using hydrodynamics as an organizing framework, we review the biomechanics of bacterial motility and look ahead to future challenges.

  4. Bacterial vaginosis -- aftercare

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/patientinstructions/000687.htm Bacterial vaginosis - aftercare To use the sharing features on this ... to back after you use the bathroom. Preventing Bacterial Vaginosis You can help prevent bacterial vaginosis by: Not ...

  5. Pregnancy Complications: Bacterial Vaginosis

    Science.gov (United States)

    ... Complications & Loss > Pregnancy complications > Bacterial vaginosis and pregnancy Bacterial vaginosis and pregnancy E-mail to a friend Please ... this page It's been added to your dashboard . Bacterial vaginosis (also called BV or vaginitis) is an infection ...

  6. 生境破坏的空间结构对集合种群动态的影响%Effect of habitat destruction structure on the dynamics of metapopulation

    Institute of Scientific and Technical Information of China (English)

    张彦宇; 罗鑫娟

    2013-01-01

    To study the effects of habitat destruction on metapopulation dynamics, a model for metapopulation dynamics has been constructed, based on the cellular automaton model, which includes not only metapopulation information about spatial structure, but also the global density and local density of destruction habitat. With the model reveals the spatial structure of destructed habitat profoundly affects the dynamics of metapopulation. The mixed distribution of destructed habitat and suitable habitat, the global density of destructed habitat is bigger than the local, which makes the danger of metapopulation extinction. While with clustering distribution, the global density of destructed habitat is smaller than the local, which will promote the persistence of metapopulation increase. General, the global and local density of metapopulation are in direct proportion to the global density of destructed habitat, and in inverse proportion to the local density of destructed habitat. But, with certain global density of destructed habitat, the global and local density of metapopulation decrease with the increase of the local density of destructed habitat. There is a threshold, which the local density of metapopulationis below, the metapopulation would extinct. All these results show that it is important to construct the connectivity among patches and the local density of metapopulation, although habitat restoration and habitat quality improvement are necessary.%构建任意生境破坏结构下集合种群动态的元胞自动机模型,研究生境破坏的空间结构对集合种群全局密度及局部密度的影响.该模型不仅包括了生境破坏的空间结构,而且能够描述集合种群的空间分布模式.模型结果表明:生境破坏的空间结构复杂地影响着集合种群的全局密度和局部密度;生境破坏的混合分布增大了集合种群灭绝的风险;生境破坏的聚集分布降低了集合种群灭绝的风险.在生境破坏比例较

  7. Coevolutionary fine-tuning: evidence for genetic tracking between a specialist wasp parasitoid and its aphid host in a dual metapopulation interaction.

    Science.gov (United States)

    Nyabuga, F N; Loxdale, H D; Heckel, D G; Weisser, W W

    2012-04-01

    In the interaction between two ecologically-associated species, the population structure of one species may affect the population structure of the other. Here, we examine the population structures of the aphid Metopeurum fuscoviride, a specialist on tansy Tanacetum vulgare, and its specialist primary hymenopterous parasitoid Lysiphlebus hirticornis, both of which are characterized by multivoltine life histories and a classic metapopulation structure. Samples of the aphid host and the parasitoid were collected from eight sites in and around Jena, Germany, where both insect species co-occur, and then were genotyped using suites of polymorphic microsatellite markers. The host aphid was greatly differentiated in terms of its spatial population genetic patterning, while the parasitoid was, in comparison, only moderately differentiated. There was a positive Mantel test correlation between pairwise shared allele distance (DAS) of the host and parasitoid, i.e. if host subpopulation samples were more similar between two particular sites, so were the parasitoid subpopulation samples. We argue that while the differences in the levels of genetic differentiation are due to the differences in the biology of the species, the correlations between host and parasitoid are indicative of dependence of the parasitoid population structure on that of its aphid host. The parasitoid is genetically tracking behind the aphid host, as can be expected in a classic metapopulation structure where host persistence depends on a delay between host and parasitoid colonization of the patch. The results may also have relevance to the Red Queen hypothesis, whereupon in the 'arms race' between parasitoid and its host, the latter 'attempts' to evolve away from the former.

  8. 生态位构建通过修复破坏生境对集合种群动态的影响%Effect of niche construction on metapopulation dynamics by modifying destroyed habitat

    Institute of Scientific and Technical Information of China (English)

    韩晓卓; 李自珍; 张彦宇; 张锋

    2006-01-01

    Based on the Levins-type models with habitat destruction, the differential model under meanfield assumption was built to illuminate the ecological consequences of niche-constructing organisms' activities for destroyed habitat in metapopulation. Through stability analysis and simulation with cellular automation model, the results show that the metapopulation persistence depends on not only the balances between extinction and colonization but also the balance between the ability of niche construction and natural dissipation of habitat, even if the colonization rate is lower than the extinction rate. The metapopulation size is positive correlated with the ability of niche construction. With the ability of niche construction enhances, metapopulation size would increase. Furthermore, there exist two threshold phenomena for metapopulation persistence, which include the ability of niche construction and the initial state of metapopulation. Therefore, organisms or populations who have strongly positive influences on their environment play an important role on maintaining the available habitat and hence provide the theoretical ground for conservation biology.%基于具有生境破碎作用下的集合种群模型,建立了在均匀场假设下的微分方程模型,充分探讨了具有生态位构建效应的有机体活动对破碎斑块修复产生的生态结果.通过稳定性分析与元胞自动机方法模拟表明:集合种群的续存条件不仅依赖于侵占力与灭绝率之间的平衡,而且也包括集合种群的生态位构建能力与生境自然消耗率之间的平衡;当灭绝率大于侵占率时,集合种群也可以在低水平上续存,并且在该过程中集合种群依赖于两个阈值条件,分别是生态位构建能力和集合种群的初始状态.集合种群的大小与其生态位构建能力成正比,即构建能力强者,集合种群数量相应增加.因此,对环境具有较强的正效应的有机体或种群在维护生境的有效性中起重要作用.

  9. Bacterial Population Genetics in a Forensic Context

    Energy Technology Data Exchange (ETDEWEB)

    Velsko, S P

    2009-11-02

    This report addresses the recent Department of Homeland Security (DHS) call for a Phase I study to (1) assess gaps in the forensically relevant knowledge about the population genetics of eight bacterial agents of concern, (2) formulate a technical roadmap to address those gaps, and (3) identify new bioinformatics tools that would be necessary to analyze and interpret population genetic data in a forensic context. The eight organisms that were studied are B. anthracis, Y. pestis, F. tularensis, Brucella spp., E. coli O157/H7, Burkholderia mallei, Burkholderia pseudomallei, and C. botulinum. Our study focused on the use of bacterial population genetics by forensic investigators to test hypotheses about the possible provenance of an agent that was used in a crime or act of terrorism. Just as human population genetics underpins the calculations of match probabilities for human DNA evidence, bacterial population genetics determines the level of support that microbial DNA evidence provides for or against certain well-defined hypotheses about the origins of an infecting strain. Our key findings are: (1) Bacterial population genetics is critical for answering certain types of questions in a probabilistic manner, akin (but not identical) to 'match probabilities' in DNA forensics. (2) A basic theoretical framework for calculating likelihood ratios or posterior probabilities for forensic hypotheses based on microbial genetic comparisons has been formulated. This 'inference-on-networks' framework has deep but simple connections to the population genetics of mtDNA and Y-STRs in human DNA forensics. (3) The 'phylogeographic' approach to identifying microbial sources is not an adequate basis for understanding bacterial population genetics in a forensic context, and has limited utility, even for generating 'leads' with respect to strain origin. (4) A collection of genotyped isolates obtained opportunistically from international locations

  10. Prevention of bacterial adhesion

    DEFF Research Database (Denmark)

    Klemm, Per; Vejborg, Rebecca Munk; Hancock, Viktoria

    2010-01-01

    Management of bacterial infections is becoming increasingly difficult due to the emergence and increasing prevalence of bacterial pathogens that are resistant to available antibiotics. Conventional antibiotics generally kill bacteria by interfering with vital cellular functions, an approach...... that imposes selection pressure for resistant bacteria. New approaches are urgently needed. Targeting bacterial virulence functions directly is an attractive alternative. An obvious target is bacterial adhesion. Bacterial adhesion to surfaces is the first step in colonization, invasion, and biofilm formation....... As such, adhesion represents the Achilles heel of crucial pathogenic functions. It follows that interference with adhesion can reduce bacterial virulence. Here, we illustrate this important topic with examples of techniques being developed that can inhibit bacterial adhesion. Some of these will become...

  11. Ways of adaptations of populations and communities of fine Mammals to conditions of wood cabins on East Caucasus. The message 1. Populations

    Directory of Open Access Journals (Sweden)

    K. Z. Omarov

    2008-01-01

    Full Text Available It is shown that reaction of rodent populations to throw is defined by the character and depth of specialization to biotopes of every species. The general consequence of spotting habitats owing to cuttings down for the most of rodent populations is a reorganization of population structure in a metapopulation, which is revealed in the changes of population parameters. Such reorganization of populations has an adaptive character, which allows supporting the optimal structure in a population nucleus.

  12. Phylogenetic Co-Occurrence of ExoR, ExoS, and ChvI, Components of the RSI Bacterial Invasion Switch, Suggests a Key Adaptive Mechanism Regulating the Transition between Free-Living and Host-Invading Phases in Rhizobiales.

    Directory of Open Access Journals (Sweden)

    Mary Ellen Heavner

    Full Text Available Both bacterial symbionts and pathogens rely on their host-sensing mechanisms to activate the biosynthetic pathways necessary for their invasion into host cells. The Gram-negative bacterium Sinorhizobium meliloti relies on its RSI (ExoR-ExoS-ChvI Invasion Switch to turn on the production of succinoglycan, an exopolysaccharide required for its host invasion. Recent whole-genome sequencing efforts have uncovered putative components of RSI-like invasion switches in many other symbiotic and pathogenic bacteria. To explore the possibility of the existence of a common invasion switch, we have conducted a phylogenomic survey of orthologous ExoR, ExoS, and ChvI tripartite sets in more than ninety proteobacterial genomes. Our analyses suggest that functional orthologs of the RSI invasion switch co-exist in Rhizobiales, an order characterized by numerous invasive species, but not in the order's close relatives. Phylogenomic analyses and reconstruction of orthologous sets of the three proteins in Alphaproteobacteria confirm Rhizobiales-specific gene synteny and congruent RSI evolutionary histories. Evolutionary analyses further revealed site-specific substitutions correlated specifically to either animal-bacteria or plant-bacteria associations. Lineage restricted conservation of any one specialized gene is in itself an indication of species adaptation. However, the orthologous phylogenetic co-occurrence of all interacting partners within this single signaling pathway strongly suggests that the development of the RSI switch was a key adaptive mechanism. The RSI invasion switch, originally found in S. meliloti, is a characteristic of the Rhizobiales, and potentially a conserved crucial activation step that may be targeted to control host invasion by pathogenic bacterial species.

  13. Combined action of time-delay and colored cross-associated multiplicative and additive noises on stability and stochastic resonance for a stochastic metapopulation system

    Science.gov (United States)

    Wang, Kang-Kang; Zong, De-Cai; Wang, Ya-Jun; Li, Sheng-Hong

    2016-05-01

    In this paper, the transition between the stable state of a big density and the extinction state and stochastic resonance (SR) for a time-delayed metapopulation system disturbed by colored cross-correlated noises are investigated. By applying the fast descent method, the small time-delay approximation and McNamara and Wiesenfeld's SR theory, we investigate the impacts of time-delay, the multiplicative, additive noises and colored cross-correlated noise on the SNR and the shift between the two states of the system. Numerical results show that the multiplicative, additive noises and time-delay can all speed up the transition from the stable state to the extinction state, while the correlation noise and its correlation time can slow down the extinction process of the population system. With respect to SNR, the multiplicative noise always weakens the SR effect, while noise correlation time plays a dual role in motivating the SR phenomenon. Meanwhile, time-delay mainly plays a negative role in stimulating the SR phenomenon. Conversely, it could motivate the SR effect to increase the strength of the cross-correlation noise in the SNR-β plot, while the increase of additive noise intensity will firstly excite SR, and then suppress the SR effect.

  14. Population genetic analysis of microsatellite variation of guppies (Poecilia reticulata) in Trinidad and Tobago: evidence for a dynamic source-sink metapopulation structure, founder events and population bottlenecks.

    Science.gov (United States)

    Barson, N J; Cable, J; Van Oosterhout, C

    2009-03-01

    Riverine fish populations are traditionally considered to be highly structured and subject to strong genetic drift. Here, we use microsatellites to analyse the population structure of the guppy (Poecilia reticulata), focussing on the headwater floodplain area of the Caroni drainage in Trinidad. We also analyse the population genetics of guppies in the Northern Drainage in Trinidad, a habitat characterized by rivers flowing directly into the sea, and a small isolated population in Tobago. Upland Caroni populations are highly differentiated and display low levels of genetic diversity. However, we found no evidence to suggest that these upland populations experienced recent population crashes and the populations appear to approach mutation-drift equilibrium. Dominant downstream migration over both short- and long-time frames has a strong impact on the population genetics of lowland Caroni populations. This drainage system could be considered a source-sink metapopulation, with the tributary furthest downstream representing a 'super sink', receiving immigrants from rivers upstream in the drainage. Moreover, the effective population size in the lowlands is surprisingly low in comparison with the apparently large census population sizes.

  15. Adaptive Lighting

    DEFF Research Database (Denmark)

    Petersen, Kjell Yngve; Søndergaard, Karin; Kongshaug, Jesper

    2015-01-01

    Adaptive Lighting Adaptive lighting is based on a partial automation of the possibilities to adjust the colour tone and brightness levels of light in order to adapt to people’s needs and desires. IT support is key to the technical developments that afford adaptive control systems. The possibilities...... offered by adaptive lighting control are created by the ways that the system components, the network and data flow can be coordinated through software so that the dynamic variations are controlled in ways that meaningfully adapt according to people’s situations and design intentions. This book discusses...... differently into an architectural body. We also examine what might occur when light is dynamic and able to change colour, intensity and direction, and when it is adaptive and can be brought into interaction with its surroundings. In short, what happens to an architectural space when artificial lighting ceases...

  16. Peritonitis - spontaneous bacterial

    Science.gov (United States)

    Spontaneous bacterial peritonitis (SBP); Ascites - peritonitis; Cirrhosis - peritonitis ... who are on peritoneal dialysis for kidney failure. Peritonitis may have other causes . These include infection from ...

  17. ADAPT Dataset

    Data.gov (United States)

    National Aeronautics and Space Administration — Advanced Diagnostics and Prognostics Testbed (ADAPT) Project Lead: Scott Poll Subject Fault diagnosis in electrical power systems Description The Advanced...

  18. Prevention of bacterial adhesion

    DEFF Research Database (Denmark)

    Klemm, Per; Vejborg, Rebecca Munk; Hancock, Viktoria

    2010-01-01

    Management of bacterial infections is becoming increasingly difficult due to the emergence and increasing prevalence of bacterial pathogens that are resistant to available antibiotics. Conventional antibiotics generally kill bacteria by interfering with vital cellular functions, an approach that ...... valuable weapons for preventing pathogen contamination and fighting infectious diseases in the future....

  19. Vimentin in Bacterial Infections

    DEFF Research Database (Denmark)

    Mak, Tim N; Brüggemann, Holger

    2016-01-01

    Despite well-studied bacterial strategies to target actin to subvert the host cell cytoskeleton, thus promoting bacterial survival, replication, and dissemination, relatively little is known about the bacterial interaction with other components of the host cell cytoskeleton, including intermediate...... filaments (IFs). IFs have not only roles in maintaining the structural integrity of the cell, but they are also involved in many cellular processes including cell adhesion, immune signaling, and autophagy, processes that are important in the context of bacterial infections. Here, we summarize the knowledge...... about the role of IFs in bacterial infections, focusing on the type III IF protein vimentin. Recent studies have revealed the involvement of vimentin in host cell defenses, acting as ligand for several pattern recognition receptors of the innate immune system. Two main aspects of bacteria...

  20. SNP design from 454 sequencing of Podosphaera plantaginis transcriptome reveals a genetically diverse pathogen metapopulation with high levels of mixed-genotype infection.

    Directory of Open Access Journals (Sweden)

    Charlotte Tollenaere

    Full Text Available BACKGROUND: Molecular tools may greatly improve our understanding of pathogen evolution and epidemiology but technical constraints have hindered the development of genetic resources for parasites compared to free-living organisms. This study aims at developing molecular tools for Podosphaera plantaginis, an obligate fungal pathogen of Plantago lanceolata. This interaction has been intensively studied in the Åland archipelago of Finland with epidemiological data collected from over 4,000 host populations annually since year 2001. PRINCIPAL FINDINGS: A cDNA library of a pooled sample of fungal conidia was sequenced on the 454 GS-FLX platform. Over 549,411 reads were obtained and annotated into 45,245 contigs. Annotation data was acquired for 65.2% of the assembled sequences. The transcriptome assembly was screened for SNP loci, as well as for functionally important genes (mating-type genes and potential effector proteins. A genotyping assay of 27 SNP loci was designed and tested on 380 infected leaf samples from 80 populations within the Åland archipelago. With this panel we identified 85 multilocus genotypes (MLG with uneven frequencies across the pathogen metapopulation. Approximately half of the sampled populations contain polymorphism. Our genotyping protocol revealed mixed-genotype infection within a single host leaf to be common. Mixed infection has been proposed as one of the main drivers of pathogen evolution, and hence may be an important process in this pathosystem. SIGNIFICANCE: The developed SNP panel offers exciting research perspectives for future studies in this well-characterized pathosystem. Also, the transcriptome provides an invaluable novel genomic resource for powdery mildews, which cause significant yield losses on commercially important crops annually. Furthermore, the features that render genetic studies in this system a challenge are shared with the majority of obligate parasitic species, and hence our results provide

  1. Maternally Derived Immunity Extends Swine Influenza A Virus Persistence within Farrow-to-Finish Pig Farms: Insights from a Stochastic Event-Driven Metapopulation Model

    Science.gov (United States)

    Cador, Charlie; Rose, Nicolas; Willem, Lander; Andraud, Mathieu

    2016-01-01

    Swine Influenza A Viruses (swIAVs) have been shown to persist in farrow-to-finish pig herds with repeated outbreaks in successive batches, increasing the risk for respiratory disorders in affected animals and being a threat for public health. Although the general routes of swIAV transmission (i.e. direct contact and exposure to aerosols) were clearly identified, the transmission process between batches is still not fully understood. Maternally derived antibodies (MDAs) were stressed as a possible factor favoring within-herd swIAV persistence. However, the relationship between MDAs and the global spread among the different subpopulations in the herds is still lacking. The aim of this study was therefore to understand the mechanisms induced by MDAs in relation with swIAV spread and persistence in farrow-to-finish pig herds. A metapopulation model has been developed representing the population dynamics considering two subpopulations—breeding sows and growing pigs—managed according to batch-rearing system. This model was coupled with a swIAV-specific epidemiological model, accounting for partial passive immunity protection in neonatal piglets and an immunity boost in re-infected animals. Airborne transmission was included by a between-room transmission rate related to the current prevalence of shedding pigs. Maternally derived partial immunity in piglets was found to extend the duration of the epidemics within their batch, allowing for efficient between-batch transmission and resulting in longer swIAV persistence at the herd level. These results should be taken into account in the design of control programmes for the spread and persistence of swIAV in swine herds. PMID:27662592

  2. Evolution of Bacterial Pathogens within the Human Host

    OpenAIRE

    Bliven, Kimberly A.; Maurelli, Anthony T.

    2016-01-01

    Selective pressures within the human host, including interactions with innate and adaptive immune responses, exposure to medical interventions such as antibiotics, and competition with commensal microbiota all facilitate the evolution of bacterial pathogens. In this chapter, we present examples of pathogen strategies which emerged as a result of selective pressures within the human host niche, and discuss the resulting co-evolutionary ‘arms race’ between these organisms. In bacterial pathogen...

  3. Adaptation, Bacteria and Maxwell's Demons

    Science.gov (United States)

    Galajda, Peter; Keymer, Juan E.; Austin, Robert H.

    2007-03-01

    We propose a method to study the adaptation of bacterial populations with an asymmetric wall of Maxwell Demon openings. A Maxwell Demon opening is a funnel which is easier to enter than to leave. The interaction of swimming cells with such a Maxwell Demon Wall results in a population density separation, in apparent (but not real) violation of the Second Law of Thermodynamics, as we will show. Bacteria can be exposed to spatial challenges in order to move to e. g. higher food levels. The question we address in these experiments is: do the bacteria adapt and overcome the Maxwell Demon Wall?

  4. Antibiotics promote aggregation within aquatic bacterial communities

    Directory of Open Access Journals (Sweden)

    Gianluca eCorno

    2014-07-01

    Full Text Available The release of antibiotics (AB into the environment poses several threats for human health due to potential development of ABresistant natural bacteria. Even though the use of low-dose antibiotics has been promoted in health care and farming, significant amounts of AB are observed in aquatic environments. Knowledge on the impact of AB on natural bacterial communities is missing both in terms of spread and evolution of resistance mechanisms, and of modifications of community composition and productivity. New approaches are required to study the response of microbial communities rather than individual resistance genes. In this study a chemostat-based experiment with 4 coexisting bacterial strains has been performed to mimicking the response of a freshwater bacterial community to the presence of antibiotics in low and high doses. Bacterial abundance rapidly decreased by 75% in the presence of AB, independently of their concentration, and remained constant until the end of the experiment. The bacterial community was mainly dominated by Aeromonas hydrophila and Brevundimonas intermedia while the other two strains, Micrococcus luteus and Rhodococcus sp. never exceed 10%. Interestingly, the bacterial strains, which were isolated at the end of the experiment, were not AB-resistant, while reassembled communities composed of the 4 strains, isolated from treatments under AB stress, significantly raised their performance (growth rate, abundance in the presence of AB compared to the communities reassembled with strains isolated from the treatment without AB. By investigating the phenotypic adaptations of the communities subjected to the different treatments, we found that the presence of AB significantly increased co-aggregation by 5-6 fold.These results represent the first observation of co-aggregation as a successful strategy of AB resistance based on phenotype in aquatic bacterial communities, and can represent a fundamental step in the understanding of

  5. Interfering with bacterial gossip

    DEFF Research Database (Denmark)

    Bjarnsholt, Thomas; Tolker-Nielsen, Tim; Givskov, Michael

    2011-01-01

    defense. Antibiotics exhibit a rather limited effect on biofilms. Furthermore, antibiotics have an ‘inherent obsolescence’ because they select for development of resistance. Bacterial infections with origin in bacterial biofilms have become a serious threat in developed countries. Pseudomonas aeruginosa...... that appropriately target bacteria in their relevant habitat with the aim of mitigating their destructive impact on patients. In this review we describe molecular mechanisms involved in “bacterial gossip” (more scientifically referred to as quorum sensing (QS) and c-di-GMP signaling), virulence, biofilm formation......, resistance and QS inhibition as future antimicrobial targets, in particular those that would work to minimize selection pressures for the development of resistant bacteria....

  6. Airborne Bacterial interactions: functions out of thin air?

    Directory of Open Access Journals (Sweden)

    Bianca eAUDRAIN

    2015-12-01

    Full Text Available Bacteria produce and release a large diversity of small molecules including organic and inorganic volatile compounds, hereafter referred to as BVCs. Whereas BVCs were often only considered as wasted metabolic by-product sometimes perceived by animal olfactory systems, it is increasingly clear that they can also mediate cross-kingdom interactions with fungi, plants and animals. Recently, in vitro studies also reported the impact of BVCs on bacterial biology through modulation of antibiotic resistance, biofilm formation and virulence. Here, we review BVCs influence on bacterial adaptation to their environment and discuss the biological relevance of recently reported inter- and intra-species bacterial interactions mediated by BVCs.

  7. Bacterial microcompartments and the modular construction of microbial metabolism.

    Science.gov (United States)

    Kerfeld, Cheryl A; Erbilgin, Onur

    2015-01-01

    Bacterial microcompartments (BMCs) are protein-bound organelles predicted to be present across 23 bacterial phyla. BMCs facilitate carbon fixation as well as the aerobic and anaerobic catabolism of a variety of organic compounds. These functions have been linked to ecological nutrient cycling, symbiosis, pathogenesis, and cardiovascular disease. Within bacterial cells, BMCs are metabolic modules that can be further dissociated into their constituent structural and functional protein domains. Viewing BMCs as genetic, structural, functional, and evolutionary modules provides a framework for understanding both BMC-mediated metabolism and for adapting their architectures for applications in synthetic biology.

  8. The role of temperate bacteriophages in bacterial infection.

    Science.gov (United States)

    Davies, Emily V; Winstanley, Craig; Fothergill, Joanne L; James, Chloe E

    2016-03-01

    Bacteriophages are viruses that infect bacteria. There are an estimated 10(31) phage on the planet, making them the most abundant form of life. We are rapidly approaching the centenary of their identification, and yet still have only a limited understanding of their role in the ecology and evolution of bacterial populations. Temperate prophage carriage is often associated with increased bacterial virulence. The rise in use of technologies, such as genome sequencing and transcriptomics, has highlighted more subtle ways in which prophages contribute to pathogenicity. This review discusses the current knowledge of the multifaceted effects that phage can exert on their hosts and how this may contribute to bacterial adaptation during infection.

  9. Bacterial Population Genetics in a Forensic Context

    Energy Technology Data Exchange (ETDEWEB)

    Velsko, S P

    2009-11-02

    networks involve complex soil communities and metapopulations about which very little is known. It is not clear that these pathogens can be brought into the inference-on-networks framework without additional conceptual advances. (11) For all 8 bacteria some combination of field studies, computational modeling, and laboratory experiments are needed to provide a useful forensic capability for bacterial genetic inference.

  10. Bacterial intermediate filaments

    DEFF Research Database (Denmark)

    Charbon, Godefroid; Cabeen, M.; Jacobs-Wagner, C.

    2009-01-01

    Crescentin, which is the founding member of a rapidly growing family of bacterial cytoskeletal proteins, was previously proposed to resemble eukaryotic intermediate filament (IF) proteins based on structural prediction and in vitro polymerization properties. Here, we demonstrate that crescentin...

  11. Bacterial Wound Culture

    Science.gov (United States)

    ... Home Visit Global Sites Search Help? Bacterial Wound Culture Share this page: Was this page helpful? Also known as: Aerobic Wound Culture; Anaerobic Wound Culture Formal name: Culture, wound Related ...

  12. Bacterial Meningitis in Infants

    Directory of Open Access Journals (Sweden)

    J Gordon Millichap

    2004-04-01

    Full Text Available A retrospective study of 80 infantile patients (ages 30-365 days; 47 male, 33 female with culture-proven bacterial meningitis seen over a 16 year period (1986-2001 is reported from Taiwan.

  13. Bacterial proteases and virulence

    DEFF Research Database (Denmark)

    Frees, Dorte; Brøndsted, Lone; Ingmer, Hanne

    2013-01-01

    Bacterial pathogens rely on proteolysis for variety of purposes during the infection process. In the cytosol, the main proteolytic players are the conserved Clp and Lon proteases that directly contribute to virulence through the timely degradation of virulence regulators and indirectly by providing....... These extracellular proteases are activated in complex cascades involving auto-processing and proteolytic maturation. Thus, proteolysis has been adopted by bacterial pathogens at multiple levels to ensure the success of the pathogen in contact with the human host....

  14. Toothbrush Adaptations.

    Science.gov (United States)

    Exceptional Parent, 1987

    1987-01-01

    Suggestions are presented for helping disabled individuals learn to use or adapt toothbrushes for proper dental care. A directory lists dental health instructional materials available from various organizations. (CB)

  15. Ambiguous Adaptation

    DEFF Research Database (Denmark)

    Møller Larsen, Marcus; Lyngsie, Jacob

    We investigate why some exchange relationships terminate prematurely. We argue that investments in informal governance structures induce premature termination in relationships already governed by formal contracts. The formalized adaptive behavior of formal governance structures and the flexible a...

  16. [Diagnosis of bacterial vaginosis].

    Science.gov (United States)

    Djukić, Slobodanka; Ćirković, Ivana; Arsić, Biljana; Garalejić, Eliana

    2013-01-01

    Bacterial vaginosis is a common, complex clinical syndrome characterized by alterations in the normal vaginal flora. When symptomatic, it is associated with a malodorous vaginal discharge and on occasion vaginal burning or itching. Under normal conditions, lactobacilli constitute 95% of the bacteria in the vagina. Bacterial vaginosis is associated with severe reduction or absence of the normal H2O2-producing lactobacilli and overgrowth of anaerobic bacteria and Gardnerella vaginalis, Atopobium vaginae, Mycoplasma hominis and Mobiluncus species. Most types of infectious disease are diagnosed by culture, by isolating an antigen or RNA/DNA from the microbe, or by serodiagnosis to determine the presence of antibodies to the microbe. Therefore, demonstration of the presence of an infectious agent is often a necessary criterion for the diagnosis of the disease. This is not the case for bacterial vaginosis, since the ultimate cause of the disease is not yet known. There are a variety of methods for the diagnosis of bacterial vaginosis but no method can at present be regarded as the best. Diagnosing bacterial vaginosis has long been based on the clinical criteria of Amsel, whereby three of four defined criteria must be satisfied. Nugent's scoring system has been further developed and includes validation of the categories of observable bacteria structures. Up-to-date molecular tests are introduced, and better understanding of vaginal microbiome, a clear definition for bacterial vaginosis, and short-term and long-term fluctuations in vaginal microflora will help to better define molecular tests within the broader clinical context.

  17. Hedonic "adaptation"

    OpenAIRE

    2008-01-01

    People live in a world in which they are surrounded by potential disgust elicitors such as ``used'' chairs, air, silverware, and money as well as excretory activities. People function in this world by ignoring most of these, by active avoidance, reframing, or adaptation. The issue is particularly striking for professions, such as morticians, surgeons, or sanitation workers, in which there is frequent contact with major disgust elicitors. In this study, we study the ``adaptation'' process to d...

  18. Strategic Adaptation

    DEFF Research Database (Denmark)

    Andersen, Torben Juul

    2015-01-01

    This article provides an overview of theoretical contributions that have influenced the discourse around strategic adaptation including contingency perspectives, strategic fit reasoning, decision structure, information processing, corporate entrepreneurship, and strategy process. The related...... concepts of strategic renewal, dynamic managerial capabilities, dynamic capabilities, and strategic response capabilities are discussed and contextualized against strategic responsiveness. The insights derived from this article are used to outline the contours of a dynamic process of strategic adaptation...

  19. Gene migration for re-emerging amebiasis in Iran's northwest-Iraq borders: a microevolutionary scale for reflecting epidemiological drift of Entamoeba histolytica metapopulations.

    Science.gov (United States)

    Mohammadzadeh, Asad; Spotin, Adel; Mahami-Oskouei, Mahmoud; Haghighi, Ali; Zebardast, Nozhat; Kohansal, Kobra

    2017-01-01

    In the microevolutionary scales of Entamoeba isolates, the gene migration shows how Entamoeba spp. has epidemiologically drifted among border countries. Five hundred fecal samples were taken from patients suffering gastrointestinal disorders, abdominal pain, and diarrhea at Saggez, northwest Iran located within the border Iraq country. Following parasitological techniques, DNA samples were extracted and amplified by polymerase chain reaction (PCR) of 18S rRNA region to identify Entamoeba infections. To distinguish the Entamoeba spp., a multiplex PCR was conducted. Amplicons were sequenced to reconfirm their heterogeneity traits and phylogenetic analysis. Additionally, Entamoeba histolytica sequences of Iraq were retrieved from GenBank database. The suspected isolates were diagnosed as E. histolytica (2.2 %), Entamoeba moshkovskii (1 %), and Entamoeba dispar (0.4 %). Mixed Entamoeba infections did not detect among isolates. A parsimonious network of the sequence haplotypes displayed star-like features in the overall isolates containing E.h1, E.d2, and E.m3 as the most common haplotypes. According to analysis of molecular variance (AMOVA) test, high partial value of haplotype diversity (0.700 to 0.800) of E. histolytica was shown the total genetic variability within populations while nucleotide diversity was low among Iranian and Iraqi metapopulations. Neutrality indices of the 18S rRNA were shown negative values in E. histolytica populations which indicating significant deviations from neutrality. A pairwise fixation index (F-statistics [Fst]) as a degree of gene flow had a low value for all populations (0.001) while the number of migrants was 2.48. The statistically Fst value indicates that E. histolytica isolates are not genetically differentiated among shared isolates of Iran and Iraq. Occurrence of E.h1 between two regional populations indicates that there is dawn of Entamoeba flow due to transfer of alleles from one population to another population through

  20. Is adaptation. Truly an adaptation? Is adaptation. Truly an adaptation?

    Directory of Open Access Journals (Sweden)

    Thais Flores Nogueira Diniz

    2008-04-01

    Full Text Available The article begins by historicizing film adaptation from the arrival of cinema, pointing out the many theoretical approaches under which the process has been seen: from the concept of “the same story told in a different medium” to a comprehensible definition such as “the process through which works can be transformed, forming an intersection of textual surfaces, quotations, conflations and inversions of other texts”. To illustrate this new concept, the article discusses Spike Jonze’s film Adaptation. according to James Naremore’s proposal which considers the study of adaptation as part of a general theory of repetition, joined with the study of recycling, remaking, and every form of retelling. The film deals with the attempt by the scriptwriter Charles Kaufman, cast by Nicholas Cage, to adapt/translate a non-fictional book to the cinema, but ends up with a kind of film which is by no means what it intended to be: a film of action in the model of Hollywood productions. During the process of creation, Charles and his twin brother, Donald, undergo a series of adventures involving some real persons from the world of film, the author and the protagonist of the book, all of them turning into fictional characters in the film. In the film, adaptation then signifies something different from itstraditional meaning. The article begins by historicizing film adaptation from the arrival of cinema, pointing out the many theoretical approaches under which the process has been seen: from the concept of “the same story told in a different medium” to a comprehensible definition such as “the process through which works can be transformed, forming an intersection of textual surfaces, quotations, conflations and inversions of other texts”. To illustrate this new concept, the article discusses Spike Jonze’s film Adaptation. according to James Naremore’s proposal which considers the study of adaptation as part of a general theory of repetition

  1. The bacterial lipocalins.

    Science.gov (United States)

    Bishop, R E

    2000-10-18

    The lipocalins were once regarded as a eukaryotic protein family, but new members have been recently discovered in bacteria. The first bacterial lipocalin (Blc) was identified in Escherichia coli as an outer membrane lipoprotein expressed under conditions of environmental stress. Blc is distinguished from most lipocalins by the absence of intramolecular disulfide bonds, but the presence of a membrane anchor is shared with two of its closest homologues, apolipoprotein D and lazarillo. Several common features of the membrane-anchored lipocalins suggest that each may play an important role in membrane biogenesis and repair. Additionally, Blc proteins are implicated in the dissemination of antibiotic resistance genes and in the activation of immunity. Recent genome sequencing efforts reveal the existence of at least 20 bacterial lipocalins. The lipocalins appear to have originated in Gram-negative bacteria and were probably transferred horizontally to eukaryotes from the endosymbiotic alpha-proteobacterial ancestor of the mitochondrion. The genome sequences also reveal that some bacterial lipocalins exhibit disulfide bonds and alternative modes of subcellular localization, which include targeting to the periplasmic space, the cytoplasmic membrane, and the cytosol. The relationships between bacterial lipocalin structure and function further illuminate the common biochemistry of bacterial and eukaryotic cells.

  2. Heterotrophic activity, bacterial types and abundance in different ecosystems of the Queen Maud Land

    Digital Repository Service at National Institute of Oceanography (India)

    Ramaiah, N.; Kodagali, J.; Nair, S.; Sheelu, G.; Chandramohan, D.

    . Distribution of bacterial populations in freshwater, terrestrial and glacial habitats in the Schirmacher Oasis showed a remarkable ecological adaptation. They were more abundant in the habitats where there was accumulation of organic matter. Interestingly...

  3. Striking the metapopulation balance : Mathematical Models & Methods Meet Metapopulation Management

    NARCIS (Netherlands)

    Etienne, R.S.

    2002-01-01

    There are two buzz words in nature management: fragmentation and connectivity. Not only (rail) roads, but also agricultural, residential and industrial areas fragment previously connected (or even continuous) habitat. Common sense tells us that the answer to habitat fragmentation is defragmentation

  4. Adaptive test

    DEFF Research Database (Denmark)

    Kjeldsen, Lars Peter; Rose, Mette

    2010-01-01

    Artikelen er en evaluering af de adaptive tests, som blev indført i folkeskolen. Artiklen sætter særligt fokus på evaluering i folkeskolen, herunder bidrager den med vejledning til evaluering, evalueringsværktøjer og fagspecifkt evalueringsmateriale.......Artikelen er en evaluering af de adaptive tests, som blev indført i folkeskolen. Artiklen sætter særligt fokus på evaluering i folkeskolen, herunder bidrager den med vejledning til evaluering, evalueringsværktøjer og fagspecifkt evalueringsmateriale....

  5. Bacterial glycosyltransferase toxins.

    Science.gov (United States)

    Jank, Thomas; Belyi, Yury; Aktories, Klaus

    2015-12-01

    Mono-glycosylation of host proteins is a common mechanism by which bacterial protein toxins manipulate cellular functions of eukaryotic target host cells. Prototypic for this group of glycosyltransferase toxins are Clostridium difficile toxins A and B, which modify guanine nucleotide-binding proteins of the Rho family. However, toxin-induced glycosylation is not restricted to the Clostridia. Various types of bacterial pathogens including Escherichia coli, Yersinia, Photorhabdus and Legionella species produce glycosyltransferase toxins. Recent studies discovered novel unexpected variations in host protein targets and amino acid acceptors of toxin-catalysed glycosylation. These findings open new perspectives in toxin as well as in carbohydrate research.

  6. Bacterial computing: a form of natural computing and its applications.

    Science.gov (United States)

    Lahoz-Beltra, Rafael; Navarro, Jorge; Marijuán, Pedro C

    2014-01-01

    The capability to establish adaptive relationships with the environment is an essential characteristic of living cells. Both bacterial computing and bacterial intelligence are two general traits manifested along adaptive behaviors that respond to surrounding environmental conditions. These two traits have generated a variety of theoretical and applied approaches. Since the different systems of bacterial signaling and the different ways of genetic change are better known and more carefully explored, the whole adaptive possibilities of bacteria may be studied under new angles. For instance, there appear instances of molecular "learning" along the mechanisms of evolution. More in concrete, and looking specifically at the time dimension, the bacterial mechanisms of learning and evolution appear as two different and related mechanisms for adaptation to the environment; in somatic time the former and in evolutionary time the latter. In the present chapter it will be reviewed the possible application of both kinds of mechanisms to prokaryotic molecular computing schemes as well as to the solution of real world problems.

  7. Macrophages Subvert Adaptive Immunity to Urinary Tract Infection.

    Directory of Open Access Journals (Sweden)

    Gabriela Mora-Bau

    2015-07-01

    Full Text Available Urinary tract infection (UTI is one of the most common bacterial infections with frequent recurrence being a major medical challenge. Development of effective therapies has been impeded by the lack of knowledge of events leading to adaptive immunity. Here, we establish conclusive evidence that an adaptive immune response is generated during UTI, yet this response does not establish sterilizing immunity. To investigate the underlying deficiency, we delineated the naïve bladder immune cell compartment, identifying resident macrophages as the most populous immune cell. To evaluate their impact on the establishment of adaptive immune responses following infection, we measured bacterial clearance in mice depleted of either circulating monocytes, which give rise to macrophages, or bladder resident macrophages. Surprisingly, mice depleted of resident macrophages, prior to primary infection, exhibited a nearly 2-log reduction in bacterial burden following secondary challenge compared to untreated animals. This increased bacterial clearance, in the context of a challenge infection, was dependent on lymphocytes. Macrophages were the predominant antigen presenting cell to acquire bacteria post-infection and in their absence, bacterial uptake by dendritic cells was increased almost 2-fold. These data suggest that bacterial uptake by tissue macrophages impedes development of adaptive immune responses during UTI, revealing a novel target for enhancing host responses to bacterial infection of the bladder.

  8. Seizures Complicating Bacterial Meningitis

    Directory of Open Access Journals (Sweden)

    J Gordon Millichap

    2004-09-01

    Full Text Available The clinical data of 116 patients, 1 month to <5 years of age, admitted for bacterial meningitis, and grouped according to those with and without seizures during hospitalization, were compared in a study at Buddhist Dalin Tzu Chi General Hospital, Chang Gung Memorial Hospital and other centers in Taiwan.

  9. The Carboxysome and Other Bacterial Microcompartments

    Energy Technology Data Exchange (ETDEWEB)

    Kerfeld, Cheryl A.; Greenleaf, William B.; Kinney, James N.

    2010-06-23

    - Carboxysomes are part of the carbon concentrating mechanism in cyanobacteria and chemoautotrophs. - Carboxysomes are a subclass of bacterial microcompartments (BMCs); BMCs can encapsulate a range of metabolic processes. - Like some viral particles, the carboxysome can be modeled as an icosahedron-in its case, having 4,000-5,000 hexameric shell subunits and 12 surface pentamers to generate curvature. - The threefold axis of symmetry of the CsoS1D protein in carboxysomes forms a pore that can open and close, allowing for selective diffusion. - Genetic modules encoding BMC shell proteins and the enzymes that they encapsulate are horizontally transferable, suggesting they enable bacteria to adapt to diverse environments.

  10. The clinical impact of bacterial biofilms

    DEFF Research Database (Denmark)

    Høiby, Niels; Ciofu, Oana; Johansen, Helle Krogh

    2011-01-01

    . Bacterial biofilms are resistant to antibiotics, disinfectant chemicals and to phagocytosis and other components of the innate and adaptive inflammatory defense system of the body. It is known, for example, that persistence of staphylococcal infections related to foreign bodies is due to biofilm formation...... and increased doubling times. These more or less dormant cells are therefore responsible for some of the tolerance to antibiotics. Biofilm growth is associated with an increased level of mutations. Bacteria in biofilms communicate by means of molecules, which activates certain genes responsible for production...

  11. Hedonic "adaptation"

    Directory of Open Access Journals (Sweden)

    Paul Rozin

    2008-02-01

    Full Text Available People live in a world in which they are surrounded by potential disgust elicitors such as ``used'' chairs, air, silverware, and money as well as excretory activities. People function in this world by ignoring most of these, by active avoidance, reframing, or adaptation. The issue is particularly striking for professions, such as morticians, surgeons, or sanitation workers, in which there is frequent contact with major disgust elicitors. In this study, we study the ``adaptation'' process to dead bodies as disgust elicitors, by measuring specific types of disgust sensitivity in medical students before and after they have spent a few months dissecting a cadaver. Using the Disgust Scale, we find a significant reduction in disgust responses to death and body envelope violation elicitors, but no significant change in any other specific type of disgust. There is a clear reduction in discomfort at touching a cold dead body, but not in touching a human body which is still warm after death.

  12. Adaptation Laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Huq, Saleemul

    2011-11-15

    Efforts to help the world's poor will face crises in coming decades as climate change radically alters conditions. Action Research for Community Adapation in Bangladesh (ARCAB) is an action-research programme on responding to climate change impacts through community-based adaptation. Set in Bangladesh at 20 sites that are vulnerable to floods, droughts, cyclones and sea level rise, ARCAB will follow impacts and adaptation as they evolve over half a century or more. National and international 'research partners', collaborating with ten NGO 'action partners' with global reach, seek knowledge and solutions applicable worldwide. After a year setting up ARCAB, we share lessons on the programme's design and move into our first research cycle.

  13. Phenotypic plasticity in bacterial plasmids.

    Science.gov (United States)

    Turner, Paul E

    2004-01-01

    Plasmid pB15 was previously shown to evolve increased horizontal (infectious) transfer at the expense of reduced vertical (intergenerational) transfer and vice versa, a key trade-off assumed in theories of parasite virulence. Whereas the models predict that susceptible host abundance should determine which mode of transfer is selectively favored, host density failed to mediate the trade-off in pB15. One possibility is that the plasmid's transfer deviates from the assumption that horizontal spread (conjugation) occurs in direct proportion to cell density. I tested this hypothesis using Escherichia coli/pB15 associations in laboratory serial culture. Contrary to most models of plasmid transfer kinetics, my data show that pB15 invades static (nonshaking) bacterial cultures only at intermediate densities. The results can be explained by phenotypic plasticity in traits governing plasmid transfer. As cells become more numerous, the plasmid's conjugative transfer unexpectedly declines, while the trade-off between transmission routes causes vertical transfer to increase. Thus, at intermediate densities the plasmid's horizontal transfer can offset selection against plasmid-bearing cells, but at high densities pB15 conjugates so poorly that it cannot invade. I discuss adaptive vs. nonadaptive causes for the phenotypic plasticity, as well as potential mechanisms that may lead to complex transfer dynamics of plasmids in liquid environments. PMID:15166133

  14. Cooperative Bacterial Foraging Optimization

    Directory of Open Access Journals (Sweden)

    Hanning Chen

    2009-01-01

    Full Text Available Bacterial Foraging Optimization (BFO is a novel optimization algorithm based on the social foraging behavior of E. coli bacteria. This paper presents a variation on the original BFO algorithm, namely, the Cooperative Bacterial Foraging Optimization (CBFO, which significantly improve the original BFO in solving complex optimization problems. This significant improvement is achieved by applying two cooperative approaches to the original BFO, namely, the serial heterogeneous cooperation on the implicit space decomposition level and the serial heterogeneous cooperation on the hybrid space decomposition level. The experiments compare the performance of two CBFO variants with the original BFO, the standard PSO and a real-coded GA on four widely used benchmark functions. The new method shows a marked improvement in performance over the original BFO and appears to be comparable with the PSO and GA.

  15. Bacterial Colony Optimization

    Directory of Open Access Journals (Sweden)

    Ben Niu

    2012-01-01

    Full Text Available This paper investigates the behaviors at different developmental stages in Escherichia coli (E. coli lifecycle and developing a new biologically inspired optimization algorithm named bacterial colony optimization (BCO. BCO is based on a lifecycle model that simulates some typical behaviors of E. coli bacteria during their whole lifecycle, including chemotaxis, communication, elimination, reproduction, and migration. A newly created chemotaxis strategy combined with communication mechanism is developed to simplify the bacterial optimization, which is spread over the whole optimization process. However, the other behaviors such as elimination, reproduction, and migration are implemented only when the given conditions are satisfied. Two types of interactive communication schemas: individuals exchange schema and group exchange schema are designed to improve the optimization efficiency. In the simulation studies, a set of 12 benchmark functions belonging to three classes (unimodal, multimodal, and rotated problems are performed, and the performances of the proposed algorithms are compared with five recent evolutionary algorithms to demonstrate the superiority of BCO.

  16. Bacterial assays for recombinagens.

    Science.gov (United States)

    Hoffmann, G R

    1992-12-01

    Two principal strategies have been used for studying recombinagenic effects of chemicals and radiation in bacteria: (1) measurement of homologous recombination involving defined alleles in a partially diploid strain, and (2) measurement of the formation and loss of genetic duplications in the bacterial chromosome. In the former category, most methods involve one allele in the bacterial chromosome and another in a plasmid, but it is also possible to detect recombination between two chromosomal alleles or between two extrachromosomal alleles. This review summarizes methods that use each of these approaches for detecting recombination and tabulates data on agents that have been found to be recombinagenic in bacteria. The assays are discussed with respect to their effectiveness in testing for recombinagens and their potential for elucidating mechanisms underlying recombinagenic effects.

  17. Bacterial transformation of terpenoids

    Science.gov (United States)

    Grishko, V. V.; Nogovitsina, Y. M.; Ivshina, I. B.

    2014-04-01

    Data on the bacterial transformation of terpenoids published in the literature in the past decade are analyzed. Possible pathways for chemo-, regio- and stereoselective modifications of terpenoids are discussed. Considerable attention is given to new technological approaches to the synthesis of terpenoid derivatives suitable for the use in the perfume and food industry and promising as drugs and chiral intermediates for fine organic synthesis. The bibliography includes 246 references.

  18. Spontaneous bacterial peritonitis

    OpenAIRE

    Al Amri Saleh

    1995-01-01

    Spontaneous bacterial peritonitis (SBP) is an infection of the ascitic fluid without obvious intra-abdominal source of sepsis; usually complicates advanced liver disease. The pathogenesis of the disease is multifactorial: low ascitic protein-content, which reflects defi-cient ascitic fluid complement and hence, reduced opsonic activity is thought to be the most important pathogenic factor. Frequent and prolonged bacteremia has been considered as another pertinent cause of SBP. This disease is...

  19. Modelling bacterial speciation

    OpenAIRE

    2006-01-01

    A central problem in understanding bacterial speciation is how clusters of closely related strains emerge and persist in the face of recombination. We use a neutral Fisher–Wright model in which genotypes, defined by the alleles at 140 house-keeping loci, change in each generation by mutation or recombination, and examine conditions in which an initially uniform population gives rise to resolved clusters. Where recombination occurs at equal frequency between all members of the population, we o...

  20. Neglected bacterial zoonoses.

    Science.gov (United States)

    Chikeka, I; Dumler, J S

    2015-05-01

    Bacterial zoonoses comprise a group of diseases in humans or animals acquired by direct contact with or by oral consumption of contaminated animal materials, or via arthropod vectors. Among neglected infections, bacterial zoonoses are among the most neglected given emerging data on incidence and prevalence as causes of acute febrile illness, even in areas where recognized neglected tropical diseases occur frequently. Although many other bacterial infections could also be considered in this neglected category, five distinct infections stand out because they are globally distributed, are acute febrile diseases, have high rates of morbidity and case fatality, and are reported as commonly as malaria, typhoid or dengue virus infections in carefully designed studies in which broad-spectrum diagnoses are actively sought. This review will focus attention on leptospirosis, relapsing fever borreliosis and rickettsioses, including scrub typhus, murine typhus and spotted fever group rickettsiosis. Of greatest interest is the lack of distinguishing clinical features among these infections when in humans, which confounds diagnosis where laboratory confirmation is lacking, and in regions where clinical diagnosis is often attributed to one of several perceived more common threats. As diseases such as malaria come under improved control, the real impact of these common and under-recognized infections will become evident, as will the requirement for the strategies and allocation of resources for their control.

  1. Collective decision making in bacterial viruses.

    Science.gov (United States)

    Weitz, Joshua S; Mileyko, Yuriy; Joh, Richard I; Voit, Eberhard O

    2008-09-15

    For many bacterial viruses, the choice of whether to kill host cells or enter a latent state depends on the multiplicity of coinfection. Here, we present a mathematical theory of how bacterial viruses can make collective decisions concerning the fate of infected cells. We base our theory on mechanistic models of gene regulatory dynamics. Unlike most previous work, we treat the copy number of viral genes as variable. Increasing the viral copy number increases the rate of transcription of viral mRNAs. When viral regulation of cell fate includes nonlinear feedback loops, very small changes in transcriptional rates can lead to dramatic changes in steady-state gene expression. Hence, we prove that deterministic decisions can be reached, e.g., lysis or latency, depending on the cellular multiplicity of infection within a broad class of gene regulatory models of viral decision-making. Comparisons of a parameterized version of the model with molecular studies of the decision structure in the temperate bacteriophage lambda are consistent with our conclusions. Because the model is general, it suggests that bacterial viruses can respond adaptively to changes in population dynamics, and that features of collective decision-making in viruses are evolvable life history traits.

  2. 3D printing of microscopic bacterial communities

    Science.gov (United States)

    Connell, Jodi L.; Ritschdorff, Eric T.; Whiteley, Marvin; Shear, Jason B.

    2013-01-01

    Bacteria communicate via short-range physical and chemical signals, interactions known to mediate quorum sensing, sporulation, and other adaptive phenotypes. Although most in vitro studies examine bacterial properties averaged over large populations, the levels of key molecular determinants of bacterial fitness and pathogenicity (e.g., oxygen, quorum-sensing signals) may vary over micrometer scales within small, dense cellular aggregates believed to play key roles in disease transmission. A detailed understanding of how cell–cell interactions contribute to pathogenicity in natural, complex environments will require a new level of control in constructing more relevant cellular models for assessing bacterial phenotypes. Here, we describe a microscopic three-dimensional (3D) printing strategy that enables multiple populations of bacteria to be organized within essentially any 3D geometry, including adjacent, nested, and free-floating colonies. In this laser-based lithographic technique, microscopic containers are formed around selected bacteria suspended in gelatin via focal cross-linking of polypeptide molecules. After excess reagent is removed, trapped bacteria are localized within sealed cavities formed by the cross-linked gelatin, a highly porous material that supports rapid growth of fully enclosed cellular populations and readily transmits numerous biologically active species, including polypeptides, antibiotics, and quorum-sensing signals. Using this approach, we show that a picoliter-volume aggregate of Staphylococcus aureus can display substantial resistance to β-lactam antibiotics by enclosure within a shell composed of Pseudomonas aeruginosa. PMID:24101503

  3. Evolution of Bacterial Pathogens Within the Human Host.

    Science.gov (United States)

    Bliven, Kimberly A; Maurelli, Anthony T

    2016-02-01

    Selective pressures within the human host, including interactions with innate and adaptive immune responses, exposure to medical interventions such as antibiotics, and competition with commensal microbiota all facilitate the evolution of bacterial pathogens. In this chapter, we present examples of pathogen strategies that emerged as a result of selective pressures within the human host niche and discuss the resulting coevolutionary "arms race" between these organisms. In bacterial pathogens, many of the genes responsible for these strategies are encoded on mobile pathogenicity islands or plasmids, underscoring the importance of horizontal gene transfer in the emergence of virulent microbial species.

  4. Catabolism of host-derived compounds during extracellular bacterial infections.

    Science.gov (United States)

    Meadows, Jamie A; Wargo, Matthew J

    2014-02-01

    Efficient catabolism of host-derived compounds is essential for bacterial survival and virulence. While these links in intracellular bacteria are well studied, such studies in extracellular bacteria lag behind, mostly for technical reasons. The field has identified important metabolic pathways, but the mechanisms by which they impact infection and in particular, establishing the importance of a compound's catabolism versus alternate metabolic roles has been difficult. In this review we will examine evidence for catabolism during extracellular bacterial infections in animals and known or potential roles in virulence. In the process, we point out key gaps in the field that will require new or newly adapted techniques.

  5. Bacteriophage functional genomics and its role in bacterial pathogen detection.

    Science.gov (United States)

    Klumpp, Jochen; Fouts, Derrick E; Sozhamannan, Shanmuga

    2013-07-01

    Emerging and reemerging bacterial infectious diseases are a major public health concern worldwide. The role of bacteriophages in the emergence of novel bacterial pathogens by horizontal gene transfer was highlighted by the May 2011 Escherichia coli O104:H4 outbreaks that originated in Germany and spread to other European countries. This outbreak also highlighted the pivotal role played by recent advances in functional genomics in rapidly deciphering the virulence mechanism elicited by this novel pathogen and developing rapid diagnostics and therapeutics. However, despite a steady increase in the number of phage sequences in the public databases, boosted by the next-generation sequencing technologies, few functional genomics studies of bacteriophages have been conducted. Our definition of 'functional genomics' encompasses a range of aspects: phage genome sequencing, annotation and ascribing functions to phage genes, prophage identification in bacterial sequences, elucidating the events in various stages of phage life cycle using genomic, transcriptomic and proteomic approaches, defining the mechanisms of host takeover including specific bacterial-phage protein interactions and identifying virulence and other adaptive features encoded by phages and finally, using prophage genomic information for bacterial detection/diagnostics. Given the breadth and depth of this definition and the fact that some of these aspects (especially phage-encoded virulence/adaptive features) have been treated extensively in other reviews, we restrict our focus only on certain aspects. These include phage genome sequencing and annotation, identification of prophages in bacterial sequences and genetic characterization of phages, functional genomics of the infection process and finally, bacterial identification using genomic information.

  6. Highly heterogeneous soil bacterial communities around Terra Nova Bay of Northern Victoria Land, Antarctica.

    Directory of Open Access Journals (Sweden)

    Mincheol Kim

    Full Text Available Given the diminished role of biotic interactions in soils of continental Antarctica, abiotic factors are believed to play a dominant role in structuring of microbial communities. However, many ice-free regions remain unexplored, and it is unclear which environmental gradients are primarily responsible for the variations among bacterial communities. In this study, we investigated the soil bacterial community around Terra Nova Bay of Victoria Land by pyrosequencing and determined which environmental variables govern the bacterial community structure at the local scale. Six bacterial phyla, Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes, were dominant, but their relative abundance varied greatly across locations. Bacterial community structures were affected little by spatial distance, but structured more strongly by site, which was in accordance with the soil physicochemical compositions. At both the phylum and species levels, bacterial community structure was explained primarily by pH and water content, while certain earth elements and trace metals also played important roles in shaping community variation. The higher heterogeneity of the bacterial community structure found at this site indicates how soil bacterial communities have adapted to different compositions of edaphic variables under extreme environmental conditions. Taken together, these findings greatly advance our understanding of the adaption of soil bacterial populations to this harsh environment.

  7. Adaptive management

    DEFF Research Database (Denmark)

    Rist, Lucy; Campbell, Bruce Morgan; Frost, Peter

    2013-01-01

    in scientific articles, policy documents and management plans, but both understanding and application of the concept is mixed. This paper reviews recent literature from conservation and natural resource management journals to assess diversity in how the term is used, highlight ambiguities and consider how...... the concept might be further assessed. AM is currently being used to describe many different management contexts, scales and locations. Few authors define the term explicitly or describe how it offers a means to improve management outcomes in their specific management context. Many do not adhere to the idea......Adaptive management (AM) emerged in the literature in the mid-1970s in response both to a realization of the extent of uncertainty involved in management, and a frustration with attempts to use modelling to integrate knowledge and make predictions. The term has since become increasingly widely used...

  8. Pseudomonas aeruginosa host-adaptation in cystic fibrosis patients

    DEFF Research Database (Denmark)

    Rau, Martin Holm

    Pseudomonas aeruginosa is an opportunistic pathogen capable of transition from an environmental lifestyle to a host-associated lifestyle, as exemplified in the life-long airway infection of cystic fibrosis (CF) patients. Long-term infection is associated with extensive genetic adaptation of P....... aeruginosa towards the CF airway environment generating variants with markedly altered phenotypes. Gaining insight into this adaptation process has great clinical relevance but simultaneously has the potential to increase our understanding of bacterial adaptation to a host environment. This has been...... to unravel the early adaptive processes possibly securing bacterial persistence. In this early stage, clinical isolates displayed few adaptive events however these included phenotypes often observed in late chronic infection isolates including the conversion to a mucoid phenotype and increased antibiotic...

  9. Bacterial chromosome segregation.

    Science.gov (United States)

    Possoz, Christophe; Junier, Ivan; Espeli, Olivier

    2012-01-01

    Dividing cells have mechanisms to ensure that their genomes are faithfully segregated into daughter cells. In bacteria, the description of these mechanisms has been considerably improved in the recent years. This review focuses on the different aspects of bacterial chromosome segregation that can be understood thanks to the studies performed with model organisms: Escherichia coli, Bacillus subtilis, Caulobacter crescentus and Vibrio cholerae. We describe the global positionning of the nucleoid in the cell and the specific localization and dynamics of different chromosomal loci, kinetic and biophysic aspects of chromosome segregation are presented. Finally, a presentation of the key proteins involved in the chromosome segregation is made.

  10. Bacterial Degradation of Pesticides

    DEFF Research Database (Denmark)

    Knudsen, Berith Elkær

    This PhD project was carried out as part of the Microbial Remediation of Contaminated Soil and Water Resources (MIRESOWA) project, funded by the Danish Council for Strategic Research (grant number 2104-08-0012). The environment is contaminated with various xenobiotic compounds e.g. pesticides......D student, to construct fungal-bacterial consortia in order to potentially stimulate pesticide degradation thereby increasing the chance of successful bioaugmentation. The results of the project are reported in three article manuscripts, included in this thesis. In manuscript I, the mineralization of 2...

  11. Spontaneous bacterial peritonitis

    Directory of Open Access Journals (Sweden)

    Al Amri Saleh

    1995-01-01

    Full Text Available Spontaneous bacterial peritonitis (SBP is an infection of the ascitic fluid without obvious intra-abdominal source of sepsis; usually complicates advanced liver disease. The pathogenesis of the disease is multifactorial: low ascitic protein-content, which reflects defi-cient ascitic fluid complement and hence, reduced opsonic activity is thought to be the most important pathogenic factor. Frequent and prolonged bacteremia has been considered as another pertinent cause of SBP. This disease is associated with high mortality and recurrence. Therefore, orompt recognition and institution of therapy and plan of prophylaxis is vital.

  12. Bacterial mitotic machineries

    DEFF Research Database (Denmark)

    Gerdes, Kenn; Møller-Jensen, Jakob; Ebersbach, Gitte;

    2004-01-01

    Here, we review recent progress that yields fundamental new insight into the molecular mechanisms behind plasmid and chromosome segregation in prokaryotic cells. In particular, we describe how prokaryotic actin homologs form mitotic machineries that segregate DNA before cell division. Thus, the Par......M protein of plasmid R1 forms F actin-like filaments that separate and move plasmid DNA from mid-cell to the cell poles. Evidence from three different laboratories indicate that the morphogenetic MreB protein may be involved in segregation of the bacterial chromosome....

  13. Arginine Metabolism in Bacterial Pathogenesis and Cancer Therapy

    Directory of Open Access Journals (Sweden)

    Lifeng Xiong

    2016-03-01

    Full Text Available Antibacterial resistance to infectious diseases is a significant global concern for health care organizations; along with aging populations and increasing cancer rates, it represents a great burden for government healthcare systems. Therefore, the development of therapies against bacterial infection and cancer is an important strategy for healthcare research. Pathogenic bacteria and cancer have developed a broad range of sophisticated strategies to survive or propagate inside a host and cause infection or spread disease. Bacteria can employ their own metabolism pathways to obtain nutrients from the host cells in order to survive. Similarly, cancer cells can dysregulate normal human cell metabolic pathways so that they can grow and spread. One common feature of the adaption and disruption of metabolic pathways observed in bacterial and cancer cell growth is amino acid pathways; these have recently been targeted as a novel approach to manage bacterial infections and cancer therapy. In particular, arginine metabolism has been illustrated to be important not only for bacterial pathogenesis but also for cancer therapy. Therefore, greater insights into arginine metabolism of pathogenic bacteria and cancer cells would provide possible targets for controlling of bacterial infection and cancer treatment. This review will summarize the recent progress on the relationship of arginine metabolism with bacterial pathogenesis and cancer therapy, with a particular focus on arginase and arginine deiminase pathways of arginine catabolism.

  14. 生境破坏的空间结构对集合种群续存的影响%Influences of Habitat Destruction with Spatially Structure on Metapopulation Persistence

    Institute of Scientific and Technical Information of China (English)

    吴诗宝; 惠苍

    2008-01-01

    Habitat destruction is one of the most important desiderate problemin ecology, and researches always focus on the influences of destruction quantity, that is the fraction of destroyed habitat, on species' persistence, in which the most importantresult is the Levins rule and the minimum amount of suitable habitat (MASH). The im-portance of spatial structure of habitat destruction is scarcely concerned. In this paper,we first introduce the pair approximation into the study of metapopulation, ubstitutingfor the mean-field approximation. And then, we fully discuss the size, spatial structureand distribution of metapopulation induced by habitat destruction with spatial struc-ture. The results show that with the increases of destroyed fraction, the metapopulationsizes will decrease and distribute far away from the destroyed habitat, the clusteringstructure of metapopulation will collapses. With the decreases of destroyed clusteringdegree, the metapopulation will atrophy and the clustering structure will break down,and the metapopulation will increases and then disappears near the destroyed habitat.According to these esults, we can analyze the edge effect: it is not the fraction of habi-tat destruction but the boundary length of destroyed habitat that can depict the fullinfluences of habitat destruction. With the edge effect, we cursorily suggest that the re-maining habitat under destruction should prior to half of the origin to protect the speciesagainst extinction in a connective habitat. And the species living in patchy habitat willhave more resistance to habitat destruction than those residing in continuous habitat.%生境破坏及其影响是生态学亟待解决的问题之一,目前的研究主要集中在破坏数量,即遭破坏生境的比例,对物种续存的影响方面;其中最主要的结论是Levins原理和适合生境斑块最小数量(MASH),而关于生境破坏的空间结构的研究却比较稀少,在本文中,我们首先将偶对近似引入到

  15. Spontaneous bacterial peritonitis

    Institute of Scientific and Technical Information of China (English)

    Anastasios Koulaouzidis; Shivaram Bhat; Athar A Saeed

    2009-01-01

    Since its initial description in 1964, research has transformed spontaneous bacterial peritonitis (SBP) from a feared disease (with reported mortality of 90%) to a treatable complication of decompensated cirrhosis,albeit with steady prevalence and a high recurrence rate. Bacterial translocation, the key mechanism in the pathogenesis of SBP, is only possible because of the concurrent failure of defensive mechanisms in cirrhosis.Variants of SBP should be treated. Leucocyte esterase reagent strips have managed to shorten the 'tap-toshot' time, while future studies should look into their combined use with ascitic fluid pH. Third generation cephalosporins are the antibiotic of choice because they have a number of advantages. Renal dysfunction has been shown to be an independent predictor of mortality in patients with SBP. Albumin is felt to reduce the risk of renal impairment by improving effective intravascular volume, and by helping to bind proinflammatory molecules. Following a single episode of SBP, patients should have long-term antibiotic prophylaxis and be considered for liver transplantation.

  16. Antimicrobials for bacterial bioterrorism agents.

    Science.gov (United States)

    Sarkar-Tyson, Mitali; Atkins, Helen S

    2011-06-01

    The limitations of current antimicrobials for highly virulent pathogens considered as potential bioterrorism agents drives the requirement for new antimicrobials that are suitable for use in populations in the event of a deliberate release. Strategies targeting bacterial virulence offer the potential for new countermeasures to combat bacterial bioterrorism agents, including those active against a broad spectrum of pathogens. Although early in the development of antivirulence approaches, inhibitors of bacterial type III secretion systems and cell division mechanisms show promise for the future.

  17. Evolutionary rewiring and reprogramming of bacterial transcription regulation

    Institute of Scientific and Technical Information of China (English)

    Li Wang; Fang-Fang Wang; Wei Qian

    2011-01-01

    Rewiring and reprogramming of transcriptional regulation took place during bacterial speciation. The mechanistic alterations among transcription factors, cis-regulatory elements and target genes confer bacteria novel ability to adapt to stochastic environmental changes. This process is critical to their survival, especially for bacterial pathogens subjected to accelerated evolution. In the past two decades, the investigators not only completed the sequences of numerous bacterial genomes, but also made great progress in understanding the molecular basis of evolution. Here we briefly reviewed the current knowledge on the mechanistic changes among orthologous, paralogous and xenogenic regulatory circuits, which were caused by genetic recombinations such as gene duplication, horizontal gene transfer, transposable elements and different genetic contexts. We also discussed the potential impact of this area on theoretical and applied studies of microbes.

  18. Recognition of bacterial plant pathogens: local, systemic and transgenerational immunity.

    Science.gov (United States)

    Henry, Elizabeth; Yadeta, Koste A; Coaker, Gitta

    2013-09-01

    Bacterial pathogens can cause multiple plant diseases and plants rely on their innate immune system to recognize and actively respond to these microbes. The plant innate immune system comprises extracellular pattern recognition receptors that recognize conserved microbial patterns and intracellular nucleotide binding leucine-rich repeat (NLR) proteins that recognize specific bacterial effectors delivered into host cells. Plants lack the adaptive immune branch present in animals, but still afford flexibility to pathogen attack through systemic and transgenerational resistance. Here, we focus on current research in plant immune responses against bacterial pathogens. Recent studies shed light onto the activation and inactivation of pattern recognition receptors and systemic acquired resistance. New research has also uncovered additional layers of complexity surrounding NLR immune receptor activation, cooperation and sub-cellular localizations. Taken together, these recent advances bring us closer to understanding the web of molecular interactions responsible for coordinating defense responses and ultimately resistance.

  19. A Straightforward Approach for 3D Bacterial Printing.

    Science.gov (United States)

    Lehner, Benjamin A E; Schmieden, Dominik T; Meyer, Anne S

    2017-03-01

    Sustainable and personally tailored materials production is an emerging challenge to society. Living organisms can produce and pattern an extraordinarily wide range of different molecules in a sustainable way. These natural systems offer an abundant source of inspiration for the development of new environmentally friendly materials production techniques. In this paper, we describe the first steps toward the 3-dimensional printing of bacterial cultures for materials production and patterning. This methodology combines the capability of bacteria to form new materials with the reproducibility and tailored approach of 3D printing systems. For this purpose, a commercial 3D printer was modified for bacterial systems, and new alginate-based bioink chemistry was developed. Printing temperature, printhead speed, and bioink extrusion rate were all adapted and customized to maximize bacterial health and spatial resolution of printed structures. Our combination of 3D printing technology with biological systems enables a sustainable approach for the production of numerous new materials.

  20. Epigenetics and bacterial infections.

    Science.gov (United States)

    Bierne, Hélène; Hamon, Mélanie; Cossart, Pascale

    2012-12-01

    Epigenetic mechanisms regulate expression of the genome to generate various cell types during development or orchestrate cellular responses to external stimuli. Recent studies highlight that bacteria can affect the chromatin structure and transcriptional program of host cells by influencing diverse epigenetic factors (i.e., histone modifications, DNA methylation, chromatin-associated complexes, noncoding RNAs, and RNA splicing factors). In this article, we first review the molecular bases of the epigenetic language and then describe the current state of research regarding how bacteria can alter epigenetic marks and machineries. Bacterial-induced epigenetic deregulations may affect host cell function either to promote host defense or to allow pathogen persistence. Thus, pathogenic bacteria can be considered as potential epimutagens able to reshape the epigenome. Their effects might generate specific, long-lasting imprints on host cells, leading to a memory of infection that influences immunity and might be at the origin of unexplained diseases.

  1. Bacterial polyhydroxyalkanoates: Still fabulous?

    Science.gov (United States)

    Możejko-Ciesielska, Justyna; Kiewisz, Robert

    2016-11-01

    Bacterial polyhydroxyalkanoates (PHA) are polyesters accumulated as carbon and energy storage materials under limited growth conditions in the presence of excess carbon sources. They have been developed as biomaterials with unique properties for the past many years being considered as a potential substitute for conventional non-degradable plastics. Due to the increasing concern towards global climate change, depleting petroleum resource and problems with an utilization of a growing number of synthetic plastics, PHAs have gained much more attention from industry and research. These environmentally friendly microbial polymers have great potential in biomedical, agricultural, and industrial applications. However, their production on a large scale is still limited. This paper describes the backgrounds of PHAs and discussed the current state of knowledge on the polyhydroxyalkanoates. Ability of bacteria to convert different carbon sources to PHAs, the opportunities and challenges of their introduction to global market as valuable renewable products have been also discussed.

  2. Adaptively robust filtering with classified adaptive factors

    Institute of Scientific and Technical Information of China (English)

    CUI Xianqiang; YANG Yuanxi

    2006-01-01

    The key problems in applying the adaptively robust filtering to navigation are to establish an equivalent weight matrix for the measurements and a suitable adaptive factor for balancing the contributions of the measurements and the predicted state information to the state parameter estimates. In this paper, an adaptively robust filtering with classified adaptive factors was proposed, based on the principles of the adaptively robust filtering and bi-factor robust estimation for correlated observations. According to the constant velocity model of Kalman filtering, the state parameter vector was divided into two groups, namely position and velocity. The estimator of the adaptively robust filtering with classified adaptive factors was derived, and the calculation expressions of the classified adaptive factors were presented. Test results show that the adaptively robust filtering with classified adaptive factors is not only robust in controlling the measurement outliers and the kinematic state disturbing but also reasonable in balancing the contributions of the predicted position and velocity, respectively, and its filtering accuracy is superior to the adaptively robust filter with single adaptive factor based on the discrepancy of the predicted position or the predicted velocity.

  3. Supporting Adaptive and Adaptable Hypermedia Presentation Semantics

    NARCIS (Netherlands)

    Bulterman, D.C.A.; Rutledge, L.; Hardman, L.; Ossenbruggen, J.R. van

    1999-01-01

    Having the content of a presentation adapt to the needs, resources and prior activities of a user can be an important benefit of electronic documents. While part of this adaptation is related to the encodings of individual data streams, much of the adaptation can/should be guided by the semantics in

  4. Modus operandi of the bacterial RNA polymerase containing the sigma54 promoter-specificity factor.

    Science.gov (United States)

    Wigneshweraraj, Sivaramesh; Bose, Daniel; Burrows, Patricia C; Joly, Nicolas; Schumacher, Jörg; Rappas, Mathieu; Pape, Tillmann; Zhang, Xiaodong; Stockley, Peter; Severinov, Konstantin; Buck, Martin

    2008-05-01

    Bacterial sigma (sigma) factors confer gene specificity upon the RNA polymerase, the central enzyme that catalyses gene transcription. The binding of the alternative sigma factor sigma(54) confers upon the RNA polymerase special functional and regulatory properties, making it suited for control of several major adaptive responses. Here, we summarize our current understanding of the interactions the sigma(54) factor makes with the bacterial transcription machinery.

  5. Personalized Adaptive Learning

    NARCIS (Netherlands)

    Kravcik, Milos; Specht, Marcus; Naeve, Ambjorn

    2009-01-01

    Kravcik, M., Specht, M., & Naeve, A. (2008). Personalized Adaptive Learning. Presentation of PROLEARN WP1 Personalized Adaptive Learning at the final review meeting. February, 27, 2008, Hannover, Germany.

  6. Bacteriophage Amplification-Coupled Detection and Identification of Bacterial Pathogens

    Science.gov (United States)

    Cox, Christopher R.; Voorhees, Kent J.

    Current methods of species-specific bacterial detection and identification are complex, time-consuming, and often require expensive specialized equipment and highly trained personnel. Numerous biochemical and genotypic identification methods have been applied to bacterial characterization, but all rely on tedious microbiological culturing practices and/or costly sequencing protocols which render them impractical for deployment as rapid, cost-effective point-of-care or field detection and identification methods. With a view towards addressing these shortcomings, we have exploited the evolutionarily conserved interactions between a bacteriophage (phage) and its bacterial host to develop species-specific detection methods. Phage amplification-coupled matrix assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS) was utilized to rapidly detect phage propagation resulting from species-specific in vitro bacterial infection. This novel signal amplification method allowed for bacterial detection and identification in as little as 2 h, and when combined with disulfide bond reduction methods developed in our laboratory to enhance MALDI-TOF-MS resolution, was observed to lower the limit of detection by several orders of magnitude over conventional spectroscopy and phage typing methods. Phage amplification has been combined with lateral flow immunochromatography (LFI) to develop rapid, easy-to-operate, portable, species-specific point-of-care (POC) detection devices. Prototype LFI detectors have been developed and characterized for Yersinia pestis and Bacillus anthracis, the etiologic agents of plague and anthrax, respectively. Comparable sensitivity and rapidity was observed when phage amplification was adapted to a species-specific handheld LFI detector, thus allowing for rapid, simple, POC bacterial detection and identification while eliminating the need for bacterial culturing or DNA isolation and amplification techniques.

  7. Bacterial degradation of aminopyrine.

    Science.gov (United States)

    Blecher, H; Blecher, R; Wegst, W; Eberspaecher, J; Lingens, F

    1981-11-01

    1. Four strains of bacteria growing with aminopyrine as sole source of carbon were isolated from soil and were identified as strains of Phenylobacterium immobilis. 2. Strain M13 and strain E, the type species of Phenylobacterium immobilis (DSM 1986), which had been isolated by enrichment with chloridazon (5-amino-4-chloro-2-phenyl-2H-pyridazin-3-one) were used to investigate the bacterial degradation of aminopyrine. 3. Three metabolites were isolated and identified as: 4-(dimethylamino)-1,2-dihydro-1,5-dimethyl-2-(2,3-dihydro-2,3-dihydroxy-4,6-cyc lohexadien-1-yl)-3H-pyrazol-3-one, 4-(dimethylamino)-1,2-dihydro-1,5-dimethyl-2-(2,3-dihydroxyphenyl)-3H-pyrazol-3 -one and 4-(dimethylamino)-1,2-dihydro-1,5-dimethyl-3H-pyrazol-3-one. 4. An enzyme extract from cells of strain m13 was shown to further metabolize the catechol derivative of aminopyrine, with the formation of 2-pyrone-6-carboxylic acid. 5. Results indicate that the benzene ring of aminopyrine is the principal site of microbial metabolism.

  8. Electromagnetism of Bacterial Growth

    Science.gov (United States)

    Ainiwaer, Ailiyasi

    2011-10-01

    There has been increasing concern from the public about personal health due to the significant rise in the daily use of electrical devices such as cell phones, radios, computers, GPS, video games and television. All of these devices create electromagnetic (EM) fields, which are simply magnetic and electric fields surrounding the appliances that simultaneously affect the human bio-system. Although these can affect the human system, obstacles can easily shield or weaken the electrical fields; however, magnetic fields cannot be weakened and can pass through walls, human bodies and most other objects. The present study was conducted to examine the possible effects of bacteria when exposed to magnetic fields. The results indicate that a strong causal relationship is not clear, since different magnetic fields affect the bacteria differently, with some causing an increase in bacterial cells, and others causing a decrease in the same cells. This phenomenon has yet to be explained, but the current study attempts to offer a mathematical explanation for this occurrence. The researchers added cultures to the magnetic fields to examine any effects to ion transportation. Researchers discovered ions such as potassium and sodium are affected by the magnetic field. A formula is presented in the analysis section to explain this effect.

  9. Evolution of Bacterial Suicide

    Science.gov (United States)

    Tchernookov, Martin; Nemenman, Ilya

    2013-03-01

    While active, controlled cellular suicide (autolysis) in bacteria is commonly observed, it has been hard to argue that autolysis can be beneficial to an individual who commits it. We propose a theoretical model that predicts that bacterial autolysis is evolutionarily advantageous to an individualand would fixate in physically structured environments for stationary phase colonies. We perform spatially resolved agent-based simulations of the model, which predict that lower mixing in the environment results in fixation of a higher autolysis rate from a single mutated cell, regardless of the colony's genetic diversity. We argue that quorum sensing will fixate as well, even if initially rare, if it is coupled to controlling the autolysis rate. The model does not predict a strong additional competitive advantage for cells where autolysis is controlled by quorum sensing systems that distinguish self from nonself. These predictions are broadly supported by recent experimental results in B. subtilisand S. pneumoniae. Research partially supported by the James S McDonnell Foundation grant No. 220020321 and by HFSP grant No. RGY0084/2011.

  10. Bacterial endocarditis prophylaxis.

    Science.gov (United States)

    Blanco-Carrión, Andrés

    2004-01-01

    Bacterial endocarditis (BE) is a disease resulting from the association of morphological alterations of the heart and bacteraemia originating from different sources that at times can be indiscernible (infectious endocarditis). It is classified on the basis of the morphological alteration involved, depending on the clinical manifestations and course of illness, which varies according to the causative microorganism and host conditions (for example, it is characteristic in I.V. drug users). The most common microorganisms involved are: Streptococcus viridans (55%), Staphylococcus aureus (30%), Enterococcus (6%) and HACEK bacteria (corresponding to the initials: Haemophilus, Actinobacillus, Cardiobacterium, Eikenella and Kingella), although on occasions it can also be caused by fungi. The oral microbiological flora plays a very important role in the aetiopathogenesis of BE, given that the condition may be of oral or dental origin. This paper will deal with the prevention of said bacteraemia. Prophylaxis will be undertaken using amoxicillin or clindamycin according to action protocols, with special emphasis placed on oral hygiene in patients with structural defects of the heart.

  11. Micro-magnet arrays for specific single bacterial cell positioning

    Energy Technology Data Exchange (ETDEWEB)

    Pivetal, Jérémy, E-mail: jeremy.piv@netcmail.com [Ecole Centrale de Lyon, CNRS UMR 5005, Laboratoire Ampère, F-69134 Écully (France); Royet, David [Ecole Centrale de Lyon, CNRS UMR 5005, Laboratoire Ampère, F-69134 Écully (France); Ciuta, Georgeta [Univ. Grenoble Alpes, Inst NEEL, F-38042 Grenoble (France); CNRS, Inst NEEL, F-38042 Grenoble (France); Frenea-Robin, Marie [Université de Lyon, Université Lyon 1, CNRS UMR 5005, Laboratoire Ampère, F-69622 Villeurbanne (France); Haddour, Naoufel [Ecole Centrale de Lyon, CNRS UMR 5005, Laboratoire Ampère, F-69134 Écully (France); Dempsey, Nora M. [Univ. Grenoble Alpes, Inst NEEL, F-38042 Grenoble (France); CNRS, Inst NEEL, F-38042 Grenoble (France); Dumas-Bouchiat, Frédéric [Univ Limoges, CNRS, SPCTS UMR 7513, 12 Rue Atlantis, F-87068 Limoges (France); Simonet, Pascal [Ecole Centrale de Lyon, CNRS UMR 5005, Laboratoire Ampère, F-69134 Écully (France)

    2015-04-15

    In various contexts such as pathogen detection or analysis of microbial diversity where cellular heterogeneity must be taken into account, there is a growing need for tools and methods that enable microbiologists to analyze bacterial cells individually. One of the main challenges in the development of new platforms for single cell studies is to perform precise cell positioning, but the ability to specifically target cells is also important in many applications. In this work, we report the development of new strategies to selectively trap single bacterial cells upon large arrays, based on the use of micro-magnets. Escherichia coli bacteria were used to demonstrate magnetically driven bacterial cell organization. In order to provide a flexible approach adaptable to several applications in the field of microbiology, cells were magnetically and specifically labeled using two different strategies, namely immunomagnetic labeling and magnetic in situ hybridization. Results show that centimeter-sized arrays of targeted, isolated bacteria can be successfully created upon the surface of a flat magnetically patterned hard magnetic film. Efforts are now being directed towards the integration of a detection tool to provide a complete micro-system device for a variety of microbiological applications. - Highlights: 1.We report a new approach to selectively micropattern bacterial cells individually upon micro-magnet arrays. 2.Permanent micro-magnets of a size approaching that of bacteria could be fabricated using a Thermo-Magnetic Patterning process. 3.Bacterial cells were labeled using two different magnetic labeling strategies providing flexible approach adaptable to several applications in the field of microbiology.

  12. Meningitis bacteriana Bacterial meningitis

    Directory of Open Access Journals (Sweden)

    Ana Teresa Alvarado Guevara

    2006-03-01

    causales son virales lo cual conlleva a las diferentes sub-clasificaciones. También en ciertos casos puede ser ocasionada por hongos, bacterias atípicas, micobacterias y parásitos.In Costa Rica the bacterial meningitis had turn into a high-priority subject in which to monitoring epidemiologist. It had been talked about in the last months, to dice an increase in the attention is published of this subject, due to this phenomenon it becomes necessary to make a revision of topic. Meningitis is an inflammation of leptomeninges and colonization of the subarachnoid cerebrospinal fluid (LCR due to different agents, which produces meningeal symptoms (ex. migraine, neck rigidity, and photophobia and pleocytosis in LCR. De pending on the variables to take into account is possible to group it in different classifications, taking into account the time of evolution are possible to be divided in acute or chronic, to first with few hours or days of beginning of the symptoms, whereas the chronicle also presents a silence course but of the disease of approximately 4 weeks of instauration. There is a difference according to its etiologic agent; they can be infectious and non-infectious. Examples of common non-infectious causes include medications (ex, nonsteroidal anti-inflammatory drugs, and antibiotics and carcinomatosis. A classification exists as well according to the causal agent. The acute bacterial meningitis remarks a bacterial origin of the syndrome, which characterizes by the by an acute onset of meningeal symptoms and neutrophilic pleocytosis. Each one of the bacteriological agents, parasitic or fungus finishes by characterizing the different presentations of the clinical features (ex, meningocóccica meningitis, Cryptococcus meningitis. Finally, there is also the aseptic meningitis, denominated in this form because it’s nonpyogenic cellular response caused by many types of agents. The patients show an acute beginning of symptoms, fever and lymphocytic pleocytosis. After

  13. Bacterial Communities: Interactions to Scale

    Directory of Open Access Journals (Sweden)

    Reed M. Stubbendieck

    2016-08-01

    Full Text Available In the environment, bacteria live in complex multispecies communities. These communities span in scale from small, multicellular aggregates to billions or trillions of cells within the gastrointestinal tract of animals. The dynamics of bacterial communities are determined by pairwise interactions that occur between different species in the community. Though interactions occur between a few cells at a time, the outcomes of these interchanges have ramifications that ripple through many orders of magnitude, and ultimately affect the macroscopic world including the health of host organisms. In this review we cover how bacterial competition influences the structures of bacterial communities. We also emphasize methods and insights garnered from culture-dependent pairwise interaction studies, metagenomic analyses, and modeling experiments. Finally, we argue that the integration of multiple approaches will be instrumental to future understanding of the underlying dynamics of bacterial communities.

  14. Bacterial Chromosome Organization and Segregation

    OpenAIRE

    Toro, Esteban; Shapiro, Lucy

    2010-01-01

    Bacterial chromosomes are generally ∼1000 times longer than the cells in which they reside, and concurrent replication, segregation, and transcription/translation of this crowded mass of DNA poses a challenging organizational problem. Recent advances in cell-imaging technology with subdiffraction resolution have revealed that the bacterial nucleoid is reliably oriented and highly organized within the cell. Such organization is transmitted from one generation to the next by progressive segrega...

  15. Bacterial Protein-Tyrosine Kinases

    DEFF Research Database (Denmark)

    Shi, Lei; Kobir, Ahasanul; Jers, Carsten

    2010-01-01

    phosphorylation. Protein-tyrosine phosphorylation in bacteria is particular with respect to very low occupancy of phosphorylation sites in vivo; this has represented a major challenge for detection techniques. Only the recent breakthroughs in gel-free high resolution mass spectrometry allowed the systematic...... and highlighted their importance in bacterial physiology. Having no orthologues in Eukarya, BY-kinases are receiving a growing attention from the biomedical field, since they represent a particularly promising target for anti-bacterial drug design....

  16. Surface micropattern limits bacterial contamination

    OpenAIRE

    Mann, Ethan E.; Manna, Dipankar; Mettetal, Michael R; May, Rhea M.; Dannemiller, Elisa M; Chung, Kenneth K.; Brennan, Anthony B; Reddy, Shravanthi T

    2014-01-01

    Background Bacterial surface contamination contributes to transmission of nosocomial infections. Chemical cleansers used to control surface contamination are often toxic and incorrectly implemented. Additional non-toxic strategies should be combined with regular cleanings to mitigate risks of human error and further decrease rates of nosocomial infections. The Sharklet micropattern (MP), inspired by shark skin, is an effective tool for reducing bacterial load on surfaces without toxic additiv...

  17. Bacterial cellulose/boehmite composites

    Energy Technology Data Exchange (ETDEWEB)

    Salvi, Denise T.B. de; Barud, Hernane S.; Messaddeq, Younes; Ribeiro, Sidney J.L. [Universidade Estadual Paulista Julio de Mesquita Filho. UNESP. Instituto de Quimica de Araraquara, SP (Brazil); Caiut, Jose Mauricio A. [Universidade de Sao Paulo. Departamento de Quimica - FFCLRP/USP, Ribeirao Preto, SP (Brazil)

    2011-07-01

    Composites based on bacterial cellulose membranes and boehmite were obtained. SEM results indicate that the bacterial cellulose (BC) membranes are totally covered by boehmite and obtained XRD patterns suggest structural changes due to this boehmite addition. Thermal stability is accessed through TG curves and is dependent on boehmite content. Transparency is high comparing to pure BC as can be seen through UV-vis absorption spectroscopy. (author)

  18. The sensory transduction pathways in bacterial chemotaxis

    Science.gov (United States)

    Taylor, Barry L.

    1989-01-01

    Bacterial chemotaxis is a useful model for investigating in molecular detail the behavioral response of cells to changes in their environment. Peritrichously flagellated bacteria such as coli and typhimurium swim by rotating helical flagella in a counterclockwise direction. If flagellar rotation is briefly reversed, the bacteria tumble and change the direction of swimming. The bacteria continuously sample the environment and use a temporal sensing mechanism to compare the present and immediate past environments. Bacteria respond to a broad range of stimuli including changes in temperature, oxygen concentration, pH and osmotic strength. Bacteria are attracted to potential sources of nutrition such as sugars and amino acids and are repelled by other chemicals. In the methylation-dependent pathways for sensory transduction and adaptation in E. coli and S. typhimurium, chemoeffectors bind to transducing proteins that span the plasma membrane. The transducing proteins are postulated to control the rate of autophosphorylation of the CheA protein, which in turn phosphorylates the CheY protein. The phospho-CheY protein binds to the switch on the flagellar motor and is the signal for clockwise rotation of the motor. Adaptation to an attractant is achieved by increasing methylation of the transducing protein until the attractant stimulus is cancelled. Responses to oxygen and certain sugars involve methylation-independent pathways in which adaption occurs without methylation of a transducing protein. Taxis toward oxygen is mediated by the electron transport system and changes in the proton motive force. Recent studies have shown that the methylation-independent pathway converges with the methylation-dependent pathway at or before the CheA protein.

  19. Host adaptation of bovine Staphylococcus aureus seems associated with bacteriological cure after lactational antimicrobial treatment

    NARCIS (Netherlands)

    Borne, van den B.H.P.; Nielen, M.; Schaik, van G.; Melchior, M.B.; Lam, T.J.G.M.; Zadoks, R.N.

    2010-01-01

    Staphylococcus aureus causes a wide range of diseases in multiple species. Some sequence types (ST) are observed in a variety of hosts, whereas other strains are mainly associated with bovine mastitis, suggesting host adaptation. We propose that host adaptation of Staph. aureus may influence bacteri

  20. The Human Vaginal Bacterial Biota and Bacterial Vaginosis

    Directory of Open Access Journals (Sweden)

    Sujatha Srinivasan

    2008-01-01

    Full Text Available The bacterial biota of the human vagina can have a profound impact on the health of women and their neonates. Changes in the vaginal microbiota have been associated with several adverse health outcomes including premature birth, pelvic inflammatory disease, and acquisition of HIV infection. Cultivation-independent molecular methods have provided new insights regarding bacterial diversity in this important niche, particularly in women with the common condition bacterial vaginosis (BV. PCR methods have shown that women with BV have complex communities of vaginal bacteria that include many fastidious species, particularly from the phyla Bacteroidetes and Actinobacteria. Healthy women are mostly colonized with lactobacilli such as Lactobacillus crispatus, Lactobacillus jensenii, and Lactobacillus iners, though a variety of other bacteria may be present. The microbiology of BV is heterogeneous. The presence of Gardnerella vaginalis and Atopobium vaginae coating the vaginal epithelium in some subjects with BV suggests that biofilms may contribute to this condition.

  1. Expressing Adaptation Strategies Using Adaptation Patterns

    Science.gov (United States)

    Zemirline, N.; Bourda, Y.; Reynaud, C.

    2012-01-01

    Today, there is a real challenge to enable personalized access to information. Several systems have been proposed to address this challenge including Adaptive Hypermedia Systems (AHSs). However, the specification of adaptation strategies remains a difficult task for creators of such systems. In this paper, we consider the problem of the definition…

  2. New Treatments for Bacterial Keratitis

    Directory of Open Access Journals (Sweden)

    Raymond L. M. Wong

    2012-01-01

    Full Text Available Purpose. To review the newer treatments for bacterial keratitis. Data Sources. PubMed literature search up to April 2012. Study Selection. Key words used for literature search: “infectious keratitis”, “microbial keratitis”, “infective keratitis”, “new treatments for infectious keratitis”, “fourth generation fluoroquinolones”, “moxifloxacin”, “gatifloxacin”, “collagen cross-linking”, and “photodynamic therapy”. Data Extraction. Over 2400 articles were retrieved. Large scale studies or publications at more recent dates were selected. Data Synthesis. Broad spectrum antibiotics have been the main stay of treatment for bacterial keratitis but with the emergence of bacterial resistance; there is a need for newer antimicrobial agents and treatment methods. Fourth-generation fluoroquinolones and corneal collagen cross-linking are amongst the new treatments. In vitro studies and prospective clinical trials have shown that fourth-generation fluoroquinolones are better than the older generation fluoroquinolones and are as potent as combined fortified antibiotics against common pathogens that cause bacterial keratitis. Collagen cross-linking was shown to improve healing of infectious corneal ulcer in treatment-resistant cases or as an adjunct to antibiotics treatment. Conclusion. Fourth-generation fluoroquinolones are good alternatives to standard treatment of bacterial keratitis using combined fortified topical antibiotics. Collagen cross-linking may be considered in treatment-resistant infectious keratitis or as an adjunct to antibiotics therapy.

  3. Bacterial carbonatogenesis; La carbonatogenese bacterienne

    Energy Technology Data Exchange (ETDEWEB)

    Castanier, S. [Angers Univ., 49 (France). Faculte des Sciences; Le Metayer-Levrel, G.; Perthuisot, J.P. [Nantes Univ., 44 (France). Laboratoire de Biogeologie, Faculte des Sciences et des Techniques

    1998-12-31

    Several series of experiments in the laboratory as well as in natural conditions teach that the production of carbonate particles by heterotrophic bacteria follows different ways. The `passive` carbonatogenesis is generated by modifications of the medium that lead to the accumulation of carbonate and bicarbonate ions and to the precipitation of solid particles. The `active` carbonatogenesis is independent of the metabolic pathways. The carbonate particles are produced by ionic exchanges through the cell membrane following still poorly known mechanisms. Carbonatogenesis appears to be the response of heterotrophic bacterial communities to an enrichment of the milieu in organic matter. The active carbonatogenesis seems to start first. It is followed by the passive one which induces the growth of initially produced particles. The yield of heterotrophic bacterial carbonatogenesis and the amounts of solid carbonates production by bacteria are potentially very high as compared to autotrophic or chemical sedimentation from marine, paralic or continental waters. Furthermore, the bacterial processes are environmentally very ubiquitous; they just require organic matter enrichment. Thus, apart from purely evaporite and autotrophic ones, all Ca and/or Mg carbonates must be considered as from heterotrophic bacterial origin. By the way, the carbon of carbonates comes from primary organic matter. Such considerations ask questions about some interpretations from isotopic data on carbonates. Finally, bacterial heterotrophic carbonatogenesis appears as a fundamental phase in the relationships between atmosphere and lithosphere and in the geo-biological evolution of Earth. (author) 43 refs.

  4. Responses of Baltic Sea ice and open-water natural bacterial communities to salinity change.

    Science.gov (United States)

    Kaartokallio, Hermanni; Laamanen, Maria; Sivonen, Kaarina

    2005-08-01

    To investigate the responses of Baltic Sea wintertime bacterial communities to changing salinity (5 to 26 practical salinity units), an experimental study was conducted. Bacterial communities of Baltic seawater and sea ice from a coastal site in southwest Finland were used in two batch culture experiments run for 17 or 18 days at 0 degrees C. Bacterial abundance, cell volume, and leucine and thymidine incorporation were measured during the experiments. The bacterial community structure was assessed using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rRNA genes with sequencing of DGGE bands from initial communities and communities of day 10 or 13 of the experiment. The sea ice-derived bacterial community was metabolically more active than the open-water community at the start of the experiment. Ice-derived bacterial communities were able to adapt to salinity change with smaller effects on physiology and community structure, whereas in the open-water bacterial communities, the bacterial cell volume evolution, bacterial abundance, and community structure responses indicated the presence of salinity stress. The closest relatives for all eight partial 16S rRNA gene sequences obtained were either organisms found in polar sea ice and other cold habitats or those found in summertime Baltic seawater. All sequences except one were associated with the alpha- and gamma-proteobacteria or the Cytophaga-Flavobacterium-Bacteroides group. The overall physiological and community structure responses were parallel in ice-derived and open-water bacterial assemblages, which points to a linkage between community structure and physiology. These results support previous assumptions of the role of salinity fluctuation as a major selective factor shaping the sea ice bacterial community structure.

  5. Bacterial Degradation of Aromatic Compounds

    Directory of Open Access Journals (Sweden)

    Qing X. Li

    2009-01-01

    Full Text Available Aromatic compounds are among the most prevalent and persistent pollutants in the environment. Petroleum-contaminated soil and sediment commonly contain a mixture of polycyclic aromatic hydrocarbons (PAHs and heterocyclic aromatics. Aromatics derived from industrial activities often have functional groups such as alkyls, halogens and nitro groups. Biodegradation is a major mechanism of removal of organic pollutants from a contaminated site. This review focuses on bacterial degradation pathways of selected aromatic compounds. Catabolic pathways of naphthalene, fluorene, phenanthrene, fluoranthene, pyrene, and benzo[a]pyrene are described in detail. Bacterial catabolism of the heterocycles dibenzofuran, carbazole, dibenzothiophene, and dibenzodioxin is discussed. Bacterial catabolism of alkylated PAHs is summarized, followed by a brief discussion of proteomics and metabolomics as powerful tools for elucidation of biodegradation mechanisms.

  6. Nonequilibrium Enhances Adaptation Efficiency of Stochastic Biochemical Systems

    Science.gov (United States)

    Jia, Chen; Qian, Minping

    2016-01-01

    Adaptation is a crucial biological function possessed by many sensory systems. Early work has shown that some influential equilibrium models can achieve accurate adaptation. However, recent studies indicate that there are close relationships between adaptation and nonequilibrium. In this paper, we provide an explanation of these two seemingly contradictory results based on Markov models with relatively simple networks. We show that as the nonequilibrium driving becomes stronger, the system under consideration will undergo a phase transition along a fixed direction: from non-adaptation to simple adaptation then to oscillatory adaptation, while the transition in the opposite direction is forbidden. This indicates that although adaptation may be observed in equilibrium systems, it tends to occur in systems far away from equilibrium. In addition, we find that nonequilibrium will improve the performance of adaptation by enhancing the adaptation efficiency. All these results provide a deeper insight into the connection between adaptation and nonequilibrium. Finally, we use a more complicated network model of bacterial chemotaxis to validate the main results of this paper. PMID:27195482

  7. Nonequilibrium Enhances Adaptation Efficiency of Stochastic Biochemical Systems.

    Directory of Open Access Journals (Sweden)

    Chen Jia

    Full Text Available Adaptation is a crucial biological function possessed by many sensory systems. Early work has shown that some influential equilibrium models can achieve accurate adaptation. However, recent studies indicate that there are close relationships between adaptation and nonequilibrium. In this paper, we provide an explanation of these two seemingly contradictory results based on Markov models with relatively simple networks. We show that as the nonequilibrium driving becomes stronger, the system under consideration will undergo a phase transition along a fixed direction: from non-adaptation to simple adaptation then to oscillatory adaptation, while the transition in the opposite direction is forbidden. This indicates that although adaptation may be observed in equilibrium systems, it tends to occur in systems far away from equilibrium. In addition, we find that nonequilibrium will improve the performance of adaptation by enhancing the adaptation efficiency. All these results provide a deeper insight into the connection between adaptation and nonequilibrium. Finally, we use a more complicated network model of bacterial chemotaxis to validate the main results of this paper.

  8. Emerging frontiers in detection and control of bacterial biofilms.

    Science.gov (United States)

    Tan, Seth Yang-En; Chew, Su Chuen; Tan, Sean Yang-Yi; Givskov, Michael; Yang, Liang

    2014-04-01

    Bacteria form surface-attached biofilm communities in nature. In contrast to free-living cells, bacterial cells within biofilms resist sanitizers and antimicrobials. While building biofilms, cells physiologically adapt to sustain the otherwise lethal impacts of a variety of environmental stress conditions. In this development, the production and embedding of cells in extracellular polymeric substances plays a key role. Biofilm bacteria can cause a range of problems to food processing including reduced heat-cold transfer, clogging water pipelines, food spoilage and they may cause infections among consumers. Recent biofilm investigations with the aim of potential control approaches include a combination of bacterial genetics, systems biology, materials and mechanic engineering and chemical biology.

  9. Bacterial iron-sulfur cluster sensors in mammalian pathogens

    Science.gov (United States)

    Miller, Halie K.; Auerbuch, Victoria

    2015-01-01

    Iron-sulfur clusters act as important cofactors for a number of transcriptional regulators in bacteria, including many mammalian pathogens. The sensitivity of iron-sulfur clusters to iron availability, oxygen tension, and reactive oxygen and nitrogen species enables bacteria to use such regulators to adapt their gene expression profiles rapidly in response to changing environmental conditions. In this review, we discuss how the [4Fe-4S] or [2Fe-2S] cluster-containing regulators FNR, Wbl, aconitase, IscR, NsrR, SoxR, and AirSR contribute to bacterial pathogenesis through control of both metabolism and classical virulence factors. In addition, we briefly review mammalian iron homeostasis as well as oxidative/nitrosative stress to provide context for understanding the function of bacterial iron-sulfur cluster sensors in different niches within the host. PMID:25738802

  10. The role of bacterial biofilms in chronic infections

    DEFF Research Database (Denmark)

    Bjarnsholt, Thomas

    2013-01-01

    treatment depends on accurate and fast diagnosis. However, in cases where the bacteria succeed in forming a biofilm within the human host, the infection often turns out to be untreatable and will develop into a chronic state. The important hallmarks of chronic biofilm-based infections are extreme resistance...... to antibiotics and many other conventional antimicrobial agents, and an extreme capacity for evading the host defences. In this thesis, I will assemble the current knowledge on biofilms with an emphasis on chronic infections, guidelines for diagnosis and treatment of these infections, before relating this to my...... previous research into the area of biofilms. I will present evidence to support a view that the biofilm lifestyle dominates chronic bacterial infections, where bacterial aggregation is the default mode, and that subsequent biofilm development progresses by adaptation to nutritional and environmental...

  11. Adaptive Rationality, Adaptive Behavior and Institutions

    Directory of Open Access Journals (Sweden)

    Volchik Vyacheslav, V.

    2015-12-01

    Full Text Available The economic literature focused on understanding decision-making and choice processes reveals a vast collection of approaches to human rationality. Theorists’ attention has moved from absolutely rational, utility-maximizing individuals to boundedly rational and adaptive ones. A number of economists have criticized the concepts of adaptive rationality and adaptive behavior. One of the recent trends in the economic literature is to consider humans irrational. This paper offers an approach which examines adaptive behavior in the context of existing institutions and constantly changing institutional environment. It is assumed that adaptive behavior is a process of evolutionary adjustment to fundamental uncertainty. We emphasize the importance of actors’ engagement in trial and error learning, since if they are involved in this process, they obtain experience and are able to adapt to existing and new institutions. The paper aims at identifying relevant institutions, adaptive mechanisms, informal working rules and practices that influence actors’ behavior in the field of Higher Education in Russia (Rostov Region education services market has been taken as an example. The paper emphasizes the application of qualitative interpretative methods (interviews and discourse analysis in examining actors’ behavior.

  12. Principles of adaptive optics

    CERN Document Server

    Tyson, Robert

    2010-01-01

    History and BackgroundIntroductionHistoryPhysical OpticsTerms in Adaptive OpticsSources of AberrationsAtmospheric TurbulenceThermal BloomingNonatmospheric SourcesAdaptive Optics CompensationPhase ConjugationLimitations of Phase ConjugationArtificial Guide StarsLasers for Guide StarsCombining the LimitationsLinear AnalysisPartial Phase ConjugationAdaptive Optics SystemsAdaptive Optics Imaging SystemsBeam Propagation Syst

  13. Amplicon sequencing for the quantification of spoilage microbiota in complex foods including bacterial spores

    NARCIS (Netherlands)

    Boer, de P.; Caspers, M.; Sanders, J.W.; Kemperman, R.; Wijman, J.; Lommerse, G.; Roeselers, G.; Montijn, R.; Abee, T.; Kort, R.

    2015-01-01

    Background
    Spoilage of food products is frequently caused by bacterial spores and lactic acid bacteria. Identification of these organisms by classic cultivation methods is limited by their ability to form colonies on nutrient agar plates. In this study, we adapted and optimized 16S rRNA amplicon

  14. Assembly and Mechanical Properties of the Cargo-Free and Cargo-Loaded Bacterial Nanocompartment Encapsulin

    NARCIS (Netherlands)

    Snijder, Joost; Kononova, Olga; Barbu, Ioana M; Uetrecht, Charlotte; Rurup, W Frederik; Koay, Melissa S T; Burnley, Rebecca J; Cornelissen, Jeroen J L M; Roos, Wouter H; Barsegov, Valeri; Wuite, Gijs J L; Heck, Albert J R

    2016-01-01

    Prokaryotes mostly lack membranous compartments that are typical of eukaryotic cells, but instead, they have various protein-based organelles. These include bacterial microcompartments like the carboxysome and the virus-like nanocompartment encapsulin. Encapsulins have an adaptable mechanism for enz

  15. Assembly and mechanical properties of the cargo-free and cargo-loaded bacterial nanocompartment encapsulin

    NARCIS (Netherlands)

    Snijder, Joost; Kononova, Olga; Barbu, Ioana M; Uetrecht, Charlotte; Rurup, W Frederik; Burnley, Rebecca J; Koay, Melissa S T; Cornelissen, Jeroen J L M; Roos, Wouter H; Barsegov, Valeri; Wuite, Gijs J L; Heck, Albert J R

    2016-01-01

    Prokaryotes mostly lack membranous compartments that are typical of eukaryotic cells, but instead they have various protein-based organelles. These include bacterial microcompartments like the carboxysome and the virus-like nanocompartment encapsulin. Encapsulins have an adaptable mechanism for enzy

  16. Bayesian prediction of bacterial growth temperature range based on genome sequences

    DEFF Research Database (Denmark)

    Jensen, Dan Børge; Vesth, Tammi Camilla; Hallin, Peter Fischer

    2012-01-01

    on a genomic sequence, would thus allow for an efficient and targeted search for production organisms, reducing the need for culturing experiments. Results: This study found a total of 40 protein families useful for distinction between three thermophilicity classes (thermophiles, mesophiles and psychrophiles...... and psychrophilic adapted bacterial genomes....

  17. Adaptation to climate change

    NARCIS (Netherlands)

    Carmin, J.; Tierney, K.; Chu, E.; Hunter, L.M.; Roberts, J.T.; Shi, L.; Dunlap, R.E.; Brulle, R.J.

    2015-01-01

    Climate change adaptation involves major global and societal challenges such as finding adequate and equitable adaptation funding and integrating adaptation and development programs. Current funding is insufficient. Debates between the Global North and South center on how best to allocate the financ

  18. Host imprints on bacterial genomes--rapid, divergent evolution in individual patients.

    Directory of Open Access Journals (Sweden)

    Jaroslaw Zdziarski

    Full Text Available Bacteria lose or gain genetic material and through selection, new variants become fixed in the population. Here we provide the first, genome-wide example of a single bacterial strain's evolution in different deliberately colonized patients and the surprising insight that hosts appear to personalize their microflora. By first obtaining the complete genome sequence of the prototype asymptomatic bacteriuria strain E. coli 83972 and then resequencing its descendants after therapeutic bladder colonization of different patients, we identified 34 mutations, which affected metabolic and virulence-related genes. Further transcriptome and proteome analysis proved that these genome changes altered bacterial gene expression resulting in unique adaptation patterns in each patient. Our results provide evidence that, in addition to stochastic events, adaptive bacterial evolution is driven by individual host environments. Ongoing loss of gene function supports the hypothesis that evolution towards commensalism rather than virulence is favored during asymptomatic bladder colonization.

  19. Molecular mechanisms underlying bacterial persisters

    DEFF Research Database (Denmark)

    Maisonneuve, Etienne; Gerdes, Kenn

    2014-01-01

    All bacteria form persisters, cells that are multidrug tolerant and therefore able to survive antibiotic treatment. Due to the low frequencies of persisters in growing bacterial cultures and the complex underlying molecular mechanisms, the phenomenon has been challenging to study. However, recent...

  20. Bacterial Cytotoxins Target Rho GTPases

    Science.gov (United States)

    Schmidt, Gudula; Aktories, Klaus

    1998-06-01

    Low molecular mass GTPases of the Rho family, which are involved in the regulation of the actin cytoskeleton and in various signal transduction processes, are the eukaryotic targets of bacterial protein toxins. The toxins covalently modify Rho proteins by ADP ribosylation, glucosylation, and deamidation, thereby inactivating and activating the GTPases.

  1. Disease notes - Bacterial root rot

    Science.gov (United States)

    Bacterial root rot initiated by lactic acid bacteria, particularly Leuconostoc, occurs every year in Idaho sugarbeet fields. Hot fall weather seems to make the problem worse. Although Leuconostoc initiates the rot, other bacteria and yeast frequently invade the tissue as well. The acetic acid bac...

  2. Bacterial canker resistance in tomato

    NARCIS (Netherlands)

    Sen, Y.

    2014-01-01

    Clavibacter michiganensis subsp. michiganensis (Cmm) is the pathogen causing bacterial  canker in tomato. The disease was described for the first time in 1910 in Michigan, USA. Cmmis considered the most harmful bacteria threatening tomato. Disease transmission occurs via seed and symptoms becom

  3. Biotechnological applications of bacterial cellulases

    Directory of Open Access Journals (Sweden)

    Esther Menendez

    2015-08-01

    Full Text Available Cellulases have numerous applications in several industries, including biofuel production, food and feed industry, brewing, pulp and paper, textile, laundry, and agriculture.Cellulose-degrading bacteria are widely spread in nature, being isolated from quite different environments. Cellulose degradation is the result of a synergic process between an endoglucanase, an exoglucanase and a,β-glucosidase. Bacterial endoglucanases degrade ß-1,4-glucan linkages of cellulose amorphous zones, meanwhile exoglucanases cleave the remaining oligosaccharide chains, originating cellobiose, which is hydrolyzed by ß-glucanases. Bacterial cellulases (EC 3.2.1.4 are comprised in fourteen Glycosil Hydrolase families. Several advantages, such as higher growth rates and genetic versatility, emphasize the suitability and advantages of bacterial cellulases over other sources for this group of enzymes. This review summarizes the main known cellulolytic bacteria and the best strategies to optimize their cellulase production, focusing on endoglucanases, as well as it reviews the main biotechnological applications of bacterial cellulases in several industries, medicine and agriculture.

  4. Food irradiation and bacterial toxins

    Energy Technology Data Exchange (ETDEWEB)

    Tranter, H.S.; Modi, N.K.; Hambleton, P.; Melling, J.; Rose, S.; Stringer, M.F.

    1987-07-04

    The authors' findings indicate that irradiation confers no advantage over heat processing in respect of bacterial toxins (clostridium botulinum, neurotoxin A and staphylococcal enterotoxin A). It follows that irradiation at doses less than the ACINF recommended upper limit of 10 kGy could not be used to improve the ambient temperature shelf life on non-acid foods.

  5. Extracardiac manifestations of bacterial endocarditis.

    Science.gov (United States)

    Heffner, J E

    1979-08-01

    Bacterial endocarditis is an elusive disease that challenges clinicians' diagnostic capabilities. Because it can present with various combinations of extravalvular signs and symptoms, the underlying primary disease can go unnoticed.A review of the various extracardiac manifestations of bacterial endocarditis suggests three main patterns by which the valvular infection can be obscured. (1) A major clinical event may be so dramatic that subtle evidence of endocarditis is overlooked. The rupture of a mycotic aneurysm may simulate a subarachnoid hemorrhage from a congenital aneurysm. (2) The symptoms of bacterial endocarditis may be constitutional complaints easily attributable to a routine, trivial illness. Symptoms of low-grade fever, myalgias, back pain and anorexia may mimic a viral syndrome. (3) Endocarditis poses a difficult diagnostic dilemma when it generates constellations of findings that are classic for other disorders. Complaints of arthritis and arthralgias accompanied by hematuria and antinuclear antibody may suggest systemic lupus erythematosus; a renal biopsy study showing diffuse proliferative glomerulonephritis may support this diagnosis. The combination of fever, petechiae, altered mental status, thrombocytopenia, azotemia and anemia may promote the diagnosis of thrombotic thrombocytopenic purpura. When the protean guises of bacterial endocarditis create these clinical difficulties, errors in diagnosis occur and appropriate therapy is delayed. Keen awareness of the varied disease presentations will improve success in managing endocarditis by fostering rapid diagnosis and prompt therapy.

  6. Resilience through adaptation

    Science.gov (United States)

    van Voorn, George A. K.; Ligtenberg, Arend; Molenaar, Jaap

    2017-01-01

    Adaptation of agents through learning or evolution is an important component of the resilience of Complex Adaptive Systems (CAS). Without adaptation, the flexibility of such systems to cope with outside pressures would be much lower. To study the capabilities of CAS to adapt, social simulations with agent-based models (ABMs) provide a helpful tool. However, the value of ABMs for studying adaptation depends on the availability of methodologies for sensitivity analysis that can quantify resilience and adaptation in ABMs. In this paper we propose a sensitivity analysis methodology that is based on comparing time-dependent probability density functions of output of ABMs with and without agent adaptation. The differences between the probability density functions are quantified by the so-called earth-mover’s distance. We use this sensitivity analysis methodology to quantify the probability of occurrence of critical transitions and other long-term effects of agent adaptation. To test the potential of this new approach, it is used to analyse the resilience of an ABM of adaptive agents competing for a common-pool resource. Adaptation is shown to contribute positively to the resilience of this ABM. If adaptation proceeds sufficiently fast, it may delay or avert the collapse of this system. PMID:28196372

  7. [Individual adaptation strategies].

    Science.gov (United States)

    Aldasheva, A A

    2014-01-01

    The article looks at the relation between adaptation strategy and individual style of activity based on the doctrine of human adaptation of V.I. Medvedev that enables opening up characteristics of professional activity in diverse environments. It illustrates a role and the relation between physiological and psychological mechanisms, which can vary, depending on individual adaptation strategies of a person. Theoretical and practical studies based on activity paradigm allow us to look at the basic principles of human interaction with the environment from a new perspective. Based on the law on the conceptual model of adaptation proposed by V.I. Medvedev, the article illustrates that humans are active figures in adaptation situations, modeling their own adaption strategies, using different individual styles manifested in the programs of adaptive behaviour.

  8. Is The Ribosome Targeted By Adaptive Mutations

    DEFF Research Database (Denmark)

    Jimenez Fernandez, Alicia; Molin, Søren; Johansen, Helle Krogh

    2015-01-01

    degree of evolutionary conservation of the cellular MMSM tend to support this view. However, under certain selective conditions the machinery itself may be targeted by adaptive mutations, which result in fitness-increasing phenotypic changes. Here we investigate and characterize the role of ribosomal...... mutations in adaptive evolution. Methods: Several mutations in ribosomal genes have been identified in the genome analysis of nearly 700 Pseudomonas aeruginosa isolates from infected cystic fibrosis patients. Among these mutations we have repeatedly identified insertions, deletions and substitutions...... in specific ribosomal genes. The bacterial phenotypes of the mutated strains will be investigated. Results: Preliminary assays show that mutant strains have reduced growth rate and an altered antibiotic resistance pattern. The selection for mutations in ribosomal protein genes is partly explainable...

  9. Prostatitis-bacterial - self-care

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/patientinstructions/000395.htm Prostatitis- bacterial - self-care To use the sharing features ... enable JavaScript. You have been diagnosed with bacterial prostatitis . This is an infection of the prostate gland. ...

  10. Cognitive outcome in adults after bacterial meningitis.

    NARCIS (Netherlands)

    Hoogman, M.; Beek, D. van de; Weisfelt, M.; Gans, J. de; Schmand, B.

    2007-01-01

    OBJECTIVE: To evaluate cognitive outcome in adult survivors of bacterial meningitis. METHODS: Data from three prospective multicentre studies were pooled and reanalysed, involving 155 adults surviving bacterial meningitis (79 after pneumococcal and 76 after meningococcal meningitis) and 72 healthy c

  11. Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests

    Science.gov (United States)

    Kaiser, Kristin; Wemheuer, Bernd; Korolkow, Vera; Wemheuer, Franziska; Nacke, Heiko; Schöning, Ingo; Schrumpf, Marion; Daniel, Rolf

    2016-01-01

    Soil bacteria provide a large range of ecosystem services such as nutrient cycling. Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils derived from three German regions by pyrotag sequencing of 16S rRNA genes. Land use type (forest and grassland) and soil edaphic properties strongly affected bacterial community structure and function, whereas management regime had a minor effect. In addition, a separation of soil bacterial communities by sampling region was encountered. Soil pH was the best predictor for bacterial community structure, diversity and function. The application of multinomial log-linear models revealed distinct responses of abundant bacterial groups towards pH. Predicted functional profiles revealed that differences in land use not only select for distinct bacterial populations but also for specific functional traits. The combination of 16S rRNA data and corresponding functional profiles provided comprehensive insights into compositional and functional adaptations to changing environmental conditions associated with differences in land use and management. PMID:27650273

  12. Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests

    Science.gov (United States)

    Kaiser, Kristin; Wemheuer, Bernd; Korolkow, Vera; Wemheuer, Franziska; Nacke, Heiko; Schöning, Ingo; Schrumpf, Marion; Daniel, Rolf

    2016-09-01

    Soil bacteria provide a large range of ecosystem services such as nutrient cycling. Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils derived from three German regions by pyrotag sequencing of 16S rRNA genes. Land use type (forest and grassland) and soil edaphic properties strongly affected bacterial community structure and function, whereas management regime had a minor effect. In addition, a separation of soil bacterial communities by sampling region was encountered. Soil pH was the best predictor for bacterial community structure, diversity and function. The application of multinomial log-linear models revealed distinct responses of abundant bacterial groups towards pH. Predicted functional profiles revealed that differences in land use not only select for distinct bacterial populations but also for specific functional traits. The combination of 16S rRNA data and corresponding functional profiles provided comprehensive insights into compositional and functional adaptations to changing environmental conditions associated with differences in land use and management.

  13. Steady at the wheel: conservative sex and the benefits of bacterial transformation

    Science.gov (United States)

    Ambur, Ole Herman; Engelstädter, Jan; Johnsen, Pål J.

    2016-01-01

    Many bacteria are highly sexual, but the reasons for their promiscuity remain obscure. Did bacterial sex evolve to maximize diversity and facilitate adaptation in a changing world, or does it instead help to retain the bacterial functions that work right now? In other words, is bacterial sex innovative or conservative? Our aim in this review is to integrate experimental, bioinformatic and theoretical studies to critically evaluate these alternatives, with a main focus on natural genetic transformation, the bacterial equivalent of eukaryotic sexual reproduction. First, we provide a general overview of several hypotheses that have been put forward to explain the evolution of transformation. Next, we synthesize a large body of evidence highlighting the numerous passive and active barriers to transformation that have evolved to protect bacteria from foreign DNA, thereby increasing the likelihood that transformation takes place among clonemates. Our critical review of the existing literature provides support for the view that bacterial transformation is maintained as a means of genomic conservation that provides direct benefits to both individual bacterial cells and to transformable bacterial populations. We examine the generality of this view across bacteria and contrast this explanation with the different evolutionary roles proposed to maintain sex in eukaryotes.  This article is part of the themed issue ‘Weird sex: the underappreciated diversity of sexual reproduction’. PMID:27619692

  14. Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests.

    Science.gov (United States)

    Kaiser, Kristin; Wemheuer, Bernd; Korolkow, Vera; Wemheuer, Franziska; Nacke, Heiko; Schöning, Ingo; Schrumpf, Marion; Daniel, Rolf

    2016-09-21

    Soil bacteria provide a large range of ecosystem services such as nutrient cycling. Despite their important role in soil systems, compositional and functional responses of bacterial communities to different land use and management regimes are not fully understood. Here, we assessed soil bacterial communities in 150 forest and 150 grassland soils derived from three German regions by pyrotag sequencing of 16S rRNA genes. Land use type (forest and grassland) and soil edaphic properties strongly affected bacterial community structure and function, whereas management regime had a minor effect. In addition, a separation of soil bacterial communities by sampling region was encountered. Soil pH was the best predictor for bacterial community structure, diversity and function. The application of multinomial log-linear models revealed distinct responses of abundant bacterial groups towards pH. Predicted functional profiles revealed that differences in land use not only select for distinct bacterial populations but also for specific functional traits. The combination of 16S rRNA data and corresponding functional profiles provided comprehensive insights into compositional and functional adaptations to changing environmental conditions associated with differences in land use and management.

  15. Bacterial Stressors in Minimally Processed Food

    Directory of Open Access Journals (Sweden)

    Giuseppe Spano

    2009-07-01

    Full Text Available Stress responses are of particular importance to microorganisms, because their habitats are subjected to continual changes in temperature, osmotic pressure, and nutrients availability. Stressors (and stress factors, may be of chemical, physical, or biological nature. While stress to microorganisms is frequently caused by the surrounding environment, the growth of microbial cells on its own may also result in induction of some kinds of stress such as starvation and acidity. During production of fresh-cut produce, cumulative mild processing steps are employed, to control the growth of microorganisms. Pathogens on plant surfaces are already stressed and stress may be increased during the multiple mild processing steps, potentially leading to very hardy bacteria geared towards enhanced survival. Cross-protection can occur because the overlapping stress responses enable bacteria exposed to one stress to become resistant to another stress. A number of stresses have been shown to induce cross protection, including heat, cold, acid and osmotic stress. Among other factors, adaptation to heat stress appears to provide bacterial cells with more pronounced cross protection against several other stresses. Understanding how pathogens sense and respond to mild stresses is essential in order to design safe and effective minimal processing regimes.

  16. Bacterial infections in Myd88-deficient mice.

    Science.gov (United States)

    Villano, Jason S; Rong, Fang; Cooper, Timothy K

    2014-04-01

    Three breeding colonies of Myd88(-/-) mice had a history of significant morbidity and mortality. Although strain-specific poor reproductive performance might explain neonatal death and dystocia, mice were found dead or required euthanasia because of moribundity, distended abdomen, head tilt, and seizures. Histopathology results included bacteremia, placentitis, metritis, peritonitis with abscess formation, and suppurative meningoencephalitis. Intralesional gram-negative coccobacilli were present, often in extremely high number. Cultures of samples of the cardiac blood of a mouse and from water-bottle sipper tubes provided to some affected mice grew Pseudomonas aeruginosa. In addition, affected tissues from 2 mice and feces from a third tested PCR-positive for P. aeruginosa. Although the mice had received autoclaved reverse-osmosis-purified drinking water, we suspect that the mice were inoculated with P. aeruginosa through contaminated sipper tubes. Because of the deficiency in most of the Toll-like receptor signaling pathways, these Myd88(-/-) mice were unlikely to have developed competitive innate and adaptive immune responses, resulting in bacterial infections. These clinical cases underscore the importance of understanding how genotype, phenotype and environment affect animal health. Sound husbandry and experimental practices are needed to prevent the exposure of immuno-deficient mice to pathogens.

  17. The bacterial lux reporter system: applications in bacterial localisation studies.

    Science.gov (United States)

    Gahan, Cormac G M

    2012-02-01

    Bacterial production of visible light is a natural phenomenon occurring in marine (Vibrio and Photobacterium) and terrestrial (Photorhabdus) species. The mechanism underpinning light production in these organisms is similar and involves the oxidation of an aldehyde substrate in a reaction catalysed by the bacterial luciferase enzyme. The genes encoding the luciferase and a fatty acid reductase complex which synthesizes the substrate are contained in a single operon (the lux operon). This provides a useful reporter system as cloning the operon into a recipient host bacterium will generate visible light without the requirement to add exogenous substrate. The light can be detected in vivo in the living animal using a sensitive detection system and is therefore ideally suited to bioluminescence imaging protocols. The system has therefore been widely used to track bacteria during infection or colonisation of the host. As bacteria are currently being examined as bactofection vectors for gene delivery, particularly to tumour tissue, the use of bioluminescence imaging offers a powerful means to investigate vector amplification in situ. The implications of this technology for bacterial localization, tumour targeting and gene transfer (bactofection) studies are discussed.

  18. Solving a Hamiltonian Path Problem with a bacterial computer

    Directory of Open Access Journals (Sweden)

    Treece Jessica

    2009-07-01

    Full Text Available Abstract Background The Hamiltonian Path Problem asks whether there is a route in a directed graph from a beginning node to an ending node, visiting each node exactly once. The Hamiltonian Path Problem is NP complete, achieving surprising computational complexity with modest increases in size. This challenge has inspired researchers to broaden the definition of a computer. DNA computers have been developed that solve NP complete problems. Bacterial computers can be programmed by constructing genetic circuits to execute an algorithm that is responsive to the environment and whose result can be observed. Each bacterium can examine a solution to a mathematical problem and billions of them can explore billions of possible solutions. Bacterial computers can be automated, made responsive to selection, and reproduce themselves so that more processing capacity is applied to problems over time. Results We programmed bacteria with a genetic circuit that enables them to evaluate all possible paths in a directed graph in order to find a Hamiltonian path. We encoded a three node directed graph as DNA segments that were autonomously shuffled randomly inside bacteria by a Hin/hixC recombination system we previously adapted from Salmonella typhimurium for use in Escherichia coli. We represented nodes in the graph as linked halves of two different genes encoding red or green fluorescent proteins. Bacterial populations displayed phenotypes that reflected random ordering of edges in the graph. Individual bacterial clones that found a Hamiltonian path reported their success by fluorescing both red and green, resulting in yellow colonies. We used DNA sequencing to verify that the yellow phenotype resulted from genotypes that represented Hamiltonian path solutions, demonstrating that our bacterial computer functioned as expected. Conclusion We successfully designed, constructed, and tested a bacterial computer capable of finding a Hamiltonian path in a three node

  19. Distribution of Triplet Separators in Bacterial Genomes

    Institute of Scientific and Technical Information of China (English)

    HU Rui; ZHENG Wei-Mou

    2001-01-01

    Distributions of triplet separator lengths for two bacterial complete genomes are analyzed. The theoretical distributions for the independent random sequence and the first-order Markov chain are derived and compared with the distributions of the bacterial genomes. A prominent double band structure, which does not exist in the theoretical distributions, is observed in the bacterial distributions for most triplets.``

  20. Technology transfer for adaptation

    Science.gov (United States)

    Biagini, Bonizella; Kuhl, Laura; Gallagher, Kelly Sims; Ortiz, Claudia

    2014-09-01

    Technology alone will not be able to solve adaptation challenges, but it is likely to play an important role. As a result of the role of technology in adaptation and the importance of international collaboration for climate change, technology transfer for adaptation is a critical but understudied issue. Through an analysis of Global Environment Facility-managed adaptation projects, we find there is significantly more technology transfer occurring in adaptation projects than might be expected given the pessimistic rhetoric surrounding technology transfer for adaptation. Most projects focused on demonstration and early deployment/niche formation for existing technologies rather than earlier stages of innovation, which is understandable considering the pilot nature of the projects. Key challenges for the transfer process, including technology selection and appropriateness under climate change, markets and access to technology, and diffusion strategies are discussed in more detail.

  1. Origins of adaptive immunity.

    Science.gov (United States)

    Liongue, Clifford; John, Liza B; Ward, Alister

    2011-01-01

    Adaptive immunity, involving distinctive antibody- and cell-mediated responses to specific antigens based on "memory" of previous exposure, is a hallmark of higher vertebrates. It has been argued that adaptive immunity arose rapidly, as articulated in the "big bang theory" surrounding its origins, which stresses the importance of coincident whole-genome duplications. Through a close examination of the key molecules and molecular processes underpinning adaptive immunity, this review suggests a less-extreme model, in which adaptive immunity emerged as part of longer evolutionary journey. Clearly, whole-genome duplications provided additional raw genetic materials that were vital to the emergence of adaptive immunity, but a variety of other genetic events were also required to generate some of the key molecules, whereas others were preexisting and simply co-opted into adaptive immunity.

  2. Antibiotic drugs targeting bacterial RNAs

    Directory of Open Access Journals (Sweden)

    Weiling Hong

    2014-08-01

    Full Text Available RNAs have diverse structures that include bulges and internal loops able to form tertiary contacts or serve as ligand binding sites. The recent increase in structural and functional information related to RNAs has put them in the limelight as a drug target for small molecule therapy. In addition, the recognition of the marked difference between prokaryotic and eukaryotic rRNA has led to the development of antibiotics that specifically target bacterial rRNA, reduce protein translation and thereby inhibit bacterial growth. To facilitate the development of new antibiotics targeting RNA, we here review the literature concerning such antibiotics, mRNA, riboswitch and tRNA and the key methodologies used for their screening.

  3. Electromagnetic Signals from Bacterial DNA

    CERN Document Server

    Widom, A; Srivastava, Y N; Sivasubramanian, S

    2011-01-01

    Chemical reactions can be induced at a distance due to the propagation of electromagnetic signals during intermediate chemical stages. Although is is well known at optical frequencies, e.g. photosynthetic reactions, electromagnetic signals hold true for muck lower frequencies. In E. coli bacteria such electromagnetic signals can be generated by electric transitions between energy levels describing electrons moving around DNA loops. The electromagnetic signals between different bacteria within a community is a "wireless" version of intercellular communication found in bacterial communities connected by "nanowires". The wireless broadcasts can in principle be of both the AM and FM variety due to the magnetic flux periodicity in electron energy spectra in bacterial DNA orbital motions.

  4. Bacterial survival in Martian conditions

    CERN Document Server

    D'Alessandro, Giuseppe Galletta; Giulio Bertoloni; Maurizio

    2010-01-01

    We shortly discuss the observable consequences of the two hypotheses about the origin of life on Earth and Mars: the Lithopanspermia (Mars to Earth or viceversa) and the origin from a unique progenitor, that for Earth is called LUCA (the LUCA hypothesis). To test the possibility that some lifeforms similar to the terrestrial ones may survive on Mars, we designed and built two simulators of Martian environments where to perform experiments with different bacterial strains: LISA and mini-LISA. Our LISA environmental chambers can reproduce the conditions of many Martian locations near the surface trough changes of temperature, pressure, UV fluence and atmospheric composition. Both simulators are open to collaboration with other laboratories interested in performing experiments on many kind of samples (biological, minerals, electronic) in situations similar to that of the red planet. Inside LISA we have studied the survival of several bacterial strains and endospores. We verified that the UV light is the major re...

  5. Bacterial streamers in curved microchannels

    Science.gov (United States)

    Rusconi, Roberto; Lecuyer, Sigolene; Guglielmini, Laura; Stone, Howard

    2009-11-01

    Biofilms, generally identified as microbial communities embedded in a self-produced matrix of extracellular polymeric substances, are involved in a wide variety of health-related problems ranging from implant-associated infections to disease transmissions and dental plaque. The usual picture of these bacterial films is that they grow and develop on surfaces. However, suspended biofilm structures, or streamers, have been found in natural environments (e.g., rivers, acid mines, hydrothermal hot springs) and are always suggested to stem from a turbulent flow. We report the formation of bacterial streamers in curved microfluidic channels. By using confocal laser microscopy we are able to directly image and characterize the spatial and temporal evolution of these filamentous structures. Such streamers, which always connect the inner corners of opposite sides of the channel, are always located in the middle plane. Numerical simulations of the flow provide evidences for an underlying hydrodynamic mechanism behind the formation of the streamers.

  6. Bacterial chromosome organization and segregation.

    Science.gov (United States)

    Badrinarayanan, Anjana; Le, Tung B K; Laub, Michael T

    2015-01-01

    If fully stretched out, a typical bacterial chromosome would be nearly 1 mm long, approximately 1,000 times the length of a cell. Not only must cells massively compact their genetic material, but they must also organize their DNA in a manner that is compatible with a range of cellular processes, including DNA replication, DNA repair, homologous recombination, and horizontal gene transfer. Recent work, driven in part by technological advances, has begun to reveal the general principles of chromosome organization in bacteria. Here, drawing on studies of many different organisms, we review the emerging picture of how bacterial chromosomes are structured at multiple length scales, highlighting the functions of various DNA-binding proteins and the impact of physical forces. Additionally, we discuss the spatial dynamics of chromosomes, particularly during their segregation to daughter cells. Although there has been tremendous progress, we also highlight gaps that remain in understanding chromosome organization and segregation.

  7. Dynamics of bacterial gene regulation

    Science.gov (United States)

    Narang, Atul

    2009-03-01

    The phenomenon of diauxic growth is a classical problem of bacterial gene regulation. The most well studied example of this phenomenon is the glucose-lactose diauxie, which occurs because the expression of the lac operon is strongly repressed in the presence of glucose. This repression is often explained by appealing to molecular mechanisms such as cAMP activation and inducer exclusion. I will begin by analyzing data showing that these molecular mechanisms cannot explain the strong lac repression because they exert a relatively weak effect. I will then present a minimal model accounting only for enzyme induction and dilution, which yields strong repression despite the absence of catabolite repression and inducer exclusion. The model also explains the growth patterns observed in batch and continuous cultures of various bacterial strains and substrate mixtures. The talk will conclude with a discussion of the experimental evidence regarding positive feedback, the key component of the minimal model.

  8. Collective Functionality through Bacterial Individuality

    Science.gov (United States)

    Ackermann, Martin

    According to the conventional view, the properties of an organism are a product of nature and nurture - of its genes and the environment it lives in. Recent experiments with unicellular organisms have challenged this view: several molecular mechanisms generate phenotypic variation independently of environmental signals, leading to variation in clonal groups. My presentation will focus on the causes and consequences of this microbial individuality. Using examples from bacterial genetic model systems, I will first discuss different molecular and cellular mechanisms that give rise to bacterial individuality. Then, I will discuss the consequences of individuality, and focus on how phenotypic variation in clonal populations of bacteria can promote interactions between individuals, lead to the division of labor, and allow clonal groups of bacteria to cope with environmental uncertainty. Variation between individuals thus provides clonal groups with collective functionality.

  9. Adaptive Pairing Reversible Watermarking.

    Science.gov (United States)

    Dragoi, Ioan-Catalin; Coltuc, Dinu

    2016-05-01

    This letter revisits the pairwise reversible watermarking scheme of Ou et al., 2013. An adaptive pixel pairing that considers only pixels with similar prediction errors is introduced. This adaptive approach provides an increased number of pixel pairs where both pixels are embedded and decreases the number of shifted pixels. The adaptive pairwise reversible watermarking outperforms the state-of-the-art low embedding bit-rate schemes proposed so far.

  10. Bacterial Interstitial Nephritis in Children

    OpenAIRE

    Bobadilla Chang, Fernando; Departamento de Ciencias Dinámicas Facultad de Medicina Universidad Nacional Mayor de San Marcos Lima, Perú; Villanueva, Dolores; Departamento de Ciencias Dinámicas Facultad de Medicina Universidad Nacional Mayor de San Marcos Lima, Perú

    2014-01-01

    OBJECTIVE: To assess the diagnosis approach to urinary tract infections in children. MATERIAL AND METHODS: Medical records from 103 children with diagnosis of interstitial bacterial nephritis were retrospectively reviewed. Diagnosis was supported by the dramatic involvement of renal parenquima, which is not addressed as "urinary tract infection". RESULTS: From all 103 patients, 49 were 2-years-old or younger, 33 were between 2 and 5-years-old, and 21 were between 6 to 10. Clinical picture inc...

  11. Bacterial canker resistance in tomato

    OpenAIRE

    Sen, Y.

    2014-01-01

    Clavibacter michiganensis subsp. michiganensis (Cmm) is the pathogen causing bacterial  canker in tomato. The disease was described for the first time in 1910 in Michigan, USA. Cmmis considered the most harmful bacteria threatening tomato. Disease transmission occurs via seed and symptoms become visible at least 20 days after infection. Due to its complex strategy and transmission, Cmm is under quarantine regulation in EU and other countries. There is no method to stop disease progress i...

  12. Small intestinal bacterial overgrowth syndrome

    Institute of Scientific and Technical Information of China (English)

    Jan; Bures; Jiri; Cyrany; Darina; Kohoutova; Miroslav; Frstl; Stanislav; Rejchrt; Jaroslav; Kvetina; Viktor; Vorisek; Marcela; Kopacova

    2010-01-01

    Human intestinal microbiota create a complex polymi-crobial ecology. This is characterised by its high population density, wide diversity and complexity of interaction. Any dysbalance of this complex intestinal microbiome, both qualitative and quantitative, might have serious health consequence for a macro-organism, including small intestinal bacterial overgrowth syndrome (SIBO).SIBO is defined as an increase in the number and/or alteration in the type of bacteria in the upper gastro-intestinal tract. There...

  13. Biotechnological applications of bacterial cellulases

    OpenAIRE

    Esther Menendez; Paula Garcia-Fraile; Raul Rivas

    2015-01-01

    Cellulases have numerous applications in several industries, including biofuel production, food and feed industry, brewing, pulp and paper, textile, laundry, and agriculture.Cellulose-degrading bacteria are widely spread in nature, being isolated from quite different environments. Cellulose degradation is the result of a synergic process between an endoglucanase, an exoglucanase and a,β-glucosidase. Bacterial endoglucanases degrade ß-1,4-glucan linkages of cellulose amorphous zones, mean...

  14. Bacterial motility on abiotic surfaces

    OpenAIRE

    Gibiansky, Maxsim

    2013-01-01

    Bacterial biofilms are structured microbial communities which are widespread both in nature and in clinical settings. When organized into a biofilm, bacteria are extremely resistant to many forms of stress, including a greatly heightened antibiotic resistance. In the early stages of biofilm formation on an abiotic surface, many bacteria make use of their motility to explore the surface, finding areas of high nutrition or other bacteria to form microcolonies. They use motility appendages, incl...

  15. [Complications of bacterial rhino-sinusitis in children: a case report and a review of the literature].

    Science.gov (United States)

    Amat, F

    2010-03-01

    Acute sinusitis in children is a controversial issue in terms of its diagnostic criteria, classification and therapeutic management. A therapeutic delay can lead to complications if the cause is bacterial. Guidelines have been set, but they are not consensual in pediatrics. Complications of acute bacterial sinusitis are uncommon in children, but they can be extremely severe and cause high morbidity and mortality. Because of their rarity, they often are not identified early, exposing the patient to an unfavorable outcome. We report on a case of acute bacterial pan-sinusitis complicated with thrombophlebitis of the cavernous sinuses and meningitis in a 9-year-old child, in spite of early and adapted antibiotic therapy. The bacterial agent was Staphylococcus aureus, which had no resistance or toxin profile. The progression was favorable under intravenous antibiotic therapy and after bilateral sphenoidectomy. This case raises the question of the best therapy for acute bacterial sinusitis in pediatrics and the management of complications.

  16. Quantifying the adaptive cycle

    Science.gov (United States)

    Angeler, David G.; Allen, Craig R.; Garmestani, Ahjond S.; Gunderson, Lance H.; Hjerne, Olle; Winder, Monika

    2015-01-01

    The adaptive cycle was proposed as a conceptual model to portray patterns of change in complex systems. Despite the model having potential for elucidating change across systems, it has been used mainly as a metaphor, describing system dynamics qualitatively. We use a quantitative approach for testing premises (reorganisation, conservatism, adaptation) in the adaptive cycle, using Baltic Sea phytoplankton communities as an example of such complex system dynamics. Phytoplankton organizes in recurring spring and summer blooms, a well-established paradigm in planktology and succession theory, with characteristic temporal trajectories during blooms that may be consistent with adaptive cycle phases. We used long-term (1994–2011) data and multivariate analysis of community structure to assess key components of the adaptive cycle. Specifically, we tested predictions about: reorganisation: spring and summer blooms comprise distinct community states; conservatism: community trajectories during individual adaptive cycles are conservative; and adaptation: phytoplankton species during blooms change in the long term. All predictions were supported by our analyses. Results suggest that traditional ecological paradigms such as phytoplankton successional models have potential for moving the adaptive cycle from a metaphor to a framework that can improve our understanding how complex systems organize and reorganize following collapse. Quantifying reorganization, conservatism and adaptation provides opportunities to cope with the intricacies and uncertainties associated with fast ecological change, driven by shifting system controls. Ultimately, combining traditional ecological paradigms with heuristics of complex system dynamics using quantitative approaches may help refine ecological theory and improve our understanding of the resilience of ecosystems.

  17. Adapt or Become Extinct!

    DEFF Research Database (Denmark)

    Goumas, Georgios; McKee, Sally A.; Själander, Magnus

    2011-01-01

    during the execution of an application can be utilized to adapt the execution context and may lead to performance gains beyond those provided by static information and compile-time adaptation. We consider specialization based on dynamic information like user input, architectural characteristics...... static analysis (either during ahead-of-time or just-in-time) compilation. We extend the notion of information-driven adaptation and outline the architecture of an infrastructure designed to enable information ow and adaptation throughout the life-cycle of an application....

  18. Adaptive Wireless Transceiver Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Wireless technologies are an increasingly attractive means for spatial data, input, manipulation, and distribution. Mobitrum is proposing an innovative Adaptive...

  19. Cytochemical Differences in Bacterial Glycocalyx

    Science.gov (United States)

    Krautgartner, Wolf Dietrich; Vitkov, Ljubomir; Hannig, Matthias; Pelz, Klaus; Stoiber, Walter

    2005-02-01

    To examine new cytochemical aspects of the bacterial adhesion, a strain 41452/01 of the oral commensal Streptococcus sanguis and a wild strain of Staphylococcus aureus were grown with and without sucrose supplementation for 6 days. Osmiumtetraoxyde (OsO4), uranyl acetate (UA), ruthenium red (RR), cupromeronic blue (CB) staining with critical electrolytic concentrations (CECs), and the tannic acid-metal salt technique (TAMST) were applied for electron microscopy. Cytochemically, only RR-positive fimbriae in S. sanguis were visualized. By contrast, some types of fimbriae staining were observed in S. aureus glycocalyx: RR-positive, OsO4-positive, tannophilic and CB-positive with ceasing point at 0.3 M MgCl2. The CB staining with CEC, used for the first time for visualization of glycoproteins of bacterial glycocalyx, also reveals intacellular CB-positive substances-probably the monomeric molecules, that is, subunits forming the fimbriae via extracellular assembly. Thus, glycosylated components of the biofilm matrix can be reliably related to single cells. The visualization of intracellular components by CB with CEC enables clear distinction between S. aureus and other bacteria, which do not produce CB-positive substances. The small quantities of tannophilic substances found in S. aureus makes the use of TAMST for the same purpose difficult. The present work protocol enables, for the first time, a partial cytochemical differentiation of the bacterial glycocalyx.

  20. DIAGNOSTIC DIFFICULTIES IN BACTERIAL SPONDYLODISCITIS

    Directory of Open Access Journals (Sweden)

    Vinicius Orso

    2015-12-01

    Full Text Available Objective : To analyze aspects related to the diagnostic difficulty in patients with bacterial spondylodiscitis. Methods : Cross-sectional observational study with retrospective data collected in the period from March 2004 to January 2014.Twenty-one patients diagnosed with bacterial spondylodiscitis were analyzed. Results : Women were the most affected, as well as older individuals. Pain in the affected region was the initial symptom in 52% of patients, and 45.5% of the patients had low back pain, and those with dorsal discitis had back pain as the main complaint; the patients with thoracolumbar discitis had pain in that region, and only one patient had sacroiliac discitis. The average time between onset of symptoms and treatment was five months. The lumbar segment was the most affected with 11 cases (52%, followed by thoracolumbar in 24%, dorsal in 19% of cases and a case in the sacroiliac segment. Only seven patients had fever. Pain in the affected level was coincidentally the most common symptom. Conclusions : Early diagnosis of bacterial spondylodiscitis remains a challenge due to the nonspecific signs and symptoms reported by the patient and the wide variability of laboratory results and imaging. The basis for early diagnosis remains the clinical suspicion at the time of initial treatment.

  1. Detergent-compatible bacterial amylases.

    Science.gov (United States)

    Niyonzima, Francois N; More, Sunil S

    2014-10-01

    Proteases, lipases, amylases, and cellulases are enzymes used in detergent formulation to improve the detergency. The amylases are specifically supplemented to the detergent to digest starchy stains. Most of the solid and liquid detergents that are currently manufactured contain alkaline enzymes. The advantages of using alkaline enzymes in the detergent formulation are that they aid in removing tough stains and the process is environmentally friendly since they reduce the use of toxic detergent ingredients. Amylases active at low temperature are preferred as the energy consumption gets reduced, and the whole process becomes cost-effective. Most microbial alkaline amylases are used as detergent ingredients. Various reviews report on the production, purification, characterization, and application of amylases in different industry sectors, but there is no specific review on bacterial or fungal alkaline amylases or detergent-compatible amylases. In this mini-review, an overview on the production and property studies of the detergent bacterial amylases is given, and the stability and compatibility of the alkaline bacterial amylases in the presence of the detergents and the detergent components are highlighted.

  2. Micro-magnet arrays for specific single bacterial cell positioning

    Science.gov (United States)

    Pivetal, Jérémy; Royet, David; Ciuta, Georgeta; Frenea-Robin, Marie; Haddour, Naoufel; Dempsey, Nora M.; Dumas-Bouchiat, Frédéric; Simonet, Pascal

    2015-04-01

    In various contexts such as pathogen detection or analysis of microbial diversity where cellular heterogeneity must be taken into account, there is a growing need for tools and methods that enable microbiologists to analyze bacterial cells individually. One of the main challenges in the development of new platforms for single cell studies is to perform precise cell positioning, but the ability to specifically target cells is also important in many applications. In this work, we report the development of new strategies to selectively trap single bacterial cells upon large arrays, based on the use of micro-magnets. Escherichia coli bacteria were used to demonstrate magnetically driven bacterial cell organization. In order to provide a flexible approach adaptable to several applications in the field of microbiology, cells were magnetically and specifically labeled using two different strategies, namely immunomagnetic labeling and magnetic in situ hybridization. Results show that centimeter-sized arrays of targeted, isolated bacteria can be successfully created upon the surface of a flat magnetically patterned hard magnetic film. Efforts are now being directed towards the integration of a detection tool to provide a complete micro-system device for a variety of microbiological applications.

  3. Growth hormone reduces mortality and bacterial translocation in irradiated rats

    Energy Technology Data Exchange (ETDEWEB)

    Gomez-de-Segura, I.A.; Miguel, E. de [`La Paz` Hospital, Madrid (Spain). Dept. of Experimental Surgery; Prieto, I. [`La Paz` Hospital, Madrid (Spain). Dept. of General and Digestive Surgery; Grande, A.G. [`La Paz` Hospital, Madrid (Spain). Dept. of Oncology Radiotherapy; Garcia, P.; Mendez, J. [`La Paz` Hospital, Madrid (Spain). Dept. of Clinical Biochemistry; Guerra, A. [`La Paz` Hospital, Madrid (Spain). Dept. of Microbiology

    1998-09-01

    Growth hormone stimulates the growth of intestinal mucosa and may reduce the severity of injury caused by radiation. Male Wistar rats underwent abdominal irradiation (12 Gy) and were treated with either human growth hormone (hGH) or saline, and sacrificed at day 4 or 7 post-irradiation. Bacterial translocation, and the ileal mucosal thickness, proliferation, and disaccharidase activity were assessed. Mortality was 65% in irradiated animals, whereas hGH caused a decrement (29%, p<0.05). Bacterial translocation was also reduced by hGH (p<0.05). Treating irradiated rats with hGH prevented body weight loss (p<0.05). Mucosal thickness increased faster in irradiated hGH-treated animals. The proliferative index showed an increment in hGH-treated animals (p<0.05). Giving hGH to irradiated rats prevented decrease in sucrose activity, and increment in lactase activity. In conclusion, giving hGH to irradiated rats promotes the adaptative process of the intestine and acute radiation-related negative effects, including mortality, bacterial translocation, and weight loss. (orig.)

  4. A proteomic approach for the diagnosis of bacterial meningitis.

    Directory of Open Access Journals (Sweden)

    Sarah Jesse

    Full Text Available BACKGROUND: The discrimination of bacterial meningitis (BM versus viral meningitis (VM shapes up as a problem, when laboratory data are not equivocal, in particular, when Gram stain is negative. METHODOLOGY/PRINCIPAL FINDINGS: With the aim to determine reliable marker for bacterial or viral meningitis, we subjected cerebrospinal fluid (CSF to a quantitative proteomic screening. By using a recently established 2D-DIGE protocol which was adapted to the individual CSF flow, we compared a small set of patients with proven BM and VM. Thereby, we identified six potential biomarkers out of which Prostaglandin-H2 D-isomerase was already described in BM, showing proof of concept. In the subsequent validation phase on a more comprehensive collective of 80 patients, we could validate that in BM high levels of glial fibrillary acidic protein (GFAP and low levels of soluble amyloid precursor protein alpha/beta (sAPPalpha/beta are present as possible binding partner of Fibulin-1. CONCLUSIONS/SIGNIFICANCE: We conclude that our CSF flow-adapted 2D-DIGE protocol is valid especially in comparing samples with high differences in total protein and suppose that GFAP and sAPPalpha/beta have a high potential as additional diagnostic markers for differentiation of BM from VM. In the clinical setting, this might lead to an improved early diagnosis and to an individual therapy.

  5. Bacterial adhesion and biofilms on surfaces

    Institute of Scientific and Technical Information of China (English)

    Trevor Roger Garrett; Manmohan Bhakoo; Zhibing Zhang

    2008-01-01

    Bacterial adhesion has become a significant problem in industry and in the domicile,and much research has been done for deeper understanding of the processes involved.A generic biological model of bacterial adhesion and population growth called the bacterial biofilm growth cycle,has been described and modified many times.The biofilm growth cycle encompasses bacterial adhesion at all levels,starting with the initial physical attraction of bacteria to a substrate,and ending with the eventual liberation of cell dusters from the biofilm matrix.When describing bacterial adhesion one is simply describing one or more stages of biofilm development,neglecting the fact that the population may not reach maturity.This article provides an overview of bacterial adhesion.cites examples of how bac-terial adhesion affects industry and summarises methods and instrumentation used to improve our understanding of the adhesive prop-erties of bacteria.

  6. Depletion of dendritic cells enhances innate anti-bacterial host defense through modulation of phagocyte homeostasis.

    Directory of Open Access Journals (Sweden)

    Stella E Autenrieth

    2012-02-01

    Full Text Available Dendritic cells (DCs as professional antigen-presenting cells play an important role in the initiation and modulation of the adaptive immune response. However, their role in the innate immune response against bacterial infections is not completely defined. Here we have analyzed the role of DCs and their impact on the innate anti-bacterial host defense in an experimental infection model of Yersinia enterocolitica (Ye. We used CD11c-diphtheria toxin (DT mice to deplete DCs prior to severe infection with Ye. DC depletion significantly increased animal survival after Ye infection. The bacterial load in the spleen of DC-depleted mice was significantly lower than that of control mice throughout the infection. DC depletion was accompanied by an increase in the serum levels of CXCL1, G-CSF, IL-1α, and CCL2 and an increase in the numbers of splenic phagocytes. Functionally, splenocytes from DC-depleted mice exhibited an increased bacterial killing capacity compared to splenocytes from control mice. Cellular studies further showed that this was due to an increased production of reactive oxygen species (ROS by neutrophils. Adoptive transfer of neutrophils from DC-depleted mice into control mice prior to Ye infection reduced the bacterial load to the level of Ye-infected DC-depleted mice, suggesting that the increased number of phagocytes with additional ROS production account for the decreased bacterial load. Furthermore, after incubation with serum from DC-depleted mice splenocytes from control mice increased their bacterial killing capacity, most likely due to enhanced ROS production by neutrophils, indicating that serum factors from DC-depleted mice account for this effect. In summary, we could show that DC depletion triggers phagocyte accumulation in the spleen and enhances their anti-bacterial killing capacity upon bacterial infection.

  7. Adaptive Multimedia Retrieval: Semantics, Context, and Adaptation

    DEFF Research Database (Denmark)

    This book constitutes the thoroughly refereed post-conference proceedings of the 10th International Conference on Adaptive Multimedia Retrieval, AMR 2012, held in Copenhagen, Denmark, in October 2012. The 17 revised full papers presented were carefully reviewed and selected from numerous submissi...

  8. Plasmid profiling of bacterial isolates from confined environments

    Science.gov (United States)

    van Houdt, Rob; Provoost, Ann; Coninx, Ilse; Leys, Natalie; Mergeay, Max

    Plasmid profiling of bacterial isolates from confined environments R. Van Houdt, I. Coninx, A. Provoost, N. Leys, and M. Mergeay Expertise group for Molecular and Cellular Biology, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK•CEN), Boeretang 200, B-2400 Mol, Belgium. Human exploration of extreme and isolated hostile environments such as space requires special confined small volume habitats to protect and house the crew. However, human confinement in such small volume habitats has restrictions on waste disposal and personal hygiene and inevitably generates a particular community of microorganisms within the habitat. These microorganisms are mainly originating from the crew (skin, mucous membranes, upper respiratory tract, mouth, and gastrointestinal tract) but also include the residing environmental microorganisms. Earth-based confined habitats such as the Antarctic Research Station Concordia are used as test beds for long-duration spaceflights to study the physiologic and psychological adaptation to isolated environments. The dynamics of the environmental microbial population in such a test bed could render additional insights in assessing the potential health risks in long-duration space missions. Not only total bacterial contamination levels are important, but it is essential to identify also the predominant microbial taxa and their mobile genetic elements (MGE). These MGEs could be exchanged between bacteria by horizontal gene transfer and may alter the pathogenic potential since they often carry antibiotic resistance or more in general adaptation-enhancing traits. In this study several bacterial strains isolated in the Concordia research station were examined for their plasmid content. An optimized protocol for extraction of large plasmids showed the present of at least one plasmid in 50% of the strains. For all strains the minimal inhibitory concentration of a range of antibiotics was determined indicating resistance to

  9. Bacterial meningitis and diseases caused by bacterial toxins.

    Science.gov (United States)

    Rings, D M

    1987-03-01

    Bacterial meningitis most commonly occurs in young calves secondary to septicemia. Clinical signs of hyperirritability are usually seen. Meningitis can be confirmed by cerebrospinal fluid analysis and culture or by necropsy. Intoxications by the exotoxins of Clostridium perfringens types C and D, C. botulinum, and C. tetani are difficult to confirm. The clinical signs of these intoxications vary from flaccid paralysis (botulism) to muscular rigidity (tetanus). Treatment of affected cattle has been unrewarding in botulism and enterotoxemia, whereas early aggressive treatment of tetanus cases can often be successfully resolved. Botulism and enterotoxemia can be proved using mouse inoculation tests, whereas tetanus is diagnosed largely by ruling out other diseases.

  10. [Postvagotomy adaptation syndrome].

    Science.gov (United States)

    Shapovalov, V A

    1998-01-01

    It was established in experiment, that the changes of the natural resistance of organism indexes and of the peritoneal cavity cytology has compensatory-adaptational character while the denervation-adaptational syndrome occurrence and progress, which may be assessed as eustress. Vagotomy and operative trauma cause qualitatively different reactions of an organism.

  11. Adaptive Wavelet Transforms

    Energy Technology Data Exchange (ETDEWEB)

    Szu, H.; Hsu, C. [Univ. of Southwestern Louisiana, Lafayette, LA (United States)

    1996-12-31

    Human sensors systems (HSS) may be approximately described as an adaptive or self-learning version of the Wavelet Transforms (WT) that are capable to learn from several input-output associative pairs of suitable transform mother wavelets. Such an Adaptive WT (AWT) is a redundant combination of mother wavelets to either represent or classify inputs.

  12. Controls on stable sulfur isotope fractionation during bacterial sulfate reduction in Arctic sediments

    DEFF Research Database (Denmark)

    Bruchert, V.; Knoblauch, C.; Jørgensen, BB

    2001-01-01

    Sulfur isotope fractionation experiments during bacterial sulfate reduction were performed with recently isolated strains of cold-adapted sulfate-reducing bacteria from Arctic marine sediments with year-round temperatures below 2 degreesC. The bacteria represent quantitatively important members...... parts per thousand and 8 parts per thousand above 25 degreesC, respectively. In absence of significant differences in sulfate reduction rates in the high and low temperature range, respectively, we infer that different genera of sulfate-reducing bacteria dominate the sulfate-reducing bacterial community...

  13. Are patch occupancy data sufficient for inferring metapopulation dynamics using spatially explicit patch occupancy models?%用空间直观模型是否足以从斑块占据性资料中推断集合种群的动态过程?

    Institute of Scientific and Technical Information of China (English)

    Weidong GU; Robert K. SWIHART

    2003-01-01

    Spatial occupancy data have been widely used to draw inferences about metapopulation dynamics using patch- occupancy models. In the context of conservation biology, parameter estimation of patch-occupancy models is crucial for interpretation of metapopulation dynamics and prediction of a species' response to habitat destruction. In this paper, we explored the uncertainties associated with parameter estimation of a spatially explicit patch-occupancy model, the incidence function model (IFM). By constructing hypothetical networks of habitat patches and metapopulations with known param-eters, we could estimate parameters based on maximum likelihood methods using different snapshots from the same metapopulation. Furthermore, we developed a variant IFM with a target-area effect, I. E. , the probability of colonization was related to the size of a focal patch as well as spatial isolation. Our results show that estimated parameters based on dif-ferent snapshots collected from the same metapopulation exhibit considerable variation. For example, estimates from one snapshot may indicate a species with good dispersal and poor local survival probabilities whereas estimates from another snapshot of the same metapopulation may suggest a poor disperser with good local survival probabilities. Failure to include a target-area effect in the model yielded a positive bias for the parameter that scaled extinction probability to patch size.We conclude that inference of metapopulation dynamics based on one snapshot of occupancy data is not reliable [ Acta Zoo-logica Sinica 49 (6): 787-794, 2003].%在集合种群的研究中,经常要根据空间占据性数据应用斑块模型来推断种群的动态过程,在保护生物学应用中,斑块占据性模型的参数估测对于阐释集合种群动态和预测种群对生境破坏的反应极为重要.我们探讨了一种广泛应用的空间直观模型--率函数模型(Incidence function model)中参数估测的不

  14. User-Centered Evaluation of Adaptive and Adaptable Systems

    NARCIS (Netherlands)

    Velsen, van Lex; Geest, van der Thea M.; Klaassen, Rob F.

    2009-01-01

    Adaptive and adaptable systems provide tailored output to various users in various contexts. While adaptive systems base their output on implicit inferences, adaptable systems use explicitly provided information. Since the presentation or output of these systems is adapted, standard user-centered ev

  15. Financing climate change adaptation.

    Science.gov (United States)

    Bouwer, Laurens M; Aerts, Jeroen C J H

    2006-03-01

    This paper examines the topic of financing adaptation in future climate change policies. A major question is whether adaptation in developing countries should be financed under the 1992 United Nations Framework Convention on Climate Change (UNFCCC), or whether funding should come from other sources. We present an overview of financial resources and propose the employment of a two-track approach: one track that attempts to secure climate change adaptation funding under the UNFCCC; and a second track that improves mainstreaming of climate risk management in development efforts. Developed countries would need to demonstrate much greater commitment to the funding of adaptation measures if the UNFCCC were to cover a substantial part of the costs. The mainstreaming of climate change adaptation could follow a risk management path, particularly in relation to disaster risk reduction. 'Climate-proofing' of development projects that currently do not consider climate and weather risks could improve their sustainability.

  16. Appraising Adaptive Management

    Directory of Open Access Journals (Sweden)

    Kai N. Lee

    1999-12-01

    Full Text Available Adaptive management is appraised as a policy implementation approach by examining its conceptual, technical, equity, and practical strengths and limitations. Three conclusions are drawn: (1 Adaptive management has been more influential, so far, as an idea than as a practical means of gaining insight into the behavior of ecosystems utilized and inhabited by humans. (2 Adaptive management should be used only after disputing parties have agreed to an agenda of questions to be answered using the adaptive approach; this is not how the approach has been used. (3 Efficient, effective social learning, of the kind facilitated by adaptive management, is likely to be of strategic importance in governing ecosystems as humanity searches for a sustainable economy.

  17. Adaptive noise cancellation

    CERN Document Server

    Akram, N

    1999-01-01

    In this report we describe the concept of adaptive noise canceling, an alternative method of estimating signals corrupted by additive noise of interference. The method uses 'primary' input containing the corrupted signal and a 'reference' input containing noise correlated in some unknown way with the primary noise, the reference input is adaptively filtered and subtracted from the primary input to obtain the signal estimate. Adaptive filtering before subtraction allows the treatment of inputs that are deterministic or stochastic, stationary or time variable. When the reference input is free of signal and certain other conditions are met then noise in the primary input can be essentially eliminated without signal distortion. It is further shown that the adaptive filter also acts as notch filter. Simulated results illustrate the usefulness of the adaptive noise canceling technique.

  18. Mercury methylation and bacterial activity associated to tropical phytoplankton

    Energy Technology Data Exchange (ETDEWEB)

    Coelho-Souza, Sergio A. [Laboratorio de Tracadores Wolfgang Pfeiffer, SL 62, Instituto de Biofisica Carlos Chagas Filho, Bloco G, Ilha do Fundao, Universidade Federal do Rio de Janeiro (IBCCF/UFRJ), RJ, CEP 21949-900 (Brazil); Guimaraes, Jean R.D. [Laboratorio de Tracadores Wolfgang Pfeiffer, SL 62, Instituto de Biofisica Carlos Chagas Filho, Bloco G, Ilha do Fundao, Universidade Federal do Rio de Janeiro (IBCCF/UFRJ), RJ, CEP 21949-900 (Brazil)]. E-mail: jeanrdg@biof.ufrj.br; Mauro, Jane B.N. [Laboratorio de Tracadores Wolfgang Pfeiffer, SL 62, Instituto de Biofisica Carlos Chagas Filho, Bloco G, Ilha do Fundao, Universidade Federal do Rio de Janeiro (IBCCF/UFRJ), RJ, CEP 21949-900 (Brazil); Miranda, Marcio R. [Laboratorio de Tracadores Wolfgang Pfeiffer, SL 62, Instituto de Biofisica Carlos Chagas Filho, Bloco G, Ilha do Fundao, Universidade Federal do Rio de Janeiro (IBCCF/UFRJ), RJ, CEP 21949-900 (Brazil); Azevedo, Sandra M.F.O. [Laboratorio de Ecofisiologia e Toxicologia de Cianobacterias, IBCCF/UFRJ, RJ (Brazil)

    2006-07-01

    The methylated form of mercury (Hg), methylmercury (MeHg), is one of the most toxic pollutants. Biotic and/or abiotic methylation, often associated to sulfate-reducing bacteria metabolism, occurs in aquatic environments and in many tropical areas, mostly in the periphyton associated to floating macrophyte roots. Data about mercury methylation by phytoplankton are scarce and the aim of this study was to verify the biotic influence in the methylation process in Microcystis aeruginosa and Sineccocystis sp. laboratory strains and in natural populations of phytoplankton from two different aquatic systems, the mesotrophic Ribeirao das Lajes reservoir and hypereutrophic oligohaline Jacarepagua lagoon, Rio de Janeiro state, Brazil. Adapted radiochemical techniques were used to measure sulfate-reduction, mercury methylation and bacterial activity in phytoplankton samples. Methyl-{sup 203}Hg formation from added inorganic {sup 203}Hg and {sup 3}H-Leucine uptake were measured by liquid scintillation as well as sulfate-reduction, estimated as H{sub 2} {sup 35}S produced from added Na{sub 2} {sup 35}SO{sub 4}. There was no significant difference in low methylation potentials (0.37%) among the two cyanobacterium species studied in laboratory conditions. At Ribeirao das Lajes reservoir, there was no significant difference in methylation, bacterial activity and sulfate-reduction of surface sediment between the sampling points. Methylation in sediments (3-4%) was higher than in phytoplankton (1.5%), the opposite being true for bacterial activity (sediment mean 6.6 against 150.3 nmol gdw{sup -1} h{sup -1} for phytoplankton samples). At Jacarepagua lagoon, an expressive bacterial activity (477.1 x 10{sup 3} nmol gdw{sup -1} h{sup -1} at a concentration of 1000 nM leucine) and sulfate-reduction ({approx}21% H{sub 2} {sup 35}S trapped) associated to phytoplankton (mostly cyanobacteria M. aeruginosa) was observed, but mercury methylation was not detected.

  19. Two-dimensional DNA displays for comparisons of bacterial genomes

    Directory of Open Access Journals (Sweden)

    Malloff Chad

    2003-01-01

    Full Text Available We have developed two whole genome-scanning techniques to aid in the discovery of polymorphisms as well as horizontally acquired genes in prokaryotic organisms. First, two-dimensional bacterial genomic display (2DBGD was developed using restriction enzyme fragmentation to separate genomic DNA based on size, and then employing denaturing gradient gel electrophoresis (DGGE in the second dimension to exploit differences in sequence composition. This technique was used to generate high-resolution displays that enable the direct comparison of > 800 genomic fragments simultaneously and can be adapted for the high-throughput comparison of bacterial genomes. 2DBGDs are capable of detecting acquired and altered DNA, however, only in very closely related strains. If used to compare more distantly related strains (e.g. different species within a genus numerous small changes (i.e. small deletions and point mutations unrelated to the interesting phenotype, would encumber the comparison of 2DBGDs. For this reason a second method, bacterial comparative genomic hybridization (BCGH, was developed to directly compare bacterial genomes to identify gain or loss of genomic DNA. BCGH relies on performing 2DBGD on a pooled sample of genomic DNA from 2 strains to be compared and subsequently hybridizing the resulting 2DBGD blot separately with DNA from each individual strain. Unique spots (hybridization signals represent foreign DNA. The identification of novel DNA is easily achieved by excising the DNA from a dried gel followed by subsequent cloning and sequencing. 2DBGD and BCGH thus represent novel high resolution genome scanning techniques for directly identifying altered and/or acquired DNA.

  20. A model of excitation and adaptation in bacterial chemotaxis

    OpenAIRE

    1997-01-01

    Bacterial chemotaxis is widely studied because of its accessibility and because it incorporates processes that are important in a number of sensory systems: signal transduction, excitation, adaptation, and a change in behavior, all in response to stimuli. Quantitative data on the change in behavior are available for this system, and the major biochemical steps in the signal transduction/processing pathway have been identified. We have incorporated recent biochemica...

  1. 色交叉关联噪声作用下集合种群的稳定性和平均灭绝时间*%The mean extinction time and stability for a metapopulation system driven by colored cross-correlated noises∗

    Institute of Scientific and Technical Information of China (English)

    王康康; 刘先斌†; 杨建华

    2013-01-01

      在Levins模型的基础上研究了色交叉关联噪声对集合种群稳定性的影响,应用Fokker-Plank方程得到了系统的稳态概率密度函数,运用最快下降法得到了平均灭绝时间的解析式。结果表明:两噪声色关联时,加性噪声强度和乘性噪声强度均弱化集合种群的稳定性;噪声关联强度强化集合种群的稳定性。两噪声之间负关联时,平均灭绝时间是加性噪声强度和乘性噪声强度的减函数,是噪声关联时间的增函数;两噪声之间正关联时,平均灭绝时间是加性噪声强度和噪声关联时间乘性噪声强度的减函数,是乘性噪声强度的非单调函数。%In this paper, the stability for a metapopulation system driven by colored cross-correlated noises is investigated based on the Levins model. The stationary probability distribution and the explicit expression of the mean extinction time are derived according to the Fokker-Planck equation. Numerical results show that in the case of colored correlation between two noises, the addictive noise and the multiplicative noise intensity weaken the stability of metapopulation, and the correlation strength enhances the stability of metapopulation. If the correlation strength between the two noises is negative, the mean extinction time is a decreasing function of intensities of the two noises, but a increasing function of correlation time;if the correlation strength between the two noises is positive, then the mean extinction time is a decreasing function of addictive noise intensity and correlation time, but a non-monotonic function of multiplicative noise intensity.

  2. Fine-scale local adaptation of weevil mouthpart length and camellia pericarp thickness: altitudinal gradient of a putative arms race.

    Science.gov (United States)

    Toju, Hirokazu

    2008-05-01

    Although coevolutionary theory predicts that evolutionary interactions between species are spatially hierarchical, few studies have examined coevolutionary processes at multiple spatial scales. In an antagonistic system involving a plant, the Japanese camellia (Camellia japonica), and its obligate seed predator, the camellia weevil (Curculio camelliae), I elucidated the local adaptation of a camellia defensive armament (pericarp thickness) and a weevil offensive armament (rostrum length) within Yakushima Island (ca. 30 km in diameter), compared to a larger-scale variation in those traits throughout Japan reported in previous studies. Results showed that camellia pericarp thickness and weevil rostrum length vary remarkably within several kilometers on this island. In addition, geographic variation in each camellia and weevil armament was best explained by the armament size of the sympatric participant than by abiotic environmental heterogeneity. However, I also found that camellia pericarp thickness significantly decreased in cool-temperate (i.e., highland) areas, suggesting the contributions of climate on the spatial structuring of the weevil-camellia interaction. Interestingly, relatively thin pericarps occurred not only in the highlands but also in some low-altitude areas, indicating that other factors such as nonrandom or asymmetric gene flow play important roles in the metapopulation processes of interspecific interactions at small spatial scales.

  3. Resource allocation for epidemic control in metapopulations.

    Directory of Open Access Journals (Sweden)

    Martial L Ndeffo Mbah

    Full Text Available Deployment of limited resources is an issue of major importance for decision-making in crisis events. This is especially true for large-scale outbreaks of infectious diseases. Little is known when it comes to identifying the most efficient way of deploying scarce resources for control when disease outbreaks occur in different but interconnected regions. The policy maker is frequently faced with the challenge of optimizing efficiency (e.g. minimizing the burden of infection while accounting for social equity (e.g. equal opportunity for infected individuals to access treatment. For a large range of diseases described by a simple SIRS model, we consider strategies that should be used to minimize the discounted number of infected individuals during the course of an epidemic. We show that when faced with the dilemma of choosing between socially equitable and purely efficient strategies, the choice of the control strategy should be informed by key measurable epidemiological factors such as the basic reproductive number and the efficiency of the treatment measure. Our model provides new insights for policy makers in the optimal deployment of limited resources for control in the event of epidemic outbreaks at the landscape scale.

  4. Metapopulation dynamics and spatial heterogeneity in cancer

    OpenAIRE

    2002-01-01

    With the advent of drugs targeting specific molecular defects in cancerous cells [Gorre, M. E., et al. (2001) Science 293, 876–880], it is important to understand the degree of genetic heterogeneity present in tumor cell populations and the rules that govern microdiversity in human cancer. Here, we first show that populations with different genotypes in genes influencing cell growth and programmed cell death coexist in advanced malignant tumors of the colon, exhibiting microsatellite instabil...

  5. [Laboratory diagnosis of bacterial meningitis: usefulness of various tests for the determination of the etiological agent].

    Science.gov (United States)

    Carbonnelle, E

    2009-01-01

    Despite breakthroughs in the diagnosis and treatment of infectious diseases, meningitis still remains an important cause of mortality and morbidity. An accurate and rapid diagnosis of acute bacterial meningitis is essential for a good outcome. The gold-standard test for diagnosis is CSF analysis. Gram staining of CSF reveals bacteria in about 50 to 80 % of cases and cultures are positive in at best 80 % of cases. However, the sensitivity of both tests is less than 50 % in patients who are already on antibiotic treatment. CSF leukocyte count and concentration of protein and glucose lack specificity and sensitivity for the diagnosis of meningitis. Other biological tests are available for the diagnosis. Latex agglutination test were adapted for rapid and direct detection of soluble bacterial antigens in CSF of patients suspected with bacterial meningitis. This test is efficient in detecting antigens of most common central nervous system bateria but lacks sensibility. Furthermore, in the early phases of acute bacterial and viral meningitis, signs and symptoms are often non specific and it is not always possible to make a differential diagnosis. Markers like CRP, procalcitonin, or sTREM-1 may be very useful for the diagnosis and to differentiate between viral and bacterial meningitis. Bacterial meningitis diagnosis and management require various biological tests and a multidisciplinary approach.

  6. Adaptation dynamics in densely clustered chemoreceptors.

    Directory of Open Access Journals (Sweden)

    William Pontius

    Full Text Available In many sensory systems, transmembrane receptors are spatially organized in large clusters. Such arrangement may facilitate signal amplification and the integration of multiple stimuli. However, this organization likely also affects the kinetics of signaling since the cytoplasmic enzymes that modulate the activity of the receptors must localize to the cluster prior to receptor modification. Here we examine how these spatial considerations shape signaling dynamics at rest and in response to stimuli. As a model system, we use the chemotaxis pathway of Escherichia coli, a canonical system for the study of how organisms sense, respond, and adapt to environmental stimuli. In bacterial chemotaxis, adaptation is mediated by two enzymes that localize to the clustered receptors and modulate their activity through methylation-demethylation. Using a novel stochastic simulation, we show that distributive receptor methylation is necessary for successful adaptation to stimulus and also leads to large fluctuations in receptor activity in the steady state. These fluctuations arise from noise in the number of localized enzymes combined with saturated modification kinetics between the localized enzymes and the receptor substrate. An analytical model explains how saturated enzyme kinetics and large fluctuations can coexist with an adapted state robust to variation in the expression levels of the pathway constituents, a key requirement to ensure the functionality of individual cells within a population. This contrasts with the well-mixed covalent modification system studied by Goldbeter and Koshland in which mean activity becomes ultrasensitive to protein abundances when the enzymes operate at saturation. Large fluctuations in receptor activity have been quantified experimentally and may benefit the cell by enhancing its ability to explore empty environments and track shallow nutrient gradients. Here we clarify the mechanistic relationship of these large

  7. Adaptive network countermeasures.

    Energy Technology Data Exchange (ETDEWEB)

    McClelland-Bane, Randy; Van Randwyk, Jamie A.; Carathimas, Anthony G.; Thomas, Eric D.

    2003-10-01

    This report describes the results of a two-year LDRD funded by the Differentiating Technologies investment area. The project investigated the use of countermeasures in protecting computer networks as well as how current countermeasures could be changed in order to adapt with both evolving networks and evolving attackers. The work involved collaboration between Sandia employees and students in the Sandia - California Center for Cyber Defenders (CCD) program. We include an explanation of the need for adaptive countermeasures, a description of the architecture we designed to provide adaptive countermeasures, and evaluations of the system.

  8. [Adaptive optics for ophthalmology].

    Science.gov (United States)

    Saleh, M

    2016-04-01

    Adaptive optics is a technology enhancing the visual performance of an optical system by correcting its optical aberrations. Adaptive optics have already enabled several breakthroughs in the field of visual sciences, such as improvement of visual acuity in normal and diseased eyes beyond physiologic limits, and the correction of presbyopia. Adaptive optics technology also provides high-resolution, in vivo imaging of the retina that may eventually help to detect the onset of retinal conditions at an early stage and provide better assessment of treatment efficacy.

  9. Adaptive Vertex Fitting

    CERN Document Server

    Frühwirth, R; Vanlaer, Pascal

    2007-01-01

    Vertex fitting frequently has to deal with both mis-associated tracks and mis-measured track errors. A robust, adaptive method is presented that is able to cope with contaminated data. The method is formulated as an iterative re-weighted Kalman filter. Annealing is introduced to avoid local minima in the optimization. For the initialization of the adaptive filter a robust algorithm is presented that turns out to perform well in a wide range of applications. The tuning of the annealing schedule and of the cut-off parameter is described, using simulated data from the CMS experiment. Finally, the adaptive property of the method is illustrated in two examples.

  10. BACTERIAL DESEASES IN SEA FISH

    Directory of Open Access Journals (Sweden)

    Ivančica Strunjak-Perović

    1997-10-01

    Full Text Available With development of the fish culturing in the sea, the interest in their health also increased. The reason for this are diseases or rather mortality that occur in such controlled cultures and cause great economic losses. By growing large quantities of fish in rather small species, natural conditions are changed, so fish is more sensitive and prone to infection agents (viruses, bacteria, parasites. Besides, a large fish density in the cultural process accelerates spreading if the diseases, but also enables a better perception of them. In wild populations sick specimen very quickly become predator’s prey, witch makes it difficult to note any pathological changes in such fish. There are lots of articles on viral, bacterial and parasitic diseases nowdays, but this work deals exclusively with bacterial deseases that occur in the controlled sea cultures (vibriosis, furunculosis, pastherelosis, nocardiosis, mycobaceriosis, edwardsielosis, yersiniosis, deseases caused by bacteria of genera Flexibacter, Pseudomonas, Aeromonas, Streptococus and bacteria nephryithis. Yet, the knowledge of these deseases vary, depending on wether a fish species is being cultured for a longer period of time or is only being introduced in the controlled culture.

  11. Bacterial Culture of Neonatal Sepsis

    Directory of Open Access Journals (Sweden)

    AH Movahedian

    2006-08-01

    Full Text Available Neonatal bacterial sepsis is one of the major cause of morbidity and mortality in neonates. This retrospective study was performed to determine the incidence of bacterial sepsis with focus on Gram negative organisms in neonates admitted at Beheshti Hospital in Kashan, during a 3-yr period, from September 2002 to September 2005. Blood culture was performed on all neonates with risk factors or signs of suggestive sepsis. Blood samples were cultured using brain heart infusion (BHI broth according to standard method. From the 1680 neonates 36% had positive blood culture for Pseudomans aeruginosa, 20.7% for Coagulase negative Staphylococci, and 17% for Klebsiella spp. Gram-negative organisms accounted for 72.1% of all positive cultures. The overall mortality rate was 19.8% (22 /111 of whom 63.6% (14 /22 were preterm. Pseudomona aeruginosa and Klebsiella spp. showed a high degree of resistance to commonly used antibiotics (ampicillin, gentamicin as well as third generation cephalosporins. Continued local surveillance studies are urged to monitor emerging antimicrobial resistance and to guide interventions to minimize its occurrence.

  12. Periodontal diseases as bacterial infection

    Directory of Open Access Journals (Sweden)

    A. Bascones Martínez

    Full Text Available The periodontal disease is conformed by a group of illnesses affecting the gums and dental support structures. They are caused by certain bacteria found in the bacterial plaque. These bacteria are essential to the onset of illness; however, there are predisposing factors in both the host and the microorganisms that will have an effect on the pathogenesis of the illness. Periodontopathogenic bacterial microbiota is needed, but by itself, it is not enough to cause the illness, requiring the presence of a susceptible host. These diseases have been classified as gingivitis, when limited to the gums, and periodontitis, when they spread to deeper tissues. Classification of periodontal disease has varied over the years.The one used in this work was approved at the International Workshop for a Classification of Periodontal Diseases and Conditions, held in 1999. This study is an overview of the different periodontal disease syndromes. Later, the systematic use of antibiotic treatment consisting of amoxicillin, amoxicillinclavulanic acid, and metronidazole as first line coadjuvant treatment of these illnesses will be reviewed.

  13. Bioinformatic Comparison of Bacterial Secretomes

    Institute of Scientific and Technical Information of China (English)

    Catharine Song; Aseem Kumar; Mazen Saleh

    2009-01-01

    The rapid increasing number of completed bacterial genomes provides a good op-portunity to compare their proteomes. This study was undertaken to specifically compare and contrast their secretomes-the fraction of the proteome with pre-dicted N-terminal signal sequences, both type Ⅰ and type Ⅱ. A total of 176 theoreti-cal bacterial proteomes were examined using the ExProt program. Compared with the Gram-positives, the Gram-negative bacteria were found, on average, to con-tain a larger number of potential Sec-dependent sequences. In the Gram-negative bacteria but not in the others, there was a positive correlation between proteome size and secretome size, while there was no correlation between secretome size and pathogenicity. Within the Gram-negative bacteria, intracellular pathogens were found to have the smallest secretomes. However, the secretomes of certain bacte-ria did not fit into the observed pattern. Specifically, the secretome of Borrelia burgdoferi has an unusually large number of putative lipoproteins, and the signal peptides of mycoplasmas show closer sequence similarity to those of the Gram-negative bacteria. Our analysis also suggests that even for a theoretical minimal genome of 300 open reading frames, a fraction of this gene pool (up to a maximum of 20%) may code for proteins with Sec-dependent signal sequences.

  14. Bacterial pericarditis in a cat

    Directory of Open Access Journals (Sweden)

    Nicole LeBlanc

    2015-09-01

    Full Text Available Case summary A 4-year-old male neutered domestic shorthair cat was presented to the Oregon State University cardiology service for suspected pericardial effusion. Cardiac tamponade was documented and pericardiocentesis yielded purulent fluid with cytologic results supportive of bacterial pericarditis. The microbial population consisted of Pasteurella multocida, Actinomyces canis, Fusobacterium and Bacteroides species. Conservative management was elected consisting of intravenous antibiotic therapy with ampicillin sodium/sulbactam sodium and metronidazole for 48 h followed by 4 weeks of oral antibiotics. Re-examination 3 months after the initial incident indicated no recurrence of effusion and the cat remained free of clinical signs 2 years after presentation. Relevance and novel information Bacterial pericarditis is a rare cause of pericardial effusion in cats. Growth of P multocida, A canis, Fusobacterium and Bacteroides species has not previously been documented in feline septic pericarditis. Conservative management with broad-spectrum antibiotics may be considered when further diagnostic imaging or exploratory surgery to search for a primary nidus of infection is not feasible or elected.

  15. Interaction between resource identity and bacterial community composition regulates bacterial respiration in aquatic ecosystems

    Directory of Open Access Journals (Sweden)

    A. P. F. Pires

    Full Text Available Abstract Resource identity and composition structure bacterial community, which in turn determines the magnitude of bacterial processes and ecological services. However, the complex interaction between resource identity and bacterial community composition (BCC has been poorly understood so far. Using aquatic microcosms, we tested whether and how resource identity interacts with BCC in regulating bacterial respiration and bacterial functional diversity. Different aquatic macrophyte leachates were used as different carbon resources while BCC was manipulated through successional changes of bacterial populations in batch cultures. We observed that the same BCC treatment respired differently on each carbon resource; these resources also supported different amounts of bacterial functional diversity. There was no clear linear pattern of bacterial respiration in relation to time succession of bacterial communities in all leachates, i.e. differences on bacterial respiration between different BCC were rather idiosyncratic. Resource identity regulated the magnitude of respiration of each BCC, e.g. Ultricularia foliosa leachate sustained the greatest bacterial functional diversity and lowest rates of bacterial respiration in all BCC. We conclude that both resource identity and the BCC interact affecting the pattern and the magnitude of bacterial respiration in aquatic ecosystems.

  16. Forensic identification using skin bacterial communities

    OpenAIRE

    FIERER Noah; Lauber, Christian L.; Zhou, Nick; McDonald, Daniel; Costello, Elizabeth K.; Knight, Rob

    2010-01-01

    Recent work has demonstrated that the diversity of skin-associated bacterial communities is far higher than previously recognized, with a high degree of interindividual variability in the composition of bacterial communities. Given that skin bacterial communities are personalized, we hypothesized that we could use the residual skin bacteria left on objects for forensic identification, matching the bacteria on the object to the skin-associated bacteria of the individual who touched the object....

  17. Drag Reduction of Bacterial Cellulose Suspensions

    Directory of Open Access Journals (Sweden)

    Satoshi Ogata

    2011-01-01

    Full Text Available Drag reduction due to bacterial cellulose suspensions with small environmental loading was investigated. Experiments were carried out by measuring the pressure drop in pipe flow. It was found that bacterial cellulose suspensions give rise to drag reduction in the turbulent flow range. We observed a maximum drag reduction ratio of 11% and found that it increased with the concentration of the bacterial cellulose suspension. However, the drag reduction effect decreased in the presence of mechanical shear.

  18. In vivo bacterial morphogenetic protein interactions

    OpenAIRE

    van der Ploeg, R.; den Blaauwen, T.; Meghea, A.

    2012-01-01

    This chapter will discuss none-invasive techniques that are widely used to study protein-protein interactions. As an example, their application in exploring interactions between proteins involved in bacterial cell division will be evaluated. First, bacterial morphology and cell division of the rod-shaped bacterium Escherichia coli will be introduced. Next, three bacterial two-hybrid methods and three Förster resonance energy transfer detection methods that are frequently applied to detect int...

  19. Exploring Adaptive Program Behavior

    DEFF Research Database (Denmark)

    Bonnichsen, Lars Frydendal; Probst, Christian W.

    Modern computer systems are increasingly complex, with ever changing bottlenecks. This makes it difficult to ensure consistent performance when porting software, or even running it. Adaptivity, ie, switching between program variations, and dynamic recompilation have been suggested as solutions. B...

  20. Adaptive digital filters

    CERN Document Server

    Kovačević, Branko; Milosavljević, Milan

    2013-01-01

    Adaptive Digital Filters” presents an important discipline applied to the domain of speech processing. The book first makes the reader acquainted with the basic terms of filtering and adaptive filtering, before introducing the field of advanced modern algorithms, some of which are contributed by the authors themselves. Working in the field of adaptive signal processing requires the use of complex mathematical tools. The book offers a detailed presentation of the mathematical models that is clear and consistent, an approach that allows everyone with a college level of mathematics knowledge to successfully follow the mathematical derivations and descriptions of algorithms.   The algorithms are presented in flow charts, which facilitates their practical implementation. The book presents many experimental results and treats the aspects of practical application of adaptive filtering in real systems, making it a valuable resource for both undergraduate and graduate students, and for all others interested in m...

  1. The genomics of adaptation.

    Science.gov (United States)

    Radwan, Jacek; Babik, Wiesław

    2012-12-22

    The amount and nature of genetic variation available to natural selection affect the rate, course and outcome of evolution. Consequently, the study of the genetic basis of adaptive evolutionary change has occupied biologists for decades, but progress has been hampered by the lack of resolution and the absence of a genome-level perspective. Technological advances in recent years should now allow us to answer many long-standing questions about the nature of adaptation. The data gathered so far are beginning to challenge some widespread views of the way in which natural selection operates at the genomic level. Papers in this Special Feature of Proceedings of the Royal Society B illustrate various aspects of the broad field of adaptation genomics. This introductory article sets up a context and, on the basis of a few selected examples, discusses how genomic data can advance our understanding of the process of adaptation.

  2. Asimovian Adaptive Agents

    CERN Document Server

    Gordon, D F

    2011-01-01

    The goal of this research is to develop agents that are adaptive and predictable and timely. At first blush, these three requirements seem contradictory. For example, adaptation risks introducing undesirable side effects, thereby making agents' behavior less predictable. Furthermore, although formal verification can assist in ensuring behavioral predictability, it is known to be time-consuming. Our solution to the challenge of satisfying all three requirements is the following. Agents have finite-state automaton plans, which are adapted online via evolutionary learning (perturbation) operators. To ensure that critical behavioral constraints are always satisfied, agents' plans are first formally verified. They are then reverified after every adaptation. If reverification concludes that constraints are violated, the plans are repaired. The main objective of this paper is to improve the efficiency of reverification after learning, so that agents have a sufficiently rapid response time. We present two solutions: ...

  3. The Adaptive Organization

    DEFF Research Database (Denmark)

    Andersen, Torben Juul; Hallin, Carina Antonia

    2016-01-01

    Contemporary organizations operate under turbulent business conditions and must adapt their strategies to ongoing changes. This article argues that sustainable organizational performance is achieved when top management directs and coordinates interactive processes anchored in emerging organizatio......Contemporary organizations operate under turbulent business conditions and must adapt their strategies to ongoing changes. This article argues that sustainable organizational performance is achieved when top management directs and coordinates interactive processes anchored in emerging...... experiential insights from the fast response processes can be aggregated systematically from frontline employees and fed into the slow process of reasoning. When the fast and slow processes interact they form a dynamic system that adapts organizational activities to the changing conditions which identifies...... the adaptive organization....

  4. Genomic islands predict functional adaptation in marine actinobacteria

    Energy Technology Data Exchange (ETDEWEB)

    Penn, Kevin; Jenkins, Caroline; Nett, Markus; Udwary, Daniel; Gontang, Erin; McGlinchey, Ryan; Foster, Brian; Lapidus, Alla; Podell, Sheila; Allen, Eric; Moore, Bradley; Jensen, Paul

    2009-04-01

    Linking functional traits to bacterial phylogeny remains a fundamental but elusive goal of microbial ecology 1. Without this information, it becomes impossible to resolve meaningful units of diversity and the mechanisms by which bacteria interact with each other and adapt to environmental change. Ecological adaptations among bacterial populations have been linked to genomic islands, strain-specific regions of DNA that house functionally adaptive traits 2. In the case of environmental bacteria, these traits are largely inferred from bioinformatic or gene expression analyses 2, thus leaving few examples in which the functions of island genes have been experimentally characterized. Here we report the complete genome sequences of Salinispora tropica and S. arenicola, the first cultured, obligate marine Actinobacteria 3. These two species inhabit benthic marine environments and dedicate 8-10percent of their genomes to the biosynthesis of secondary metabolites. Despite a close phylogenetic relationship, 25 of 37 secondary metabolic pathways are species-specific and located within 21 genomic islands, thus providing new evidence linking secondary metabolism to ecological adaptation. Species-specific differences are also observed in CRISPR sequences, suggesting that variations in phage immunity provide fitness advantages that contribute to the cosmopolitan distribution of S. arenicola 4. The two Salinispora genomes have evolved by complex processes that include the duplication and acquisition of secondary metabolite genes, the products of which provide immediate opportunities for molecular diversification and ecological adaptation. Evidence that secondary metabolic pathways are exchanged by Horizontal Gene Transfer (HGT) yet are fixed among globally distributed populations 5 supports a functional role for their products and suggests that pathway acquisition represents a previously unrecognized force driving bacterial diversification

  5. Modified niche optima and breadths explain the historical contingency of bacterial community responses to eutrophication in coastal sediments.

    Science.gov (United States)

    Fodelianakis, S; Moustakas, A; Papageorgiou, N; Manoli, O; Tsikopoulou, I; Michoud, G; Daffonchio, D; Karakassis, I; Ladoukakis, E D

    2016-09-23

    Previous studies have shown that the response of bacterial communities to disturbances depends on their environmental history. Historically fluctuating habitats host communities that respond better to disturbance than communities of historically stable habitats. However, the exact ecological mechanism that drives this dependency remains unknown. Here, we experimentally demonstrate that modifications of niche optima and niche breadths of the community members are driving this dependency of bacterial responses to past environmental conditions. First, we develop a novel, simple method to calculate the niche optima and breadths of bacterial taxa regarding single environmental gradients. Then, we test this method on sediment bacterial communities of three habitats, one historically stable and less loaded and two historically more variable and more loaded habitats in terms of historical chlorophyll-α water concentration, that we subject to hypoxia via organic matter addition ex situ. We find that communities containing bacterial taxa differently adapted to hypoxia show different structural and functional responses, depending on the sediment's environmental history. Specifically, in the historically less fluctuating and loaded sediments where we find more taxa poorly adapted to hypoxic conditions, communities change a lot over time and organic matter is not degraded efficiently. The opposite is true for the historically more fluctuating and loaded sediments where we find more taxa well adapted to hypoxia. Based on the community responses observed here, we also propose an alternative calculation of community resistance that takes into account how rapidly the communities respond to disturbances and not just the initial and final states of the community.

  6. Modified niche optima and breadths explain the historical contingency of bacterial community responses to eutrophication in coastal sediments

    KAUST Repository

    Fodelianakis, Stylianos

    2016-09-23

    Previous studies have shown that the response of bacterial communities to disturbances depends on their environmental history. Historically fluctuating habitats host communities that respond better to disturbance than communities of historically stable habitats. However, the exact ecological mechanism that drives this dependency remains unknown. Here, we experimentally demonstrate that modifications of niche optima and niche breadths of the community members are driving this dependency of bacterial responses to past environmental conditions. First, we develop a novel, simple method to calculate the niche optima and breadths of bacterial taxa regarding single environmental gradients. Then, we test this method on sediment bacterial communities of three habitats, one historically stable and less loaded and two historically more variable and more loaded habitats in terms of historical chlorophyll-α water concentration, that we subject to hypoxia via organic matter addition ex situ. We find that communities containing bacterial taxa differently adapted to hypoxia show different structural and functional responses, depending on the sediment\\'s environmental history. Specifically, in the historically less fluctuating and loaded sediments where we find more taxa poorly adapted to hypoxic conditions, communities change a lot over time and organic matter is not degraded efficiently. The opposite is true for the historically more fluctuating and loaded sediments where we find more taxa well adapted to hypoxia. Based on the community responses observed here, we also propose an alternative calculation of community resistance that takes into account how rapidly the communities respond to disturbances and not just the initial and final states of the community.

  7. Bacterial contamination of hospital physicians' stethoscopes.

    Science.gov (United States)

    Bernard, L; Kereveur, A; Durand, D; Gonot, J; Goldstein, F; Mainardi, J L; Acar, J; Carlet, J

    1999-09-01

    Because stethoscopes might be potential vectors of nosocomial infections, this study, conducted in a 450-bed general hospital, was devised to evaluate the bacterial contamination of stethoscopes; bacterial survival on stethoscope membranes; the kinetics of the bacterial load on stethoscope membranes during clinical use; and the efficacy of 70% alcohol or liquid soap for membrane disinfection. Among the 355 stethoscopes tested, 234 carried > or =2 different bacterial species; 31 carried potentially pathogenic bacteria. Although some bacteria deposited onto membranes could survive 6 to 18 hours, none survived after disinfection.

  8. Bacterial Nanocellulose as a Microbiological Derived Nanomaterial

    Directory of Open Access Journals (Sweden)

    Stanisławska A.

    2016-12-01

    Full Text Available Bacterial nanocellulose (BNC is a nanofibrilar polymer produced by strains such as Gluconacetobacter xylinus, one of the best bacterial species which given the highest efficiency in cellulose production. Bacterial cellulose is a biomaterial having unique properties such as: chemical purity, good mechanical strength, high flexibility, high absorbency, possibility of forming any shape and size and many others. Such a large number of advantages contributes to the widespread use of the BNC in food technology, paper, electronic industry, but also the architecture in use. However, the greatest hopes are using the BNC in medicine. This text contains information about bacterial nanocellulose, its specific mechanical and biological properties and current applications.

  9. Frustratingly Easy Domain Adaptation

    CERN Document Server

    Daumé, Hal

    2009-01-01

    We describe an approach to domain adaptation that is appropriate exactly in the case when one has enough ``target'' data to do slightly better than just using only ``source'' data. Our approach is incredibly simple, easy to implement as a preprocessing step (10 lines of Perl!) and outperforms state-of-the-art approaches on a range of datasets. Moreover, it is trivially extended to a multi-domain adaptation problem, where one has data from a variety of different domains.

  10. From equivalence to adaptation

    Directory of Open Access Journals (Sweden)

    Paulina Borowczyk

    2009-01-01

    Full Text Available The aim of this paper is to illustrate in which cases the translators use the adaptation when they are confronted with a term related to sociocultural aspects. We will discuss the notions of equivalence and adaptation and their limits in the translation. Some samples from Arte TV news and from the American film Shrek translated into Polish, German and French will be provided as a support for this article.

  11. Adaptable DC offset correction

    Science.gov (United States)

    Golusky, John M. (Inventor); Muldoon, Kelly P. (Inventor)

    2009-01-01

    Methods and systems for adaptable DC offset correction are provided. An exemplary adaptable DC offset correction system evaluates an incoming baseband signal to determine an appropriate DC offset removal scheme; removes a DC offset from the incoming baseband signal based on the appropriate DC offset scheme in response to the evaluated incoming baseband signal; and outputs a reduced DC baseband signal in response to the DC offset removed from the incoming baseband signal.

  12. Network and adaptive sampling

    CERN Document Server

    Chaudhuri, Arijit

    2014-01-01

    Combining the two statistical techniques of network sampling and adaptive sampling, this book illustrates the advantages of using them in tandem to effectively capture sparsely located elements in unknown pockets. It shows how network sampling is a reliable guide in capturing inaccessible entities through linked auxiliaries. The text also explores how adaptive sampling is strengthened in information content through subsidiary sampling with devices to mitigate unmanageable expanding sample sizes. Empirical data illustrates the applicability of both methods.

  13. Adaptive context exploitation

    Science.gov (United States)

    Steinberg, Alan N.; Bowman, Christopher L.

    2013-05-01

    This paper presents concepts and an implementation scheme to improve information exploitation processes and products by adaptive discovery and processing of contextual information. Context is used in data fusion - and in inferencing in general - to provide expectations and to constrain processing. It also is used to infer or refine desired information ("problem variables") on the basis of other available information ("context variables"). Contextual exploitation becomes critical in several classes of inferencing problems in which traditional information sources do not provide sufficient resolution between entity states or when such states are poorly or incompletely modeled. An adaptive evidence-accrual inference method - adapted from developments in target recognition and scene understanding - is presented; whereby context variables are selected on the basis of (a) their utility in refining explicit problem variables, (b) the probability of evaluating these variables to within a given accuracy, given candidate system actions (data collection, mining or processing), and (c) the cost of such actions. The Joint Directors of Laboratories (JDL) Data Fusion Model, with its extension to dual Resource Management functions, has been adapted to accommodate adaptive information exploitation, to include adaptive context exploitation. The interplay of Data Fusion and Resource Management (DF&RM) functionality in exploiting contextual information is illustrated in terms of the dual-node DF&RM architecture. An important advance is in the integration of data mining methods for data search/discovery and for abductive model refinement.

  14. Adaptation through proportion

    Science.gov (United States)

    Xiong, Liyang; Shi, Wenjia; Tang, Chao

    2016-08-01

    Adaptation is a ubiquitous feature in biological sensory and signaling networks. It has been suggested that adaptive systems may follow certain simple design principles across diverse organisms, cells and pathways. One class of networks that can achieve adaptation utilizes an incoherent feedforward control, in which two parallel signaling branches exert opposite but proportional effects on the output at steady state. In this paper, we generalize this adaptation mechanism by establishing a steady-state proportionality relationship among a subset of nodes in a network. Adaptation can be achieved by using any two nodes in the sub-network to respectively regulate the output node positively and negatively. We focus on enzyme networks and first identify basic regulation motifs consisting of two and three nodes that can be used to build small networks with proportional relationships. Larger proportional networks can then be constructed modularly similar to LEGOs. Our method provides a general framework to construct and analyze a class of proportional and/or adaptation networks with arbitrary size, flexibility and versatile functional features.

  15. Bacterial Community in Different Populations of Rice Brown Planthopper Nilaparvata lugens (Stål)

    Institute of Scientific and Technical Information of China (English)

    XU Hong-xing; ZHENG Xu-song; YANG Ya-jun; WANG Xin; YE Gong-yin; LU Zhong-xian

    2014-01-01

    The structures of bacterial communities in the brown planthopper (BPH) Nilaparvata lugens (Stål) from different geographic and resistant virulent populations were analyzed by using denatured gradient gel electrophoresis (DGGE). Results showed that the bacterial communities in BPH nymph from the first to the fifth instars varied with nymphal growth and development. The bacterial communities in the first-instar BPH nymph were similar to those in adults. Nine geographic BPH populations were divided into three groups based on the cluster analysis of DGGE fingerprint. The first group was from the Philippines;the second group was from Thailand and Hainan, Yunnan and Zhejiang provinces of China; and the third group was from Vietnam and Guangxi, Hunan and Jiangxi provinces of China. BPH populations adapted to different resistant rice varieties. The BPH populations from Mudgo (with resistant gene Bph1) and ASD7 (with resistant gene bph2) differed with those of the susceptible rice variety TN1.

  16. Extended recombinant bacterial ghost system.

    Science.gov (United States)

    Lubitz, W; Witte, A; Eko, F O; Kamal, M; Jechlinger, W; Brand, E; Marchart, J; Haidinger, W; Huter, V; Felnerova, D; Stralis-Alves, N; Lechleitner, S; Melzer, H; Szostak, M P; Resch, S; Mader, H; Kuen, B; Mayr, B; Mayrhofer, P; Geretschläger, R; Haslberger, A; Hensel, A

    1999-08-20

    Controlled expression of cloned PhiX174 gene E in Gram-negative bacteria results in lysis of the bacteria by formation of an E-specific transmembrane tunnel structure built through the cell envelope complex. Bacterial ghosts from a variety of bacteria are used as non-living candidate vaccines. In the recombinant ghost system, foreign proteins are attached on the inside of the inner membrane as fusions with specific anchor sequences. Ghosts have a sealed periplasmic space and the export of proteins into this space vastly extends the capacity of ghosts or recombinant ghosts to function as carriers of foreign antigens. In addition, S-layer proteins forming shell-like self assembly structures can be expressed in candidate vaccine strains prior to E-mediated lysis. Such recombinant S-layer proteins carrying foreign epitopes further extend the possibilities of ghosts as carriers of foreign epitopes. As ghosts have inherent adjuvant properties, they can be used as adjuvants in combination with subunit vaccines. Subunits or other ligands can also be coupled to matrixes like dextran which are used to fill the internal lumen of ghosts. Oral, aerogenic or parenteral immunization of experimental animals with recombinant ghosts induced specific humoral and cellular immune responses against bacterial and target components including protective mucosal immunity. The most relevant advantage of recombinant bacterial ghosts as immunogens is that no inactivation procedures that denature relevant immunogenic determinants are employed in this production. This fact explains the superior quality of ghosts when compared to other inactivated vaccines. The endotoxic component of the outer membrane does not limit the use of ghosts as vaccine candidates but triggers the release of several potent immunoregulatory cytokines. As carriers, there is no limitation in the size of foreign antigens that can be inserted in the membrane and the capacity of all spaces including the membranes, peri

  17. Primordial soup was edible: abiotically produced Miller-Urey mixture supports bacterial growth.

    Science.gov (United States)

    Xie, Xueshu; Backman, Daniel; Lebedev, Albert T; Artaev, Viatcheslav B; Jiang, Liying; Ilag, Leopold L; Zubarev, Roman A

    2015-09-28

    Sixty years after the seminal Miller-Urey experiment that abiotically produced a mixture of racemized amino acids, we provide a definite proof that this primordial soup, when properly cooked, was edible for primitive organisms. Direct admixture of even small amounts of Miller-Urey mixture strongly inhibits E. coli bacteria growth due to the toxicity of abundant components, such as cyanides. However, these toxic compounds are both volatile and extremely reactive, while bacteria are highly capable of adaptation. Consequently, after bacterial adaptation to a mixture of the two most abundant abiotic amino acids, glycine and racemized alanine, dried and reconstituted MU soup was found to support bacterial growth and even accelerate it compared to a simple mixture of the two amino acids. Therefore, primordial Miller-Urey soup was perfectly suitable as a growth media for early life forms.

  18. Influence Of Used Bacterial Culture On Zinc And Aluminium Bioleaching From Printed Circuit Boards

    Directory of Open Access Journals (Sweden)

    Mrazikova Anna

    2015-06-01

    Full Text Available Bioleaching processes were used to solubilize metals (Cu, Ni, Zn and Al from printed circuit boards (PCBs. In this study, a PCBs-adapted pure culture of Acidithiobacillus ferrooxidans, pure culture of Acidithiobacillus thiooxidans and PCBs-adapted mixed culture of A. ferrooxidans and A. thiooxidans were used for recovery of the metals. The study showed that the mixed bacterial culture has the greatest potential to dissolve metals. The maximum metal bioleaching efficiencies were found to be 100, 92, 89 and 20% of Cu, Ni, Zn and Al, respectively. The mixed culture revealed higher bacterial stability. The main factor responsible for high metal recovery was the ability of the mixed culture to maintain the low pH during the whole process. The pure culture of A. thiooxidans had no significant effect on metal bioleaching from PCBs.

  19. Bacterial lipopolysaccharide inhibits influenza virus infection of human macrophages and the consequent induction of CD8+ T cell immunity

    NARCIS (Netherlands)

    Short, K.R.; Vissers, M.; Kleijn, S. de; Zomer, A.L.; Kedzierska, K.; Grant, E.; Reading, P.C.; Hermans, P.W.M.; Ferwerda, G.; Diavatopoulos, D.A.

    2014-01-01

    It is well established that infection with influenza A virus (IAV) facilitates secondary bacterial disease. However, there is a growing body of evidence that the microbial context in which IAV infection occurs can affect both innate and adaptive responses to the virus. To date, these studies have be

  20. New pathways for bacterial polythioesters.

    Science.gov (United States)

    Wübbeler, Jan Hendrik; Steinbüchel, Alexander

    2014-10-01

    Polythioesters (PTE) contain sulfur in the backbone and represent persistent biopolymers, which are produced by certain chemical procedures as well as biotechnological in vitro and in vivo techniques. Different building blocks can be incorporated, resulting in PTE with variable features that could become interesting for special purposes. Particularly, the option to produce PTE in large-scale and in accordance with the methods of white biotechnology or green chemistry is valuable due to economical potentials and public environmental consciousness. This review is focused on the synthesis of PTE by the three established bacterial production strains Ralstonia eutropha, Escherichia coli and Advenella mimigardefordensis. In addition, an overview of the in vitro production and degradation of PTE is depicted.

  1. Cooperative Model of Bacterial Sensing

    CERN Document Server

    Shi, Y; Shi, Yu; Duke, Thomas

    1998-01-01

    Bacterial chemotaxis is controlled by the signalling of a cluster of receptors. A cooperative model is presented, in which coupling between neighbouring receptor dimers enhances the sensitivity with which stimuli can be detected, without diminishing the range of chemoeffector concentration over which chemotaxis can operate. Individual receptor dimers have two stable conformational states: one active, one inactive. Noise gives rise to a distribution between these states, with the probability influenced by ligand binding, and also by the conformational states of adjacent receptor dimers. The two-state model is solved, based on an equivalence with the Ising model in a randomly distributed magnetic field. The model has only two effective parameters, and unifies a number of experimental findings. According to the value of the parameter comparing coupling and noise, the signal can be arbitrarily sensitive to changes in the fraction of receptor dimers to which ligand is bound. The counteracting effect of a change of...

  2. Antigenic Variation in Bacterial Pathogens.

    Science.gov (United States)

    Palmer, Guy H; Bankhead, Troy; Seifert, H Steven

    2016-02-01

    Antigenic variation is a strategy used by a broad diversity of microbial pathogens to persist within the mammalian host. Whereas viruses make use of a minimal proofreading capacity combined with large amounts of progeny to use random mutation for variant generation, antigenically variant bacteria have evolved mechanisms which use a stable genome, which aids in protecting the fitness of the progeny. Here, three well-characterized and highly antigenically variant bacterial pathogens are discussed: Anaplasma, Borrelia, and Neisseria. These three pathogens display a variety of mechanisms used to create the structural and antigenic variation needed for immune escape and long-term persistence. Intrahost antigenic variation is the focus; however, the role of these immune escape mechanisms at the population level is also presented.

  3. Bacterial interactions in dental biofilm.

    Science.gov (United States)

    Huang, Ruijie; Li, Mingyun; Gregory, Richard L

    2011-01-01

    Biofilms are masses of microorganisms that bind to and multiply on a solid surface, typically with a fluid bathing the microbes. The microorganisms that are not attached but are free floating in an aqueous environment are termed planktonic cells. Traditionally, microbiology research has addressed results from planktonic bacterial cells. However, many recent studies have indicated that biofilms are the preferred form of growth of most microbes and particularly those of a pathogenic nature. Biofilms on animal hosts have significantly increased resistance to various antimicrobials compared to planktonic cells. These microbial communities form microcolonies that interact with each other using very sophisticated communication methods (i.e., quorum-sensing). The development of unique microbiological tools to detect and assess the various biofilms around us is a tremendously important focus of research in many laboratories. In the present review, we discuss the major biofilm mechanisms and the interactions among oral bacteria.

  4. Autoproteolytic Activation of Bacterial Toxins

    Directory of Open Access Journals (Sweden)

    Aimee Shen

    2010-05-01

    Full Text Available Protease domains within toxins typically act as the primary effector domain within target cells. By contrast, the primary function of the cysteine protease domain (CPD in Multifunctional Autoprocessing RTX-like (MARTX and Clostridium sp. glucosylating toxin families is to proteolytically cleave the toxin and release its cognate effector domains. The CPD becomes activated upon binding to the eukaryotic-specific small molecule, inositol hexakisphosphate (InsP6, which is found abundantly in the eukaryotic cytosol. This property allows the CPD to spatially and temporally regulate toxin activation, making it a prime candidate for developing anti-toxin therapeutics. In this review, we summarize recent findings related to defining the regulation of toxin function by the CPD and the development of inhibitors to prevent CPD-mediated activation of bacterial toxins.

  5. Bacterial Ice Crystal Controlling Proteins

    Directory of Open Access Journals (Sweden)

    Janet S. H. Lorv

    2014-01-01

    Full Text Available Across the world, many ice active bacteria utilize ice crystal controlling proteins for aid in freezing tolerance at subzero temperatures. Ice crystal controlling proteins include both antifreeze and ice nucleation proteins. Antifreeze proteins minimize freezing damage by inhibiting growth of large ice crystals, while ice nucleation proteins induce formation of embryonic ice crystals. Although both protein classes have differing functions, these proteins use the same ice binding mechanisms. Rather than direct binding, it is probable that these protein classes create an ice surface prior to ice crystal surface adsorption. Function is differentiated by molecular size of the protein. This paper reviews the similar and different aspects of bacterial antifreeze and ice nucleation proteins, the role of these proteins in freezing tolerance, prevalence of these proteins in psychrophiles, and current mechanisms of protein-ice interactions.

  6. Cold-adapted proteases as an emerging class of therapeutics.

    Science.gov (United States)

    Fornbacke, Marcus; Clarsund, Mats

    2013-06-01

    Proteases have been used in medicine for several decades and are an established and well tolerated class of therapeutic agent. These proteases were sourced from mammals or bacteria that exist or have adapted to moderate temperatures (mesophilic organisms); however, proteases derived from organisms from cold environments-cold-adapted or psychrophilic proteases-generally have high specific activity, low substrate affinity, and high catalytic rates at low and moderate temperatures. Made possible by greater flexibility, psychrophilic enzymes interact with and transform the substrate at lower energy costs. Cold-adapted proteases have been used in a wide range of applications, including industrial functions, textiles, cleaning/hygiene products, molecular biology, environmental bioremediations, consumer food products, cosmetics, and pharmaceutical production. In addition to these applications, they have also shown promise as therapeutic modalities for cosmeceutical applications (by reducing glabellar [frown] lines) and a number of disease conditions, including bacterial infections (by disrupting biofilms to prevent bacterial infection), topical wound management (when used as a debridement agent to remove necrotic tissue and fibrin clots), oral/dental health management (by removing plaque and preventing periodontal disease), and in viral infections (by reducing the infectivity of viruses, such as human rhinovirus 16 and herpes simplex virus). Psychrophilic proteases with greater activity and stability (than the original organism-derived variant) have been developed; this coupled with available manufacturing recombinant production techniques suggests that cold-adapted proteases have a promising future as a distinct therapeutic class with diverse clinical applications.

  7. Multiple bacterial species reside in chronic wounds

    DEFF Research Database (Denmark)

    Gjødsbøl, Kristine; Christensen, Jens Jørgen; Karlsmark, Tonny;

    2006-01-01

    The aim of the study was to investigate the bacterial profile of chronic venous leg ulcers and the importance of the profile to ulcer development. Patients with persisting venous leg ulcers were included and followed for 8 weeks. Every second week, ulcer samples were collected and the bacterial s...

  8. Bacterial biofilms: prokaryotic adventures in multicellularity

    DEFF Research Database (Denmark)

    Webb, J.S.; Givskov, Michael Christian; Kjelleberg, S.

    2003-01-01

    The development of bacterial biofilms includes both the initial social behavior of undifferentiated cells, as well as cell death and differentiation in the mature biofilm, and displays several striking similarities with higher organisms. Recent advances in the field provide new insight...... into differentiation and cell death events in bacterial biofilm development and propose that biofilms have an unexpected level of multicellularity....

  9. Bacterial Flora of the Female Genital Tract

    Directory of Open Access Journals (Sweden)

    Pongsakdi Chaisilwattana

    1995-01-01

    Full Text Available Objective: The purpose of this study was to analyze the ability of septicemic and nonsepticemic isolates of group B streptococci (GBS to inhibit in vitro the principal bacterial groups found in the normal bacterial flora of the female genital tract.

  10. Use of Bacteriophages to control bacterial pathogens

    Science.gov (United States)

    Lytic bacteriophages can provide a natural method and an effective alternative to antibiotics to reduce bacterial pathogens in animals, foods, and other environments. Bacteriophages (phages) are viruses which infect bacterial cells and eventually kill them through lysis, and represent the most abun...

  11. Cerebral infarction in childhood bacterial meningitis

    OpenAIRE

    Snyder, R.D.; Stovring, J; Cushing, A H; Davis, L. E.; Hardy, T. L.

    1981-01-01

    Forty-nine children with complicated bacterial meningitis were studied. Thirteen had abnormalities on computed tomography compatible with the diagnosis of brain infarction; one had a brain biopsy with the histological appearance of infarction. Factors exist in childhood bacterial meningitis which are associated with the development of brain infraction.

  12. In vivo bacterial morphogenetic protein interactions

    NARCIS (Netherlands)

    van der Ploeg, R.; den Blaauwen, T.; Meghea, A.

    2012-01-01

    This chapter will discuss none-invasive techniques that are widely used to study protein-protein interactions. As an example, their application in exploring interactions between proteins involved in bacterial cell division will be evaluated. First, bacterial morphology and cell division of the rod-s

  13. Adaptation and risk management

    Energy Technology Data Exchange (ETDEWEB)

    Preston, Benjamin L [ORNL

    2011-01-01

    Adaptation assessment methods are compatible with the international risk management standard ISO:31000. Risk management approaches are increasingly being recommended for adaptation assessments at both national and local levels. Two orientations to assessments can commonly be identified: top-down and bottom-up, and prescriptive and diagnostic. Combinations of these orientations favor different types of assessments. The choice of orientation can be related to uncertainties in prediction and taking action, in the type of adaptation and in the degree of system stress. Adopting multiple viewpoints is to be encouraged, especially in complex situations. The bulk of current guidance material is consistent with top-down and predictive approaches, thus is most suitable for risk scoping and identification. Abroad range ofmaterial fromwithin and beyond the climate change literature can be used to select methods to be used in assessing and implementing adaptation. The framing of risk, correct formulation of the questions being investigated and assessment methodology are critical aspects of the scoping phase. Only when these issues have been addressed should be issue of specific methods and tools be addressed. The reorientation of adaptation from an assessment focused solely on anthropogenic climate change to broader issues of vulnerability/resilience, sustainable development and disaster risk, especially through a risk management framework, can draw from existing policy and management understanding in communities, professions and agencies, incorporating existing agendas, knowledge, risks, and issues they already face.

  14. Solar tomography adaptive optics.

    Science.gov (United States)

    Ren, Deqing; Zhu, Yongtian; Zhang, Xi; Dou, Jiangpei; Zhao, Gang

    2014-03-10

    Conventional solar adaptive optics uses one deformable mirror (DM) and one guide star for wave-front sensing, which seriously limits high-resolution imaging over a large field of view (FOV). Recent progress toward multiconjugate adaptive optics indicates that atmosphere turbulence induced wave-front distortion at different altitudes can be reconstructed by using multiple guide stars. To maximize the performance over a large FOV, we propose a solar tomography adaptive optics (TAO) system that uses tomographic wave-front information and uses one DM. We show that by fully taking advantage of the knowledge of three-dimensional wave-front distribution, a classical solar adaptive optics with one DM can provide an extra performance gain for high-resolution imaging over a large FOV in the near infrared. The TAO will allow existing one-deformable-mirror solar adaptive optics to deliver better performance over a large FOV for high-resolution magnetic field investigation, where solar activities occur in a two-dimensional field up to 60'', and where the near infrared is superior to the visible in terms of magnetic field sensitivity.

  15. Solar Adaptive Optics

    Directory of Open Access Journals (Sweden)

    Thomas R. Rimmele

    2011-06-01

    Full Text Available Adaptive optics (AO has become an indispensable tool at ground-based solar telescopes. AO enables the ground-based observer to overcome the adverse effects of atmospheric seeing and obtain diffraction limited observations. Over the last decade adaptive optics systems have been deployed at major ground-based solar telescopes and revitalized ground-based solar astronomy. The relatively small aperture of solar telescopes and the bright source make solar AO possible for visible wavelengths where the majority of solar observations are still performed. Solar AO systems enable diffraction limited observations of the Sun for a significant fraction of the available observing time at ground-based solar telescopes, which often have a larger aperture than equivalent space based observatories, such as HINODE. New ground breaking scientific results have been achieved with solar adaptive optics and this trend continues. New large aperture telescopes are currently being deployed or are under construction. With the aid of solar AO these telescopes will obtain observations of the highly structured and dynamic solar atmosphere with unprecedented resolution. This paper reviews solar adaptive optics techniques and summarizes the recent progress in the field of solar adaptive optics. An outlook to future solar AO developments, including a discussion of Multi-Conjugate AO (MCAO and Ground-Layer AO (GLAO will be given.

  16. Structural biology of bacterial RNA polymerase.

    Science.gov (United States)

    Murakami, Katsuhiko S

    2015-05-11

    Since its discovery and characterization in the early 1960s (Hurwitz, J. The discovery of RNA polymerase. J. Biol. Chem. 2005, 280, 42477-42485), an enormous amount of biochemical, biophysical and genetic data has been collected on bacterial RNA polymerase (RNAP). In the late 1990s, structural information pertaining to bacterial RNAP has emerged that provided unprecedented insights into the function and mechanism of RNA transcription. In this review, I list all structures related to bacterial RNAP (as determined by X-ray crystallography and NMR methods available from the Protein Data Bank), describe their contributions to bacterial transcription research and discuss the role that small molecules play in inhibiting bacterial RNA transcription.

  17. The adaptive genome of Desulfovibrio vulgaris Hildenborough.

    Science.gov (United States)

    Santana, Margarida; Crasnier-Mednansky, Martine

    2006-07-01

    Peculiar attributes revealed by sequencing the genome of Desulfovibrio vulgaris Hildenborough are analyzed, particularly in relation to the presence of a phosphotransferase system (PTS). The PTS is a typical bacterial carbohydrate transport system functioning via group translocation. Novel avenues for investigations are proposed emphasizing the metabolic diversity of D. vulgaris Hildenborough, especially the likely utilization of mannose-type sugars. Comparative analysis with PTS from other Gram-negative and Gram-positive bacteria indicates regulatory functions for the PTS of D. vulgaris Hildenborough, including catabolite repression and inducer exclusion. Chemotaxis towards PTS substrates is considered. Evidence suggests that this organism may not be a strict anaerobic sulfate reducer typical of the ocean, but a versatile organism capable of bidirectional transmigration and adaptation to both water and terrestrial environments.

  18. Oral bacterial DNA findings in pericardial fluid

    Directory of Open Access Journals (Sweden)

    Anne-Mari Louhelainen

    2014-11-01

    Full Text Available Background: We recently reported that large amounts of oral bacterial DNA can be found in thrombus aspirates of myocardial infarction patients. Some case reports describe bacterial findings in pericardial fluid, mostly done with conventional culturing and a few with PCR; in purulent pericarditis, nevertheless, bacterial PCR has not been used as a diagnostic method before. Objective: To find out whether bacterial DNA can be measured in the pericardial fluid and if it correlates with pathologic–anatomic findings linked to cardiovascular diseases. Methods: Twenty-two pericardial aspirates were collected aseptically prior to forensic autopsy at Tampere University Hospital during 2009–2010. Of the autopsies, 10 (45.5% were free of coronary artery disease (CAD, 7 (31.8% had mild and 5 (22.7% had severe CAD. Bacterial DNA amounts were determined using real-time quantitative PCR with specific primers and probes for all bacterial strains associated with endodontic disease (Streptococcus mitis group, Streptococcus anginosus group, Staphylococcus aureus/Staphylococcus epidermidis, Prevotella intermedia, Parvimonas micra and periodontal disease (Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Treponema denticola, Fusobacterium nucleatus, and Dialister pneumosintes. Results: Of 22 cases, 14 (63.6% were positive for endodontic and 8 (36.4% for periodontal-disease-associated bacteria. Only one case was positive for bacterial culturing. There was a statistically significant association between the relative amount of bacterial DNA in the pericardial fluid and the severity of CAD (p=0.035. Conclusions: Oral bacterial DNA was detectable in pericardial fluid and an association between the severity of CAD and the total amount of bacterial DNA in pericardial fluid was found, suggesting that this kind of measurement might be useful for clinical purposes.

  19. Investigation on artificial blood vessels prepared from bacterial cellulose.

    Science.gov (United States)

    Zang, Shanshan; Zhang, Ran; Chen, Hua; Lu, Yudong; Zhou, Jianhai; Chang, Xiao; Qiu, Guixing; Wu, Zhihong; Yang, Guang

    2015-01-01

    BC (bacterial cellulose) exhibits quite distinctive properties than plant cellulose. The outstanding properties make BC a promising material for preparation of artificial blood vessel. By taking advantage of the high oxygen permeability of PDMS (polydimethylsiloxane) as a tubular template material, a series of BC tubes with a length of 100 mm, a thickness of 1mm and an outer diameter of 4 or 6mm were biosynthesized with the help of Gluconacetobacter xylinum. Through characterization by SEM (scanning electron microscope), tensile testing and thermal analysis, it is demonstrated that BC tubes are good enough for artificial blood vessel with elaborated nano-fiber architecture, qualified mechanical properties and high thermal stability. In addition, measurement of biocompatibility also shows that BC tubes are greatly adaptable to the in vivo environment. The results indicate that BC tubes have great potential for being utilized as tubular scaffold materials in the field of tissue engineering.

  20. Effects of low-level deuterium enrichment on bacterial growth.

    Directory of Open Access Journals (Sweden)

    Xueshu Xie

    Full Text Available Using very precise (±0.05% measurements of the growth parameters for bacteria E. coli grown on minimal media, we aimed to determine the lowest deuterium concentration at which the adverse effects that are prominent at higher enrichments start to become noticeable. Such a threshold was found at 0.5% D, a surprisingly high value, while the ultralow deuterium concentrations (≤0.25% D showed signs of the opposite trend. Bacterial adaptation for 400 generations in isotopically different environment confirmed preference for ultralow (≤0.25% D enrichment. This effect appears to be similar to those described in sporadic but multiple earlier reports. Possible explanations include hormesis and isotopic resonance phenomena, with the latter explanation being favored.

  1. Impact of genome reduction on bacterial metabolism and its regulation.

    Science.gov (United States)

    Yus, Eva; Maier, Tobias; Michalodimitrakis, Konstantinos; van Noort, Vera; Yamada, Takuji; Chen, Wei-Hua; Wodke, Judith A H; Güell, Marc; Martínez, Sira; Bourgeois, Ronan; Kühner, Sebastian; Raineri, Emanuele; Letunic, Ivica; Kalinina, Olga V; Rode, Michaela; Herrmann, Richard; Gutiérrez-Gallego, Ricardo; Russell, Robert B; Gavin, Anne-Claude; Bork, Peer; Serrano, Luis

    2009-11-27

    To understand basic principles of bacterial metabolism organization and regulation, but also the impact of genome size, we systematically studied one of the smallest bacteria, Mycoplasma pneumoniae. A manually curated metabolic network of 189 reactions catalyzed by 129 enzymes allowed the design of a defined, minimal medium with 19 essential nutrients. More than 1300 growth curves were recorded in the presence of various nutrient concentrations. Measurements of biomass indicators, metabolites, and 13C-glucose experiments provided information on directionality, fluxes, and energetics; integration with transcription profiling enabled the global analysis of metabolic regulation. Compared with more complex bacteria, the M. pneumoniae metabolic network has a more linear topology and contains a higher fraction of multifunctional enzymes; general features such as metabolite concentrations, cellular energetics, adaptability, and global gene expression responses are similar, however.

  2. Adaptive Alternating Minimization Algorithms

    CERN Document Server

    Niesen, Urs; Wornell, Gregory

    2007-01-01

    The classical alternating minimization (or projection) algorithm has been successful in the context of solving optimization problems over two variables or equivalently of finding a point in the intersection of two sets. The iterative nature and simplicity of the algorithm has led to its application to many areas such as signal processing, information theory, control, and finance. A general set of sufficient conditions for the convergence and correctness of the algorithm is quite well-known when the underlying problem parameters are fixed. In many practical situations, however, the underlying problem parameters are changing over time, and the use of an adaptive algorithm is more appropriate. In this paper, we study such an adaptive version of the alternating minimization algorithm. As a main result of this paper, we provide a general set of sufficient conditions for the convergence and correctness of the adaptive algorithm. Perhaps surprisingly, these conditions seem to be the minimal ones one would expect in ...

  3. Adaptation investments and homeownership

    DEFF Research Database (Denmark)

    Hansen, Jørgen Drud; Skak, Morten

    2008-01-01

    This article develops a model where ownership improves the efficiency of the housing market as it enhances the utility of housing consumption for some consumers. The model is based on an extended Hotelling-Lancaster utility approach in which the ideal variant of housing is obtainable only...... by adapting the home through a supplementary investment. Ownership offers low costs of adaptation, but has high contract costs compared with renting. Consumers simultaneously choose housing demand and tenure, and because of the different cost structure only consumers with strong preferences for individual...... adaptation of the home choose ownership. This article analyses the consumer's optimization. The model provides an explanation for the observation that homeowners typically live in larger dwelling units than tenants. It also provides an explanation for a high price of housing services tending to reduce...

  4. Adaptation investments and homeownership

    DEFF Research Database (Denmark)

    Hansen, Jørgen Drud; Skak, Morten

    2008-01-01

    This article develops a model where ownership improves efficiency of the housing market as it enhances the utility of housing consumption for some consumers. The model is based on an extended Hotelling-Lancaster utility approach in which the ideal variant of housing is obtainable only by adapting...... the home through a supplementary investment. Ownership offers low costs of adaptation, but has high contract costs compared with renting. Consumers simultaneously decide housing demand and tenure, and because of the different cost structure only consumers with strong preferences for individual adaptation...... of the home choose ownership. This article analyses the consumer's optimization. The model provides an explanation for the observation that homeowners typically live in larger dwelling units than tenants. It also provides and explanation for a high price on housing services tending to reduce homeownership...

  5. Adaptable Embedded Systems

    CERN Document Server

    Lisbôa, Carlos; Carro, Luigi

    2013-01-01

    As embedded systems become more complex, designers face a number of challenges at different levels: they need to boost performance, while keeping energy consumption as low as possible, they need to reuse existent software code, and at the same time they need to take advantage of the extra logic available in the chip, represented by multiple processors working together.  This book describes several strategies to achieve such different and interrelated goals, by the use of adaptability. Coverage includes reconfigurable systems, dynamic optimization techniques such as binary translation and trace reuse, new memory architectures including homogeneous and heterogeneous multiprocessor systems, communication issues and NOCs, fault tolerance against fabrication defects and soft errors, and finally, how one can combine several of these techniques together to achieve higher levels of performance and adaptability.  The discussion also includes how to employ specialized software to improve this new adaptive system, and...

  6. Experimental adaptive process tomography

    Science.gov (United States)

    Pogorelov, I. A.; Struchalin, G. I.; Straupe, S. S.; Radchenko, I. V.; Kravtsov, K. S.; Kulik, S. P.

    2017-01-01

    Adaptive measurements were recently shown to significantly improve the performance of quantum state tomography. Utilizing information about the system for the online choice of optimal measurements allows one to reach the ultimate bounds of precision for state reconstruction. In this article we generalize an adaptive Bayesian approach to the case of process tomography and experimentally show its superiority in the task of learning unknown quantum operations. Our experiments with photonic polarization qubits cover all types of single-qubit channels. We also discuss instrumental errors and the criteria for evaluation of the ultimate achievable precision in an experiment. It turns out that adaptive tomography provides a lower noise floor in the presence of strong technical noise.

  7. Engineering Adaptive Web Applications

    DEFF Research Database (Denmark)

    Dolog, Peter

    2007-01-01

    suit the user profile the most. This paper summarizes the domain engineering framework for such adaptive web applications. The framework provides guidelines to develop adaptive web applications as members of a family. It suggests how to utilize the design artifacts as knowledge which can be used......Information and services on the web are accessible for everyone. Users of the web differ in their background, culture, political and social environment, interests and so on. Ambient intelligence was envisioned as a concept for systems which are able to adapt to user actions and needs....... With the growing amount of information and services, the web applications become natural candidates to adopt the concepts of ambient intelligence. Such applications can deal with divers user intentions and actions based on the user profile and can suggest the combination of information content and services which...

  8. Bacterial coronal leakage after obturation with three root canal sealers.

    Science.gov (United States)

    Timpawat, S; Amornchat, C; Trisuwan, W R

    2001-01-01

    The purpose of this study was to compare the bacterial leakage of root canals obturated with three root canal sealers, using Endodontalis faecalis as a microbial tracer to determine the length of time for bacteria to penetrate through the obturated root canal to the root apex. Seventy-five, single-rooted teeth with straight root canals had the crown cut off at the cementoenamel junction. Root canals were instrumented by a step-back technique. The prepared teeth were randomly divided into 3 groups of 19 teeth each and another 2 groups as positive and negative controls (9 teeth each). The experimental groups were dependent on the sealer used: AH-Plus, Apexit, and Ketac-Endo. The root canals were obturated using a lateral condensation technique. After 24 h the teeth were attached to microcentrifuge tubes with 2 mm of the root apex submerged in Brain Heart Infusion broth in glass test tubes. The coronal portions of the root canal filling materials were placed in contact with E. faecalis. The teeth were observed for bacterial leakage daily for 30 and 60 days. With the chi2 test for comparing pairs of groups at the 0.05 level (p 0.06), but Apexit had significantly higher leakage (p 0.05), but Apexit leaked more than AH-Plus. The conclusion drawn from this experiment was that epoxy resin root canal sealer was found to be more adaptable to the root canal wall and filling material than a calcium hydroxide sealer when bacterial coronal leakage was studied.

  9. Intestinal mucosal adaptation

    Institute of Scientific and Technical Information of China (English)

    Laurie Drozdowski; Alan BR Thomson

    2006-01-01

    Intestinal failure is a condition characterized by malnutrition and/or dehydration as a result of the inadequate digestion and absorption of nutrients. The most common cause of intestinal failure is short bowel syndrome, which occurs when the functional gut mass is reduced below the level necessary for adequate nutrient and water absorption. This condition may be congenital, or may be acquired as a result of a massive resection of the small bowel. Following resection, the intestine is capable of adaptation in response to enteral nutrients as well as other trophic stimuli. Identifying factors that may enhance the process of intestinal adaptation is an exciting area of research with important potential clinical applications.

  10. Adaptive radar resource management

    CERN Document Server

    Moo, Peter

    2015-01-01

    Radar Resource Management (RRM) is vital for optimizing the performance of modern phased array radars, which are the primary sensor for aircraft, ships, and land platforms. Adaptive Radar Resource Management gives an introduction to radar resource management (RRM), presenting a clear overview of different approaches and techniques, making it very suitable for radar practitioners and researchers in industry and universities. Coverage includes: RRM's role in optimizing the performance of modern phased array radars The advantages of adaptivity in implementing RRMThe role that modelling and

  11. Adaptive Learning Management System

    Directory of Open Access Journals (Sweden)

    Violeta Moisa

    2013-06-01

    Full Text Available This article is an introduction to a new model for an adaptive Learning Management System. It presents the current e-learning standards and describes the elements that can be used to create the system: the sequencing control modes, sequencing rules, navigation controls, learning records and learning record stores. The model is based on artificial intelligent algorithms that analyze the data captured for each user and creates an adaptive navigation path through the learning content of the system, allowing each user to experience the content in different ways

  12. Postnatal Cardiovascular Adaptation

    Directory of Open Access Journals (Sweden)

    Ferda Ozlu

    2016-06-01

    Full Text Available Fetus depends on placental circulation in utero. A successful transition from intrauterin to extrauterine life depends on succesful physiological changes during labor. During delivery, fetus transfers from a liquid environment where oxygen comes via umbilical vein to air environement where oxygenation is supported via air breathing. Endocrinological changes are important for fetus to adapt to extrauterine life. In addition to these, cord clemping plays a crucial role in postnatal adaptation. Establishment of neonatal postnatal life and succesful overcome, the fetal cardiovascular transition period are important to stay on. [Archives Medical Review Journal 2016; 25(2.000: 181-190

  13. Adaptive Architectural Envelope

    DEFF Research Database (Denmark)

    Foged, Isak Worre; Kirkegaard, Poul Henning

    2010-01-01

    . The general scopes of this paper are to develop a new adaptive kinetic architectural structure, particularly a reconfigurable architectural structure which can transform body shape from planar geometries to hyper-surfaces using different control strategies, i.e. a transformation into more than one or two...... different shape alternatives. The adaptive structure is a proposal for a responsive building envelope which is an idea of a first level operational framework for present and future investigations towards performance based responsive architectures through a set of responsive typologies. A mock- up concept...

  14. STUDYING COMPLEX ADAPTIVE SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    John H. Holland

    2006-01-01

    Complex adaptive systems (cas) - systems that involve many components that adapt or learn as they interact - are at the heart of important contemporary problems. The study of cas poses unique challenges: Some of our most powerful mathematical tools, particularly methods involving fixed points, attractors, and the like, are of limited help in understanding the development of cas. This paper suggests ways to modify research methods and tools, with an emphasis on the role of computer-based models, to increase our understanding of cas.

  15. Host plant species determines symbiotic bacterial community mediating suppression of plant defenses

    Science.gov (United States)

    Chung, Seung Ho; Scully, Erin D.; Peiffer, Michelle; Geib, Scott M.; Rosa, Cristina; Hoover, Kelli; Felton, Gary W.

    2017-01-01

    Herbivore associated bacteria are vital mediators of plant and insect interactions. Host plants play an important role in shaping the gut bacterial community of insects. Colorado potato beetles (CPB; Leptinotarsa decemlineata) use several Solanum plants as hosts in their natural environment. We previously showed that symbiotic gut bacteria from CPB larvae suppressed jasmonate (JA)-induced defenses in tomato. However, little is known about how changes in the bacterial community may be involved in the manipulation of induced defenses in wild and cultivated Solanum plants of CPB. Here, we examined suppression of JA-mediated defense in wild and cultivated hosts of CPB by chemical elicitors and their symbiotic bacteria. Furthermore, we investigated associations between the gut bacterial community and suppression of plant defenses using 16 S rRNA amplicon sequencing. Symbiotic bacteria decreased plant defenses in all Solanum hosts and there were different gut bacterial communities in CPB fed on different host plants. When larvae were reared on different hosts, defense suppression differed among host plants. These results demonstrate that host plants influence herbivore gut bacterial communities and consequently affect the herbivore’s ability to manipulate JA-mediated plant defenses. Thus, the presence of symbiotic bacteria that suppress plant defenses might help CPB adapt to host plants. PMID:28045052

  16. CRISPR/Cas systems: new players in gene regulation and bacterial physiology

    Directory of Open Access Journals (Sweden)

    David eWeiss

    2014-04-01

    Full Text Available CRISPR-Cas systems are bacterial defenses against foreign nucleic acids derived from bacteriophages, plasmids or other sources. These systems are targeted in an RNA-dependent, sequence-specific manner, and are also adaptive, providing protection against previously encountered foreign elements. In addition to their canonical function in defense against foreign nucleic acid, their roles in various aspects of bacterial physiology are now being uncovered. We recently revealed a role for a Cas9-based Type II CRISPR-Cas system in the control of endogenous gene expression, a novel form of prokaryotic gene regulation. Cas9 functions in association with two small RNAs to target and alter the stability of an endogenous transcript encoding a bacterial lipoprotein (BLP. Since BLPs are recognized by the host innate immune protein Toll-like Receptor 2 (TLR2, CRISPR-Cas-mediated repression of BLP expression facilitates evasion of TLR2 by the intracellular bacterial pathogen Francisella novicida, and is essential for its virulence. Here we describe the Cas9 regulatory system in detail, as well as data on its role in controlling virulence traits of Neisseria meningitidis and Campylobacter jejuni. We also discuss potential roles of CRISPR-Cas systems in the response to envelope stress and other aspects of bacterial physiology. Since ~45% of bacteria and ~83% of Archaea encode these machineries, the newly appreciated regulatory functions of CRISPR-Cas systems are likely to play broad roles in controlling the pathogenesis and physiology of diverse prokaryotes.

  17. Molecular profiling of rhizosphere bacterial communities associated with Prosopis juliflora and Parthenium hysterophorus.

    Science.gov (United States)

    Jothibasu, K; Chinnadurai, C; Sundaram, Sp; Kumar, K; Balachandar, Dananjeyan

    2012-03-01

    Prosopis juliflora and Parthenium hysterophorus are the two arid, exotic weeds of India that are characterized by distinct, profuse growth even in nutritionally poor soils and environmentally stressed conditions. Owing to the exceptional growth nature of these two plants, they are believed to harbor some novel bacterial communities with wide adaptability in their rhizosphere. Hence, in the present study, the bacterial communities associated with the rhizosphere of Prosopis and Parthenium were characterized by clonal 16S rRNA gene sequence analysis. The culturable microbial counts in the rhizosphere of these two plants were higher than bulk soils, possibly influenced by the root exudates of these two plants. The phylogenetic analysis of V1_V2 domains of the 16S rRNA gene indicated a wider range of bacterial communities present in the rhizosphere of these two plants than in bulk soils and the predominant genera included Acidobacteria, Gammaproteobacteria, and Bacteriodetes in the rhizosphere of Prosopis, and Acidobacteria, Betaproteobacteria, and Nitrospirae in the Parthenium rhizosphere. The diversity of bacterial communities was more pronounced in the Parthenium rhizosphere than in the Prosopis rhizosphere. This culture-independent bacterial analysis offered extensive possibilities of unraveling novel microbes in the rhizospheres of Prosopis and Parthenium with genes for diverse functions, which could be exploited for nutrient transformation and stress tolerance in cultivated crops.

  18. Investigation on artificial blood vessels prepared from bacterial cellulose

    Energy Technology Data Exchange (ETDEWEB)

    Zang, Shanshan; Zhang, Ran; Chen, Hua; Lu, Yudong; Zhou, Jianhai [Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074 (China); Chang, Xiao; Qiu, Guixing; Wu, Zhihong [Department of Orthopaedics, Peking Union Medical College Hospital, Beijing 100730 (China); Yang, Guang, E-mail: yang_sunny@yahoo.com [Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074 (China)

    2015-01-01

    BC (bacterial cellulose) exhibits quite distinctive properties than plant cellulose. The outstanding properties make BC a promising material for preparation of artificial blood vessel. By taking advantage of the high oxygen permeability of PDMS (polydimethylsiloxane) as a tubular template material, a series of BC tubes with a length of 100 mm, a thickness of 1 mm and an outer diameter of 4 or 6 mm were biosynthesized with the help of Gluconacetobacter xylinum. Through characterization by SEM (scanning electron microscope), tensile testing and thermal analysis, it is demonstrated that BC tubes are good enough for artificial blood vessel with elaborated nano-fiber architecture, qualified mechanical properties and high thermal stability. In addition, measurement of biocompatibility also shows that BC tubes are greatly adaptable to the in vivo environment. The results indicate that BC tubes have great potential for being utilized as tubular scaffold materials in the field of tissue engineering. - Highlights: • Bacterial cellulose (BC) can be made into tubular shape through PDMS mold. • BC represents a fine nanofiber network. • The mechanical and thermal properties of BC mimic the situation of real vessel. • BC exhibits attractive biocompatible properties as a substitution of vessel.

  19. A processed noncoding RNA regulates an altruistic bacterial antiviral system.

    Science.gov (United States)

    Blower, Tim R; Pei, Xue Y; Short, Francesca L; Fineran, Peter C; Humphreys, David P; Luisi, Ben F; Salmond, George P C

    2011-02-01

    The ≥ 10³⁰ bacteriophages on Earth relentlessly drive adaptive coevolution, forcing the generation of protective mechanisms in their bacterial hosts. One such bacterial phage-resistance system, ToxIN, consists of a protein toxin (ToxN) that is inhibited in vivo by a specific RNA antitoxin (ToxI); however, the mechanisms for this toxicity and inhibition have not been defined. Here we present the crystal structure of the ToxN-ToxI complex from Pectobacterium atrosepticum, determined to 2.75-Å resolution. ToxI is a 36-nucleotide noncoding RNA pseudoknot, and three ToxI monomers bind to three ToxN monomers to generate a trimeric ToxN-ToxI complex. Assembly of this complex is mediated entirely through extensive RNA-protein interactions. Furthermore, a 2'-3' cyclic phosphate at the 3' end of ToxI, and catalytic residues, identify ToxN as an endoRNase that processes ToxI from a repetitive precursor but is regulated by its own catalytic product.

  20. Enhanced diffusion of tracer particles in dilute bacterial suspensions.

    Science.gov (United States)

    Morozov, Alexander; Marenduzzo, Davide

    2014-04-28

    Swimming bacteria create long-range velocity fields that stir a large volume of fluid and move around passive particles dispersed in the fluid. Recent experiments and simulations have shown that long-time mean-squared displacement of passive particles in a bath of swimming bacteria exhibits diffusive behaviour with an effective diffusion coefficient significantly larger than its thermal counterpart. A comprehensive theoretical prediction of this effective diffusion coefficient and the understanding of the enhancement mechanism remain a challenge. Here, we adapt the kinetic theory by Lin et al., J. Fluid Mech., 2011, 669, 167 developed for 'squirmers' to the bacterial case to quantitatively predict enhanced diffusivity of tracer particles in dilute two- and three-dimensional suspensions of swimming bacteria. We demonstrate that the effective diffusion coefficient is a product of the bacterial number density, their swimming speed, a geometric factor characterising the velocity field created by a single bacterium, and a numerical factor. We show that the numerical factor is, in fact, a rather strong function of the system parameters, most notably the run length of the bacteria, and that these dependencies have to be taken into account to quantitatively predict the enhanced diffusivity. We perform molecular-dynamics-type simulations to confirm the conclusions of the kinetic theory. Our results are in good agreement with the values of enhanced diffusivity measured in recent two- and three-dimensional experiments.

  1. Segrosome complex formation during DNA trafficking in bacterial cell division

    Directory of Open Access Journals (Sweden)

    Maria A. Oliva

    2016-09-01

    Full Text Available Bacterial extrachromosomal DNAs often contribute to virulence in pathogenic organisms or facilitate adaptation to particular environments. The transmission of genetic information from one generation to the next requires sufficient partitioning of DNA molecules to ensure that at least one copy reaches each side of the division plane and is inherited by the daughter cells. Segregation of the bacterial chromosome occurs during or after replication and probably involves a strategy in which several protein complexes participate to modify the folding pattern and distribution first of the origin domain and then of the rest of the chromosome. Low-copy number plasmids rely on specialised partitioning systems, which in some cases use a mechanism that show striking similarity to eukaryotic DNA segregation. Overall, there have been multiple systems implicated in the dynamic transport of DNA cargo to a new cellular position during the cell cycle but most seem to share a common initial DNA partitioning step, involving the formation of a nucleoprotein complex called the segrosome. The particular features and complex topologies of individual segrosomes depend on both the nature of the DNA binding protein involved and on the recognized centromeric DNA sequence, both of which vary across systems. The combination of in vivo and in vitro approaches, with structural biology has significantly furthered our understanding of the mechanisms underlying DNA trafficking in bacteria. Here, I discuss recent advances and the molecular details of the DNA segregation machinery, focusing on the formation of the segrosome complex.

  2. Seasonal variation of bacterial endophytes in urban trees

    Directory of Open Access Journals (Sweden)

    Shu Yi eShen

    2015-05-01

    Full Text Available Bacterial endophytes, non-pathogenic bacteria residing within plants, contribute to the growth and development of plants and their ability to adapt to adverse conditions. In order to fully exploit the capabilities of these bacteria, it is necessary to understand the extent to which endophytic communities vary between species and over time. The endophytes of Acer negundo, Ulmus pumila and Ulmus parvifolia were sampled over three seasons and analyzed using culture dependent and independent methods (culture on two media, terminal restriction fragment length polymorphism, and tagged pyrosequencing of 16S ribosomal amplicons. The majority of culturable endophytes isolated were Actinobacteria, and all the samples harbored Bacillus, Curtobacterium, Frigoribacterium, Methylobacterium, Paenibacilllus and Sphingomonas species. Regardless of culture medium used, only the culturable communities obtained in the winter for A. negundo could be distinguished from those of Ulmus spp.. In contrast, the nonculturable communities were dominated by Proteobacteria and Actinobacteria, particularly Erwinia, Ralstonia and Sanguibacter spp.. The presence and abundance of various bacterial classes and phyla changed with the changing seasons. Multivariate analysis on the culture independent data revealed significant community differences between the endophytic communities of A. negundo and Ulmus spp., but overall season was the main determinant of endophytic community structure. This study suggests investigations of the studies ofendophytic populations of urban trees should expect to find significant seasonal and species-specific community differences and sampling should proceed accordingly.

  3. Transcriptional response of Musca domestica larvae to bacterial infection.

    Directory of Open Access Journals (Sweden)

    Ting Tang

    Full Text Available The house fly Musca domestica, a cosmopolitan dipteran insect, is a significant vector for human and animal bacterial pathogens, but little is known about its immune response to these pathogens. To address this issue, we inoculated the larvae with a mixture of Escherichia coli and Staphylococcus aureus and profiled the transcriptome 6, 24, and 48 h thereafter. Many genes known to controlling innate immunity in insects were induced following infection, including genes encoding pattern recognition proteins (PGRPs, various components of the Toll and IMD signaling pathways and of the proPO-activating and redox systems, and multiple antimicrobial peptides. Interestingly, we also uncovered a large set of novel immune response genes including two broad-spectrum antimicrobial peptides (muscin and domesticin, which might have evolved to adapt to house-fly's unique ecological environments. Finally, genes mediating oxidative phosphorylation were repressed at 48 h post-infection, suggesting disruption of energy homeostasis and mitochondrial function at the late stages of infection. Collectively, our data reveal dynamic changes in gene expression following bacterial infection in the house fly, paving the way for future in-depth analysis of M. domestica's immune system.

  4. Bacterial Histidine Kinases as Novel Antibacterial Drug Targets

    NARCIS (Netherlands)

    Bem, A.E.; Velikova, N.R.; Pellicer, M.T.; Baarlen, van P.; Marina, A.; Wells, J.M.

    2015-01-01

    Bacterial histidine kinases (HKs) are promising targets for novel antibacterials. Bacterial HKs are part of bacterial two-component systems (TCSs), the main signal transduction pathways in bacteria, regulating various processes including virulence, secretion systems and antibiotic resistance. In thi

  5. Parallel evolution of a type IV secretion system in radiating lineages of the host-restricted bacterial pathogen Bartonella.

    Directory of Open Access Journals (Sweden)

    Philipp Engel

    2011-02-01

    Full Text Available Adaptive radiation is the rapid origination of multiple species from a single ancestor as the result of concurrent adaptation to disparate environments. This fundamental evolutionary process is considered to be responsible for the genesis of a great portion of the diversity of life. Bacteria have evolved enormous biological diversity by exploiting an exceptional range of environments, yet diversification of bacteria via adaptive radiation has been documented in a few cases only and the underlying molecular mechanisms are largely unknown. Here we show a compelling example of adaptive radiation in pathogenic bacteria and reveal their genetic basis. Our evolutionary genomic analyses of the α-proteobacterial genus Bartonella uncover two parallel adaptive radiations within these host-restricted mammalian pathogens. We identify a horizontally-acquired protein secretion system, which has evolved to target specific bacterial effector proteins into host cells as the evolutionary key innovation triggering these parallel adaptive radiations. We show that the functional versatility and adaptive potential of the VirB type IV secretion system (T4SS, and thereby translocated Bartonella effector proteins (Beps, evolved in parallel in the two lineages prior to their radiations. Independent chromosomal fixation of the virB operon and consecutive rounds of lineage-specific bep gene duplications followed by their functional diversification characterize these parallel evolutionary trajectories. Whereas most Beps maintained their ancestral domain constitution, strikingly, a novel type of effector protein emerged convergently in both lineages. This resulted in similar arrays of host cell-targeted effector proteins in the two lineages of Bartonella as the basis of their independent radiation. The parallel molecular evolution of the VirB/Bep system displays a striking example of a key innovation involved in independent adaptive processes and the emergence of bacterial

  6. Parallel evolution of a type IV secretion system in radiating lineages of the host-restricted bacterial pathogen Bartonella.

    Science.gov (United States)

    Engel, Philipp; Salzburger, Walter; Liesch, Marius; Chang, Chao-Chin; Maruyama, Soichi; Lanz, Christa; Calteau, Alexandra; Lajus, Aurélie; Médigue, Claudine; Schuster, Stephan C; Dehio, Christoph

    2011-02-10

    Adaptive radiation is the rapid origination of multiple species from a single ancestor as the result of concurrent adaptation to disparate environments. This fundamental evolutionary process is considered to be responsible for the genesis of a great portion of the diversity of life. Bacteria have evolved enormous biological diversity by exploiting an exceptional range of environments, yet diversification of bacteria via adaptive radiation has been documented in a few cases only and the underlying molecular mechanisms are largely unknown. Here we show a compelling example of adaptive radiation in pathogenic bacteria and reveal their genetic basis. Our evolutionary genomic analyses of the α-proteobacterial genus Bartonella uncover two parallel adaptive radiations within these host-restricted mammalian pathogens. We identify a horizontally-acquired protein secretion system, which has evolved to target specific bacterial effector proteins into host cells as the evolutionary key innovation triggering these parallel adaptive radiations. We show that the functional versatility and adaptive potential of the VirB type IV secretion system (T4SS), and thereby translocated Bartonella effector proteins (Beps), evolved in parallel in the two lineages prior to their radiations. Independent chromosomal fixation of the virB operon and consecutive rounds of lineage-specific bep gene duplications followed by their functional diversification characterize these parallel evolutionary trajectories. Whereas most Beps maintained their ancestral domain constitution, strikingly, a novel type of effector protein emerged convergently in both lineages. This resulted in similar arrays of host cell-targeted effector proteins in the two lineages of Bartonella as the basis of their independent radiation. The parallel molecular evolution of the VirB/Bep system displays a striking example of a key innovation involved in independent adaptive processes and the emergence of bacterial pathogens

  7. How hyperthermophiles adapt to change their lives : DNA exchange in extreme conditions

    NARCIS (Netherlands)

    van Wolferen, Marleen; Ajon, Malgorzata; Driessen, Arnold J. M.; Albers, Sonja-Verena; Ajon, Małgorzata; Huang, L.

    2013-01-01

    Transfer of DNA has been shown to be involved in genome evolution. In particular with respect to the adaptation of bacterial species to high temperatures, DNA transfer between the domains of bacteria and archaea seems to have played a major role. In addition, DNA exchange between similar species lik

  8. Adaptation and heterogeneity of Escherichia coli MC1000 growing in complex environments

    NARCIS (Netherlands)

    Puentes Téllez, Pilar; Hansen, M.A.; Sørensen, S.J.; van Elsas, J.D.

    2013-01-01

    In a study aiming to assess bacterial evolution in complex growth media, we evaluated the long-term adaptive response of Escherichia coli MC1000 in Luria-Bertani (LB) medium. Seven parallel populations were founded and followed over 150 days in sequential batch cultures under three different oxygen

  9. Adaptation and heterogeneity of Escherichia coli MC1000 growing in complex environments

    DEFF Research Database (Denmark)

    Puentes-Téllez, Pilar; Hansen, Martin Asser; Sørensen, Søren

    2013-01-01

    In a study aiming to assess bacterial evolution in complex growth media, we evaluated the long-term adaptive response of Escherichia coli MC1000 in Luria-Bertani (LB) medium. Seven parallel populations were founded and followed over 150 days in sequential batch cultures under three different oxyg...

  10. BIOSYNTHESIS OF BACTERIAL CELLULOSE BY МEDUSOMYCES GISEVII

    OpenAIRE

    E. K. Gladysheva; E. A. Skiba

    2015-01-01

    Summary: Bacterial cellulose is an organic material that is synthesized by microorganisms extracellularly. Bacterial cellulose can be used in various industries. Especially, bacterial cellulose has found its application basically in medicine. The production of bacterial cellulose is a complicated and long process. The principal criterion for the process to be successful is bacterial cellulose to be obtained in a higher yield. Russia is lacking an operating facility to produce bacterial cellul...

  11. BACTERIAL FLORA IN DIABETIC ULCER

    Directory of Open Access Journals (Sweden)

    Anitha Lavanya

    2015-04-01

    Full Text Available BACKGROUND : Diabetic foot infections are one of the most feared complications of diabetes. This study was undertaken to determine the common etiological agents of diabetic foot infections and their in vitro antibiotic susceptibility. METHODS : A prospective study was p erformed over a period of two years in a tertiary care hospital. The aerobic and anaerobic bacterial agents were isolated and their antibiotic susceptibility pattern was determined . RESULTS : One hundred patients with Diabetic ulcer were studied, of which 6 5 were males and 35 were females. Majority of patients were in the age group of 51 to 60 years (37% and polymicrobial etiology was 64 % and monomicrobial etiology was 36%. A total of 187 organisms were isolated of which 165 were aerobic and 22 were anaero bic. Most frequently isolated aerobic organisms were Pseudomonas Sp., Klebsiella Sp., E coli Sp., and Staphylococcus aureus. The common anaerobic organisms isolated were Peptostreptococcus Sp. And Bacterioids Sp. CONCLUSION : High prevalence of multi - drug r esistant pathogens was observed. Amikacin, Imipenem were active against gram - negative bacilli, while vancomycin was found to be active against gram - positive bacteria.

  12. Initiation of bacterial spore germination.

    Science.gov (United States)

    Vary, J C; Halvorson, H O

    1968-04-01

    To investigate the problem of initiation in bacterial spore germination, we isolated, from extracts of dormant spores of Bacillus cereus strain T and B. licheniformis, a protein that initiated spore germination when added to a suspension of heat-activated spores. The optimal conditions for initiatory activity of this protein (the initiator) were 30 C in 0.01 to 0.04 m NaCl and 0.01 m tris(hydroxymethyl)aminomethane (pH 8.5). The initiator was inhibited by phosphate but required two co-factors, l-alanine (1/7 of K(m) for l-alanine-inhibited germination) and nicotinamide adenine dinucleotide (1.25 x 10(-4)m). In the crude extract, the initiator activity was increased 3.5-fold by heating the extract at 65 C for 10 min, but the partially purified initiator preparation was completely heat-sensitive (65 C for 5 min). Heat stability could be conferred on the purified initiator by adding 10(-3)m dipicolinic acid. A fractionation of this protein that excluded l-alanine dehydrogenase and adenosine deaminase from the initiator activity was developed. The molecular weight of the initiator was estimated as 7 x 10(4). The kinetics of germination in the presence of initiator were examined at various concentrations of l-alanine and nicotinamide adenine dinucleotide.

  13. Acute bacterial sinusitis in children.

    Science.gov (United States)

    DeMuri, Gregory; Wald, Ellen R

    2013-10-01

    On the basis of strong research evidence, the pathogenesis of sinusitis involves 3 key factors: sinusostia obstruction, ciliary dysfunction, and thickening of sinus secretions. On the basis of studies of the microbiology of otitis media, H influenzae is playing an increasingly important role in the etiology of sinusitis, exceeding that of S pneumoniae in some areas, and b-lactamase production by H influenzae is increasing in respiratory isolates in the United States. On the basis of some research evidence and consensus,the presentation of acute bacterial sinusitis conforms to 1 of 3 predicable patterns; persistent, severe, and worsening symptoms. On the basis of some research evidence and consensus,the diagnosis of sinusitis should be made by applying strict clinical criteria. This approach will select children with upper respiratory infection symptoms who are most likely to benefit from an antibiotic. On the basis of some research evidence and consensus,imaging is not indicated routinely in the diagnosis of sinusitis. Computed tomography or magnetic resonance imaging provides useful information when complications of sinusitis are suspected. On the basis of some research evidence and consensus,amoxicillin-clavulanate should be considered asa first-line agent for the treatment of sinusitis.

  14. Marine mesocosm bacterial colonisation of volcanic ash

    Science.gov (United States)

    Witt, Verena; Cimarelli, Corrado; Ayris, Paul; Kueppers, Ulrich; Erpenbeck, Dirk; Dingwell, Donald; Woerheide, Gert

    2015-04-01

    Volcanic eruptions regularly eject large quantities of ash particles into the atmosphere, which can be deposited via fallout into oceanic environments. Such fallout has the potential to alter pH, light and nutrient availability at local scales. Shallow-water coral reef ecosystems - "rainforests of the sea" - are highly sensitive to disturbances, such as ocean acidification, sedimentation and eutrophication. Therefore, wind-delivered volcanic ash may lead to burial and mortality of such reefs. Coral reef ecosystem resilience may depend on pioneer bacterial colonisation of the ash layer, supporting subsequent establishment of the micro- and ultimately the macro-community. However, which bacteria are involved in pioneer colonisation remain unknown. We hypothesize that physico-chemical properties (i.e., morphology, mineralogy) of the ash may dictate bacterial colonisation. The effect of substrate properties on bacterial colonisation was tested by exposing five substrates: i) quartz sand ii) crystalline ash (Sakurajima, Japan) iii) volcanic glass iv) carbonate reef sand and v) calcite sand of similar grain size, in controlled marine coral reef aquaria under low light conditions for six months. Bacterial communities were screened every month by Automated Ribosomal Intergenic Spacer Analysis of the 16S-23S rRNA Internal Transcribed Spacer region. Multivariate statistics revealed discrete groupings of bacterial communities on substrates of volcanic origin (ash and glass) and reef origin (three sands). Analysis of Similarity supported significantly different communities associated with all substrates (p=0.0001), only quartz did not differ from both carbonate and calcite sands. The ash substrate exhibited the most diverse bacterial community with the most substrate-specific bacterial operational taxonomic units. Our findings suggest that bacterial diversity and community composition during colonisation of volcanic ash in a coral reef-like environment is controlled by the

  15. Adaptive metric kernel regression

    DEFF Research Database (Denmark)

    Goutte, Cyril; Larsen, Jan

    2000-01-01

    regression by minimising a cross-validation estimate of the generalisation error. This allows to automatically adjust the importance of different dimensions. The improvement in terms of modelling performance is illustrated on a variable selection task where the adaptive metric kernel clearly outperforms...

  16. Adaptive Metric Kernel Regression

    DEFF Research Database (Denmark)

    Goutte, Cyril; Larsen, Jan

    1998-01-01

    by minimising a cross-validation estimate of the generalisation error. This allows one to automatically adjust the importance of different dimensions. The improvement in terms of modelling performance is illustrated on a variable selection task where the adaptive metric kernel clearly outperforms the standard...

  17. Adaptive MGS Phase Retrieval

    Science.gov (United States)

    Basinger, Scott A.; Bikkannavar, Siddarayappa; Cohen, David; Green, Joseph J.; Lou, John; Ohara, Catherine; Redding, David; Shi, Fang

    2008-01-01

    Adaptive MGS Phase Retrieval software uses the Modified Gerchberg-Saxton (MGS) algorithm, an image-based sensing method that can turn any focal plane science instrument into a wavefront sensor, avoiding the need to use external metrology equipment. Knowledge of the wavefront enables intelligent control of active optical systems.

  18. Cooperative adaptive cruise control

    NARCIS (Netherlands)

    Naus, G.J.L.; Molengraft, R. van de; Ploeg, J.

    2009-01-01

    Adaptive Cruise Control (ACC) enables automatic following of a preceding vehicle, based on measurements of the inter-vehicle distance xr,i and the relative velocity ˙ xr,i. Commonly, a radar is used for these measurements, see Figure 1. Decreasing the inter-vehicle distance to a small value of only

  19. Adapting Bulls to Florida

    Science.gov (United States)

    The adaptation of bulls used for natural breeding purposes to the Gulf Coast region of the United States including all of Florida is an important topic. Nearly 40% of the U.S. cow/calf population resides in the Gulf Coast and Southeast. Thus, as A.I. is relatively rare, the number of bulls used for ...

  20. The Adaptability of Teams

    DEFF Research Database (Denmark)

    Jørgensen, Frances; Boer, Harry

    2006-01-01

    to the premise that “fit” between an organization’s external context and its internal structure may enhance performance, but also to the suggestion that the adaptation process may be asymmetric (Moon et al., 2004). Further, the paper contributes to practice by highlighting both the opportunities and risks...

  1. Compiler Assisted Runtime Adaptation

    NARCIS (Netherlands)

    Sima, V.M.

    2012-01-01

    In this dissertation, we address the problem of runtime adaptation of the application to its execution environment. A typical example is changing theprocessing element on which a computation is executed, considering the available processing elements in the system. This is done based on the informati

  2. The governance of adaptation

    NARCIS (Netherlands)

    Huitema, Dave; Adger, William Neil; Berkhout, Frans; Massey, Eric; Mazmanian, Daniel; Munaretto, Stefania; Plummer, Ryan; Termeer, Katrien

    2016-01-01

    The governance of climate adaptation involves the collective efforts of multiple societal actors to address problems, or to reap the benefits, associated with impacts of climate change. Governing involves the creation of institutions, rules and organizations, and the selection of normative princi

  3. Engineering Adaptive Applications

    DEFF Research Database (Denmark)

    Dolog, Peter

    for a domain.In this book, we propose a new domain engineering framework which extends a development process of Web applications with techniques required when designing such adaptive customizable Web applications. The framework is provided with design abstractions which deal separately with information served...

  4. Adaptive municipal electronic forms

    NARCIS (Netherlands)

    Kuiper, Pieter; Dijk, van Betsy; Bondarouk, Tanya; Ruël, Huub; Guiderdoni-Jourdain, Karine; Oiry, Ewan

    2009-01-01

    Adaptation of electronic forms (e-forms) seems to be a step forward to reduce the burden for people who fill in forms. Municipalities more and more offer e-forms online that can be used by citizens to request a municipal product or service or by municipal employees to place a request on behalf of a

  5. Bacterial binding to extracellular proteins - in vitro adhesion

    DEFF Research Database (Denmark)

    Schou, C.; Fiehn, N.-E.

    1999-01-01

    Viridans streptococci, bacterial adherence, extracellular matrix proteins, surface receptors, endocarditis......Viridans streptococci, bacterial adherence, extracellular matrix proteins, surface receptors, endocarditis...

  6. Tobacco use increases susceptibility to bacterial infection

    Directory of Open Access Journals (Sweden)

    Demuth Donald R

    2008-12-01

    Full Text Available Abstract Active smokers and those exposed to secondhand smoke are at increased risk of bacterial infection. Tobacco smoke exposure increases susceptibility to respiratory tract infections, including tuberculosis, pneumonia and Legionnaires disease; bacterial vaginosis and sexually transmitted diseases, such as chlamydia and gonorrhoea; Helicobacter pylori infection; periodontitis; meningitis; otitis media; and post-surgical and nosocomial infections. Tobacco smoke compromises the anti-bacterial function of leukocytes, including neutrophils, monocytes, T cells and B cells, providing a mechanistic explanation for increased infection risk. Further epidemiological, clinical and mechanistic research into this important area is warranted.

  7. Spontaneous Bacterial Peritonitis in Subclinical Hypothyroidism

    Directory of Open Access Journals (Sweden)

    Dalip Gupta

    2013-11-01

    Full Text Available Hypothyroidism is an uncommon cause of ascites. Here we describe a case of a 75 year-old female patient with spontaneous bacterial peritonitis and subclinical hypothyroidism that resolved with thyroid replacement and antibiotic therapy respectively. Ascitic fluid analysis revealed a gram-positive bacterium on gram staining. A review of the literature revealed just one other reported case of myxoedema ascites with concomitant spontaneous bacterial peritonitis and no case has till been reported of spontaneous bacterial peritonitis in subclinical hypothyroidism.

  8. Biochemistry of Bacterial Multidrug Efflux Pumps

    Directory of Open Access Journals (Sweden)

    Sanath Kumar

    2012-04-01

    Full Text Available Bacterial pathogens that are multi-drug resistant compromise the effectiveness of treatment when they are the causative agents of infectious disease. These multi-drug resistance mechanisms allow bacteria to survive in the presence of clinically useful antimicrobial agents, thus reducing the efficacy of chemotherapy towards infectious disease. Importantly, active multi-drug efflux is a major mechanism for bacterial pathogen drug resistance. Therefore, because of their overwhelming presence in bacterial pathogens, these active multi-drug efflux mechanisms remain a major area of intense study, so that ultimately measures may be discovered to inhibit these active multi-drug efflux pumps.

  9. Bacterial gasotransmitters: an innate defense against antibiotics.

    Science.gov (United States)

    Luhachack, Lyly; Nudler, Evgeny

    2014-10-01

    In recent decades, there has been growing interest in the field of gasotransmitters, endogenous gaseous signaling molecules (NO, H2S, and CO), as regulators of a multitude of biochemical pathways and physiological processes. Most of the concerted effort has been on eukaryotic gasotransmitters until the subsequent discovery of bacterial counterparts. While the fundamental aspects of bacterial gasotransmitters remain undefined and necessitate further research, we will discuss a known specific role they play in defense against antibiotics. Considering the current dilemma of multidrug-resistant bacteria we consider it particularly prudent to exploring novel targets and approaches, of which the bacterial gasotransmitters, nitric oxide and hydrogen sulfide represent.

  10. Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis

    DEFF Research Database (Denmark)

    Marvig, Rasmus Lykke; Madsen Sommer, Lea Mette; Molin, Søren;

    2015-01-01

    fibrosis. Our analysis of 36 P. aeruginosa lineages identified convergent molecular evolution in 52 genes. This list of genes suggests a role in host adaptation for remodeling of regulatory networks and central metabolism, acquisition of antibiotic resistance and loss of extracellular virulence factors....... Furthermore, we find an ordered succession of mutations in key regulatory networks. Accordingly, mutations in downstream transcriptional regulators were contingent upon mutations in upstream regulators, suggesting that remodeling of regulatory networks might be important in adaptation. The characterization...... of genes involved in host adaptation may help in predicting bacterial evolution in patients with cystic fibrosis and in the design of future intervention strategies....

  11. Transformational adaptation when incremental adaptations to climate change are insufficient.

    Science.gov (United States)

    Kates, Robert W; Travis, William R; Wilbanks, Thomas J

    2012-05-08

    All human-environment systems adapt to climate and its natural variation. Adaptation to human-induced change in climate has largely been envisioned as increments of these adaptations intended to avoid disruptions of systems at their current locations. In some places, for some systems, however, vulnerabilities and risks may be so sizeable that they require transformational rather than incremental adaptations. Three classes of transformational adaptations are those that are adopted at a much larger scale, that are truly new to a particular region or resource system, and that transform places and shift locations. We illustrate these with examples drawn from Africa, Europe, and North America. Two conditions set the stage for transformational adaptation to climate change: large vulnerability in certain regions, populations, or resource systems; and severe climate change that overwhelms even robust human use systems. However, anticipatory transformational adaptation may be difficult to implement because of uncertainties about climate change risks and adaptation benefits, the high costs of transformational actions, and institutional and behavioral actions that tend to maintain existing resource systems and policies. Implementing transformational adaptation requires effort to initiate it and then to sustain the effort over time. In initiating transformational adaptation focusing events and multiple stresses are important, combined with local leadership. In sustaining transformational adaptation, it seems likely that supportive social contexts and the availability of acceptable options and resources for actions are key enabling factors. Early steps would include incorporating transformation adaptation into risk management and initiating research to expand the menu of innovative transformational adaptations.

  12. Adaptation: Needs, Financing and Institutions

    Energy Technology Data Exchange (ETDEWEB)

    Klein, Richard J.T.; Kartha, Sivan; Persson, Aasa; Watkiss, Paul; Ackerman, Frank; Downing, Thomas E.; Kjellen, Bo; Schipper, Lisa (Stockholm Environment Institute, Stockholm (SE))

    2008-07-01

    Regardless of the efforts put into mitigation, some impacts of climate change are already unavoidable. Adaptation to climate change has therefore become a key component of domestic climate policy, along with mitigation. Adaptation has also become key to the success of global climate policy. Without an agreement on supporting adaptation in developing countries, there will be no agreement on mitigation. Strong mitigation efforts make it more likely that adaptation will be effective and affordable. The world cannot rely on adaptation alone: it would eventually lead to a level of climate change to which adaptation is no longer feasible. Government action is needed to create an enabling environment for adaptation. This includes removing existing financial, legal, institutional and knowledge barriers to adaptation, and strengthening the capacity of people and organisations to adapt. The success of adaptation relies on the success of development, and vice versa. Poverty reduction, good governance, education, environmental protection, health and gender equality all contribute to adaptive capacity. Substantially more money is needed to support adaptation in developing countries. Current levels of funding will soon have to be scaled up by two orders of magnitude (from US$ hundreds of million to US$ tens of billion per year). An agreement on adaptation in Copenhagen in 2009 will need to include concrete steps towards a strengthened knowledge base for adaptation, substantially more funding for developing countries, and enhanced adaptation planning and implementation at the national level. Recommendations: Developed countries should accept a transparent, principle-based allocation of responsibility for adaptation funding, resulting in adequate, new and additional money to support adaptation programmes in developing countries. Levies on carbon market transactions and auctioning emission permits are two existing mechanisms of generating new and additional funds consistent with

  13. The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time.

    Science.gov (United States)

    Koskella, Britt; Parr, Nicole

    2015-08-19

    Insight to the spatial and temporal scales of coevolution is key to predicting the outcome of host-parasite interactions and spread of disease. For bacteria infecting long-lived hosts, selection to overcome host defences is just one factor shaping the course of evolution; populations will also be competing with other microbial species and will themselves be facing infection by bacteriophage viruses. Here, we examine the temporal and spatial patterns of bacterial adaptation against natural phage populations from within leaves of horse chestnut trees. Using a time-shift experiment with both sympatric and allopatric phages from either contemporary or earlier points in the season, we demonstrate that bacterial resistance is higher against phages from the past, regardless of spatial sympatry or how much earlier in the season phages were collected. Similarly, we show that future bacterial hosts are more resistant to both sympatric and allopatric phages than contemporary bacterial hosts. Together, our results suggest the evolution of relatively general bacterial resistance against phages in nature and are contrasting to previously observed patterns of phage adaptation to bacteria from the same tree hosts over the same time frame, indicating a potential asymmetry in coevolutionary dynamics.

  14. Positively regulated bacterial expression systems.

    Science.gov (United States)

    Brautaset, Trygve; Lale, Rahmi; Valla, Svein

    2009-01-01

    Regulated promoters are useful tools for many aspects related to recombinant gene expression in bacteria, including for high-level expression of heterologous proteins and for expression at physiological levels in metabolic engineering applications. In general, it is common to express the genes of interest from an inducible promoter controlled either by a positive regulator or by a repressor protein. In this review, we discuss established and potentially useful positively regulated bacterial promoter systems, with a particular emphasis on those that are controlled by the AraC-XylS family of transcriptional activators. The systems function in a wide range of microorganisms, including enterobacteria, soil bacteria, lactic bacteria and streptomycetes. The available systems that have been applied to express heterologous genes are regulated either by sugars (L-arabinose, L-rhamnose, xylose and sucrose), substituted benzenes, cyclohexanone-related compounds, ε-caprolactam, propionate, thiostrepton, alkanes or peptides. It is of applied interest that some of the inducers require the presence of transport systems, some are more prone than others to become metabolized by the host and some have been applied mainly in one or a limited number of species. Based on bioinformatics analyses, the AraC-XylS family of regulators contains a large number of different members (currently over 300), but only a small fraction of these, the XylS/Pm, AraC/P(BAD), RhaR-RhaS/rhaBAD, NitR/PnitA and ChnR/Pb regulator/promoter systems, have so far been explored for biotechnological applications.

  15. Survival of acid adapted and non-acid adapted Salmonella Typhimurium in pasteurized orange juice and yogurt under different storage temperatures.

    Science.gov (United States)

    Álvarez-Ordóñez, Avelino; Valdés, Lorena; Bernardo, Ana; Prieto, Miguel; López, Mercedes

    2013-10-01

    The survival capacity of Salmonella enterica serovar Typhimurium acid adapted and non-acid adapted cells was monitored in pasteurized yogurt (pH 4.1) and orange juice (pH 3.6) during storage at different temperatures (4, 10, 25 and 37 ). Acid adapted and non-acid adapted cells were obtained by means of their growth for 36 h in Brain Heart Infusion broth acidified at pH 4.8 with citric acid and buffered (pH 7.0) Brain Heart Infusion broth, respectively. S. typhimurium showed a great ability to survive in both foodstuffs and, especially, in yogurt, where both acid adapted and non-acid adapted populations suffered only a reduction of about 1.3-1.9 log10 cycles after 43 days of storage in the range of temperatures 4-25 . At 37  a higher bacterial inactivation was observed (4.0-4.4 log10 cycles). In orange juice, a different behaviour was observed for acid-adapted and non-acid adapted cells. Whereas non-acid adapted cells survived better than acid adapted cells at 4 and 10 , acid adapted cells showed enhanced survival abilities at higher temperatures (25 and 37 ). Thus, the times required to achieve a 5 log10 cycles reduction for non-acid adapted and acid adapted cells were 10.2 and 6.0 (4 ), 6.3 and 4.2 (10 ), 0.6 and 1.0 (25 ) and 0.10 and 0.15 (37 ) days, respectively. Evidence found in this study demonstrates that refrigeration temperatures protect S. typhimurium from inactivation in acid foods and indicates that S. typhimurium acid tolerance response (ATR) is determined by storage temperature and food composition.

  16. Endolymphatic sac involvement in bacterial meningitis

    DEFF Research Database (Denmark)

    Møller, Martin Nue; Brandt, Christian; Andersen, Christian Østergaard;

    2015-01-01

    The commonest sequelae of bacterial meningitis are related to the inner ear. Little is known about the inner ear immune defense. Evidence suggests that the endolymphatic sac provides some protection against infection. A potential involvement of the endolymphatic sac in bacterial meningitis......-inoculated. The rats were killed when reaching terminal illness or on day 7, followed by light microscopy preparation and PAS-Alcian blue staining. The endolymphatic sac was examined for bacterial invasion and leukocyte infiltration. Neither bacteria nor leukocytes infiltrated the endolymphatic sac during the first...... days. Bacteria invaded the inner ear through the cochlear aquaduct. On days 5-6, the bacteria invaded the endolymphatic sac through the endolymphatic duct subsequent to invasion of the vestibular endolymphatic compartment. No evidence of direct bacterial invasion of the sac through the meninges...

  17. Bacterial bioluminescence in marine pollution assessment

    Digital Repository Service at National Institute of Oceanography (India)

    Ramaiah, N.; Chandramohan, D.

    Warm water marine luminous bacterial species, particularly Vibrio harveyi, V. fischeri and Photobacterium leiognathi, are easy to isolate, maintain and handle in the laboratories without strict temperature requirements, which is an important...

  18. The bacterial microbiota in inflammatory lung diseases.

    Science.gov (United States)

    Huffnagle, Gary B; Dickson, Robert P

    2015-08-01

    Numerous lines of evidence, ranging from recent studies back to those in the 1920s, have demonstrated that the lungs are NOT bacteria-free during health. We have recently proposed that the entire respiratory tract should be considered a single ecosystem extending from the nasal and oral cavities to the alveoli, which includes gradients and niches that modulate microbiome dispersion, retention, survival and proliferation. Bacterial exposure and colonization of the lungs during health is most likely constant and transient, respectively. Host microanatomy, cell biology and innate defenses are altered during chronic lung disease, which in turn, alters the dynamics of bacterial turnover in the lungs and can lead to longer term bacterial colonization, as well as blooms of well-recognized respiratory bacterial pathogens. A few new respiratory colonizers have been identified by culture-independent methods, such as Pseudomonas fluorescens; however, the role of these bacteria in respiratory disease remains to be determined.

  19. Respiratory bacterial infections in cystic fibrosis

    DEFF Research Database (Denmark)

    Ciofu, Oana; Hansen, Christine R; Høiby, Niels

    2013-01-01

    Bacterial respiratory infections are the main cause of morbidity and mortality in patients with cystic fibrosis (CF). Pseudomonas aeruginosa remains the main pathogen in adults, but other Gram-negative bacteria such as Achromobacter xylosoxidans and Stenotrophomonas maltophilia as well...

  20. The Bacterial Microbiota in Inflammatory Lung Diseases

    Science.gov (United States)

    Huffnagle, Gary B.; Dickson, Robert P.

    2016-01-01

    Numerous lines of evidence, ranging from recent studies back to those in the 1920's, have demonstrated that the lungs are NOT bacteria-free during health. We have recently proposed that the entire respiratory tract should be considered a single ecosystem extending from the nasal and oral cavities to the alveoli, which includes gradients and niches that modulate microbiome dispersion, retention, survival and proliferation. Bacterial exposure and colonization of the lungs during health is most likely constant and transient, respectively. Host microanatomy, cell biology and innate defenses are altered during chronic lung disease, which in turn, alters the dynamics of bacterial turnover in the lungs and can lead to longer term bacterial colonization, as well as blooms of well-recognized respiratory bacterial pathogens. A few new respiratory colonizers have been identified by culture-independent methods, such as Pseudomonas fluorescens; however, the role of these bacteria in respiratory disease remains to be determined. PMID:26122174

  1. Plant growth-promoting bacterial endophytes.

    Science.gov (United States)

    Santoyo, Gustavo; Moreno-Hagelsieb, Gabriel; Orozco-Mosqueda, Ma del Carmen; Glick, Bernard R

    2016-02-01

    Bacterial endophytes ubiquitously colonize the internal tissues of plants, being found in nearly every plant worldwide. Some endophytes are able to promote the growth of plants. For those strains the mechanisms of plant growth-promotion known to be employed by bacterial endophytes are similar to the mechanisms used by rhizospheric bacteria, e.g., the acquisition of resources needed for plant growth and modulation of plant growth and development. Similar to rhizospheric plant growth-promoting bacteria, endophytic plant growth-promoting bacteria can act to facilitate plant growth in agriculture, horticulture and silviculture as well as in strategies for environmental cleanup (i.e., phytoremediation). Genome comparisons between bacterial endophytes and the genomes of rhizospheric plant growth-promoting bacteria are starting to unveil potential genetic factors involved in an endophytic lifestyle, which should facilitate a better understanding of the functioning of bacterial endophytes.

  2. Dynamics of immune system gene expression upon bacterial challenge and wounding in a social insect (Bombus terrestris).

    Science.gov (United States)

    Erler, Silvio; Popp, Mario; Lattorff, H Michael G

    2011-03-29

    The innate immune system which helps individuals to combat pathogens comprises a set of genes representing four immune system pathways (Toll, Imd, JNK and JAK/STAT). There is a lack of immune genes in social insects (e.g. honeybees) when compared to Diptera. Potentially, this might be compensated by an advanced system of social immunity (synergistic action of several individuals). The bumble bee, Bombus terrestris, is a primitively eusocial species with an annual life cycle and colonies headed by a single queen. We used this key pollinator to study the temporal dynamics of immune system gene expression in response to wounding and bacterial challenge.Antimicrobial peptides (AMP) (abaecin, defensin 1, hymenoptaecin) were strongly up-regulated by wounding and bacterial challenge, the latter showing a higher impact on the gene expression level. Sterile wounding down-regulated TEP A, an effector gene of the JAK/STAT pathway, and bacterial infection influenced genes of the Imd (relish) and JNK pathway (basket). Relish was up-regulated within the first hour after bacterial challenge, but decreased strongly afterwards. AMP expression following wounding and bacterial challenge correlates with the expression pattern of relish whereas correlated expression with dorsal was absent. Although expression of AMPs was high, continuous bacterial growth was observed throughout the experiment.Here we demonstrate for the first time the temporal dynamics of immune system gene expression in a social insect. Wounding and bacterial challenge affected the innate immune system significantly. Induction of AMP expression due to wounding might comprise a pre-adaptation to accompanying bacterial infections. Compared with solitary species this social insect exhibits reduced immune system efficiency, as bacterial growth could not be inhibited. A negative feedback loop regulating the Imd-pathway is suggested. AMPs, the end product of the Imd-pathway, inhibited the up-regulation of the transcription

  3. Dynamics of immune system gene expression upon bacterial challenge and wounding in a social insect (Bombus terrestris.

    Directory of Open Access Journals (Sweden)

    Silvio Erler

    Full Text Available The innate immune system which helps individuals to combat pathogens comprises a set of genes representing four immune system pathways (Toll, Imd, JNK and JAK/STAT. There is a lack of immune genes in social insects (e.g. honeybees when compared to Diptera. Potentially, this might be compensated by an advanced system of social immunity (synergistic action of several individuals. The bumble bee, Bombus terrestris, is a primitively eusocial species with an annual life cycle and colonies headed by a single queen. We used this key pollinator to study the temporal dynamics of immune system gene expression in response to wounding and bacterial challenge.Antimicrobial peptides (AMP (abaecin, defensin 1, hymenoptaecin were strongly up-regulated by wounding and bacterial challenge, the latter showing a higher impact on the gene expression level. Sterile wounding down-regulated TEP A, an effector gene of the JAK/STAT pathway, and bacterial infection influenced genes of the Imd (relish and JNK pathway (basket. Relish was up-regulated within the first hour after bacterial challenge, but decreased strongly afterwards. AMP expression following wounding and bacterial challenge correlates with the expression pattern of relish whereas correlated expression with dorsal was absent. Although expression of AMPs was high, continuous bacterial growth was observed throughout the experiment.Here we demonstrate for the first time the temporal dynamics of immune system gene expression in a social insect. Wounding and bacterial challenge affected the innate immune system significantly. Induction of AMP expression due to wounding might comprise a pre-adaptation to accompanying bacterial infections. Compared with solitary species this social insect exhibits reduced immune system efficiency, as bacterial growth could not be inhibited. A negative feedback loop regulating the Imd-pathway is suggested. AMPs, the end product of the Imd-pathway, inhibited the up-regulation of the

  4. Adaptive resistance in bacteria requires epigenetic inheritance, genetic noise, and cost of efflux pumps.

    Directory of Open Access Journals (Sweden)

    Santiago Sandoval Motta

    Full Text Available Adaptive resistance emerges when populations of bacteria are subjected to gradual increases of antibiotics. It is characterized by a rapid emergence of resistance and fast reversibility to the non-resistant phenotype when the antibiotic is removed from the medium. Recent work shows that adaptive resistance requires epigenetic inheritance and heterogeneity of gene expression patterns that are, in particular, associated with the production of porins and efflux pumps. However, the precise mechanisms by which inheritance and variability govern adaptive resistance, and what processes cause its reversibility remain unclear. Here, using an efflux pump regulatory network (EPRN model, we show that the following three mechanisms are essential to obtain adaptive resistance in a bacterial population: 1 intrinsic variability in the expression of the EPRN transcription factors; 2 epigenetic inheritance of the transcription rate of EPRN associated genes; and 3 energetic cost of the efflux pumps activity that slows down cell growth. While the first two mechanisms acting together are responsible for the emergence and gradual increase of the resistance, the third one accounts for its reversibility. In contrast with the standard assumption, our model predicts that adaptive resistance cannot be explained by increased mutation rates. Our results identify the molecular mechanism of epigenetic inheritance as the main target for therapeutic treatments against the emergence of adaptive resistance. Finally, our theoretical framework unifies known and newly identified determinants such as the burden of efflux pumps that underlie bacterial adaptive resistance to antibiotics.

  5. [Combination therapy of chronic bacterial prostatitis].

    Science.gov (United States)

    Khryanin, A A; Reshetnikov, O V

    2016-08-01

    The article discusses the possible etiological factors in the development of chronic bacterial prostatitis. The authors presented a comparative long-term analysis of morbidity from non-viral sexually transmitted infections (STIs) in Russia. Against the background of general decline in STIs incidence, a significant percentage of them is made up by urogenital trichomoniasis. The findings substantiated the advantages of combination therapy (ornidazole and ofloxacin) for bacterial urinary tract infections.

  6. Jellyfish modulate bacterial dynamic and community structure.

    Science.gov (United States)

    Tinta, Tinkara; Kogovšek, Tjaša; Malej, Alenka; Turk, Valentina

    2012-01-01

    Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into possible changes in

  7. Jellyfish modulate bacterial dynamic and community structure.

    Directory of Open Access Journals (Sweden)

    Tinkara Tinta

    Full Text Available Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into

  8. Pattern Formation in a Bacterial Colony Model

    Directory of Open Access Journals (Sweden)

    Xinze Lian

    2014-01-01

    Full Text Available We investigate the spatiotemporal dynamics of a bacterial colony model. Based on the stability analysis, we derive the conditions for Hopf and Turing bifurcations. Furthermore, we present novel numerical evidence of time evolution of patterns controlled by parameters in the model and find that the model dynamics exhibit a diffusion controlled formation growth to spots, holes and stripes pattern replication, which show that the bacterial colony model is useful in revealing the spatial predation dynamics in the real world.

  9. Asynchronous exponential growth of a bacterial population

    Directory of Open Access Journals (Sweden)

    Mohamed Boulanouar

    2014-01-01

    Full Text Available In this work, we complete a study started earlier in [1,2] wherein a model of growing bacterial population has been the matter of a mathematical analysis. We show that the full model is governed by a strongly continuous semigroup. Beside the positivity and the irreducibility of the generated semigroup, we describe its asymptotic behavior in the uniform topology which leads to the asynchronous exponential growth of the bacterial population.

  10. Volatiles in Inter-Specific Bacterial Interactions.

    Science.gov (United States)

    Tyc, Olaf; Zweers, Hans; de Boer, Wietse; Garbeva, Paolina

    2015-01-01

    The importance of volatile organic compounds for functioning of microbes is receiving increased research attention. However, to date very little is known on how inter-specific bacterial interactions effect volatiles production as most studies have been focused on volatiles produced by monocultures of well-described bacterial genera. In this study we aimed to understand how inter-specific bacterial interactions affect the composition, production and activity of volatiles. Four phylogenetically different bacterial species namely: Chryseobacterium, Dyella, Janthinobacterium, and Tsukamurella were selected. Earlier results had shown that pairwise combinations of these bacteria induced antimicrobial activity in agar media whereas this was not the case for monocultures. In the current study, we examined if these observations were also reflected by the production of antimicrobial volatiles. Thus, the identity and antimicrobial activity of volatiles produced by the bacteria were determined in monoculture as well in pairwise combinations. Antimicrobial activity of the volatiles was assessed against fungal, oomycetal, and bacterial model organisms. Our results revealed that inter-specific bacterial interactions affected volatiles blend composition. Fungi and oomycetes showed high sensitivity to bacterial volatiles whereas the effect of volatiles on bacteria varied between no effects, growth inhibition to growth promotion depending on the volatile blend composition. In total 35 volatile compounds were detected most of which were sulfur-containing compounds. Two commonly produced sulfur-containing volatile compounds (dimethyl disulfide and dimethyl trisulfide) were tested for their effect on three target bacteria. Here, we display the importance of inter-specific interactions on bacterial volatiles production and their antimicrobial activities.

  11. Rho-modifying bacterial protein toxins.

    Science.gov (United States)

    Aktories, Klaus

    2015-12-01

    Rho proteins are targets of numerous bacterial protein toxins, which manipulate the GTP-binding proteins by covalent modifications, including ADP ribosylation, glycosylation, adenylylation, proteolytic cleavage and deamidation. Bacterial toxins are important virulence factors but are also potent and efficient pharmacological tools to study the physiological functions of their eukaryotic targets. Recent studies indicate that amazing variations exist in the molecular mechanisms by which toxins attack Rho proteins, which are discussed here.

  12. Mechanistic investigations on six bacterial terpene cyclases

    Directory of Open Access Journals (Sweden)

    Patrick Rabe

    2016-08-01

    Full Text Available The products obtained by incubation of farnesyl diphosphate (FPP with six purified bacterial terpene cyclases were characterised by one- and two-dimensional NMR spectroscopic methods, allowing for a full structure elucidation. The absolute configurations of four terpenes were determined based on their optical rotary powers. Incubation experiments with 13C-labelled isotopomers of FPP in buffers containing water or deuterium oxide allowed for detailed insights into the cyclisation mechanisms of the bacterial terpene cyclases.

  13. Recombination and the nature of bacterial speciation

    OpenAIRE

    2007-01-01

    Genetic surveys are uncovering the diversity of bacteria, and are causing the species concepts used to categorize these to be questioned. One difficulty in defining bacterial species arises from the high rates of recombination that results in the transfer of DNA between relatively distantly related bacteria. Barriers to this process, which could be used to define species naturally, are not apparent. Here, we have reviewed conceptual models of bacterial speciation and simulate speciation in si...

  14. Soil carbon quality and nitrogen fertilization structure bacterial communities with predictable responses of major bacterial phyla

    OpenAIRE

    2014-01-01

    Agricultural practices affect the soil ecosystem in multiple ways and the soil microbial communities represent an integrated and dynamic measure of soil status. Our aim was to test whether the soil bacterial community and the relative abundance of major bacterial phyla responded predictably to long-term organic amendments representing different carbon qualities (peat and straw) in combination with nitrogen fertilization levels and if certain bacterial groups were indicative of specific treatm...

  15. The role of the adaptive immune system in regulation of gut microbiota.

    Science.gov (United States)

    Kato, Lucia M; Kawamoto, Shimpei; Maruya, Mikako; Fagarasan, Sidonia

    2014-07-01

    The gut nourishes rich bacterial communities that affect profoundly the functions of the immune system. The relationship between gut microbiota and the immune system is one of reciprocity. The microbiota contributes to nutrient processing and the development, maturation, and function of the immune system. Conversely, the immune system, particularly the adaptive immune system, plays a key role in shaping the repertoire of gut microbiota. The fitness of host immune system is reflected in the gut microbiota, and deficiencies in either innate or adaptive immunity impact on diversity and structures of bacterial communities in the gut. Here, we discuss the mechanisms that underlie this reciprocity and emphasize how the adaptive immune system via immunoglobulins (i.e. IgA) contributes to diversification and balance of gut microbiota required for immune homeostasis.

  16. Comprehensive phylogenetic analysis of bacterial reverse transcriptases.

    Directory of Open Access Journals (Sweden)

    Nicolás Toro

    Full Text Available Much less is known about reverse transcriptases (RTs in prokaryotes than in eukaryotes, with most prokaryotic enzymes still uncharacterized. Two surveys involving BLAST searches for RT genes in prokaryotic genomes revealed the presence of large numbers of diverse, uncharacterized RTs and RT-like sequences. Here, using consistent annotation across all sequenced bacterial species from GenBank and other sources via RAST, available from the PATRIC (Pathogenic Resource Integration Center platform, we have compiled the data for currently annotated reverse transcriptases from completely sequenced bacterial genomes. RT sequences are broadly distributed across bacterial phyla, but green sulfur bacteria and cyanobacteria have the highest levels of RT sequence diversity (≤85% identity per genome. By contrast, phylum Actinobacteria, for which a large number of genomes have been sequenced, was found to have a low RT sequence diversity. Phylogenetic analyses revealed that bacterial RTs could be classified into 17 main groups: group II introns, retrons/retron-like RTs, diversity-generating retroelements (DGRs, Abi-like RTs, CRISPR-Cas-associated RTs, group II-like RTs (G2L, and 11 other groups of RTs of unknown function. Proteobacteria had the highest potential functional diversity, as they possessed most of the RT groups. Group II introns and DGRs were the most widely distributed RTs in bacterial phyla. Our results provide insights into bacterial RT phylogeny and the basis for an update of annotation systems based on sequence/domain homology.

  17. Role of quorum sensing in bacterial infections

    Science.gov (United States)

    Castillo-Juárez, Israel; Maeda, Toshinari; Mandujano-Tinoco, Edna Ayerim; Tomás, María; Pérez-Eretza, Berenice; García-Contreras, Silvia Julieta; Wood, Thomas K; García-Contreras, Rodolfo

    2015-01-01

    Quorum sensing (QS) is cell communication that is widely used by bacterial pathogens to coordinate the expression of several collective traits, including the production of multiple virulence factors, biofilm formation, and swarming motility once a population threshold is reached. Several lines of evidence indicate that QS enhances virulence of bacterial pathogens in animal models as well as in human infections; however, its relative importance for bacterial pathogenesis is still incomplete. In this review, we discuss the present evidence from in vitro and in vivo experiments in animal models, as well as from clinical studies, that link QS systems with human infections. We focus on two major QS bacterial models, the opportunistic Gram negative bacteria Pseudomonas aeruginosa and the Gram positive Staphylococcus aureus, which are also two of the main agents responsible of nosocomial and wound infections. In addition, QS communication systems in other bacterial, eukaryotic pathogens, and even immune and cancer cells are also reviewed, and finally, the new approaches proposed to combat bacterial infections by the attenuation of their QS communication systems and virulence are also discussed. PMID:26244150

  18. An Adaptive Robot Game

    DEFF Research Database (Denmark)

    Hansen, Søren Tranberg; Svenstrup, Mikael; Dalgaard, Lars

    2010-01-01

    The goal of this paper is to describe an adaptive robot game, which motivates elderly people to do a regular amount of physical exercise while playing. One of the advantages of robot based games is that the initiative to play can be taken autonomously by the robot. In this case, the goal...... is to improve the mental and physical state of the user by playing a physical game with the robot. Ideally, a robot game should be simple to learn but difficult to master, providing an appropriate degree of challenge for players with different skills. In order to achieve that, the robot should be able to adapt...... to the behavior of the interacting person. This paper presents a simple ball game between a single player and a mobile robot platform. The algorithm has been validated using simulation and real world experiments....

  19. Adaptive manifold learning.

    Science.gov (United States)

    Zhang, Zhenyue; Wang, Jing; Zha, Hongyuan

    2012-02-01

    Manifold learning algorithms seek to find a low-dimensional parameterization of high-dimensional data. They heavily rely on the notion of what can be considered as local, how accurately the manifold can be approximated locally, and, last but not least, how the local structures can be patched together to produce the global parameterization. In this paper, we develop algorithms that address two key issues in manifold learning: 1) the adaptive selection of the local neighborhood sizes when imposing a connectivity structure on the given set of high-dimensional data points and 2) the adaptive bias reduction in the local low-dimensional embedding by accounting for the variations in the curvature of the manifold as well as its interplay with the sampling density of the data set. We demonstrate the effectiveness of our methods for improving the performance of manifold learning algorithms using both synthetic and real-world data sets.

  20. Adaptive Algebraic Multigrid Methods

    Energy Technology Data Exchange (ETDEWEB)

    Brezina, M; Falgout, R; MacLachlan, S; Manteuffel, T; McCormick, S; Ruge, J

    2004-04-09

    Our ability to simulate physical processes numerically is constrained by our ability to solve the resulting linear systems, prompting substantial research into the development of multiscale iterative methods capable of solving these linear systems with an optimal amount of effort. Overcoming the limitations of geometric multigrid methods to simple geometries and differential equations, algebraic multigrid methods construct the multigrid hierarchy based only on the given matrix. While this allows for efficient black-box solution of the linear systems associated with discretizations of many elliptic differential equations, it also results in a lack of robustness due to assumptions made on the near-null spaces of these matrices. This paper introduces an extension to algebraic multigrid methods that removes the need to make such assumptions by utilizing an adaptive process. The principles which guide the adaptivity are highlighted, as well as their application to algebraic multigrid solution of certain symmetric positive-definite linear systems.

  1. Adaptive method of lines

    CERN Document Server

    Saucez, Ph

    2001-01-01

    The general Method of Lines (MOL) procedure provides a flexible format for the solution of all the major classes of partial differential equations (PDEs) and is particularly well suited to evolutionary, nonlinear wave PDEs. Despite its utility, however, there are relatively few texts that explore it at a more advanced level and reflect the method''s current state of development.Written by distinguished researchers in the field, Adaptive Method of Lines reflects the diversity of techniques and applications related to the MOL. Most of its chapters focus on a particular application but also provide a discussion of underlying philosophy and technique. Particular attention is paid to the concept of both temporal and spatial adaptivity in solving time-dependent PDEs. Many important ideas and methods are introduced, including moving grids and grid refinement, static and dynamic gridding, the equidistribution principle and the concept of a monitor function, the minimization of a functional, and the moving finite elem...

  2. Unconsciously triggered conflict adaptation.

    Directory of Open Access Journals (Sweden)

    Simon van Gaal

    Full Text Available In conflict tasks such as the Stroop, the Eriksen flanker or the Simon task, it is generally observed that the detection of conflict in the current trial reduces the impact of conflicting information in the subsequent trial; a phenomenon termed conflict adaptation. This higher-order cognitive control function has been assumed to be restricted to cases where conflict is experienced consciously. In the present experiment we manipulated the awareness of conflict-inducing stimuli in a metacontrast masking paradigm to directly test this assumption. Conflicting response tendencies were elicited either consciously (through primes that were weakly masked or unconsciously (strongly masked primes. We demonstrate trial-by-trial conflict adaptation effects after conscious as well as unconscious conflict, which could not be explained by direct stimulus/response repetitions. These findings show that unconscious information can have a longer-lasting influence on our behavior than previously thought and further stretch the functional boundaries of unconscious cognition.

  3. Adaptive Large Neighbourhood Search

    DEFF Research Database (Denmark)

    Røpke, Stefan

    Large neighborhood search is a metaheuristic that has gained popularity in recent years. The heuristic repeatedly moves from solution to solution by first partially destroying the solution and then repairing it. The best solution observed during this search is presented as the final solution....... This tutorial introduces the large neighborhood search metaheuristic and the variant adaptive large neighborhood search that dynamically tunes parameters of the heuristic while it is running. Both heuristics belong to a broader class of heuristics that are searching a solution space using very large...... neighborhoods. The tutorial also present applications of the adaptive large neighborhood search, mostly related to vehicle routing problems for which the heuristic has been extremely successful. We discuss how the heuristic can be parallelized and thereby take advantage of modern desktop computers...

  4. Adapt or Die

    DEFF Research Database (Denmark)

    Brody, Joshua Eric; Larsen, Kasper Green

    2015-01-01

    read cells. We study such non-adaptive data structures in the cell probe model. This model is one of the least restrictive lower bound models and in particular, cell probe lower bounds apply to data structures developed in the popular word-RAM model. Unfortunately, this generality comes at a high cost...... several different notions of non-adaptivity and identify key properties that must be dealt with if we are to prove polynomial lower bounds without restrictions on the data structures. Finally, our results also unveil an interesting connection between data structures and depth-2 circuits. This allows us...... to translate conjectured hard data structure problems into good candidates for high circuit lower bounds; in particular, in the area of linear circuits for linear operators. Building on lower bound proofs for data structures in slightly more restrictive models, we also present a number of properties of linear...

  5. Adapted Active Appearance Models

    Directory of Open Access Journals (Sweden)

    Renaud Séguier

    2009-01-01

    Full Text Available Active Appearance Models (AAMs are able to align efficiently known faces under duress, when face pose and illumination are controlled. We propose Adapted Active Appearance Models to align unknown faces in unknown poses and illuminations. Our proposal is based on the one hand on a specific transformation of the active model texture in an oriented map, which changes the AAM normalization process; on the other hand on the research made in a set of different precomputed models related to the most adapted AAM for an unknown face. Tests on public and private databases show the interest of our approach. It becomes possible to align unknown faces in real-time situations, in which light and pose are not controlled.

  6. Adaptive semantics visualization

    CERN Document Server

    Nazemi, Kawa

    2016-01-01

    This book introduces a novel approach for intelligent visualizations that adapts the different visual variables and data processing to human’s behavior and given tasks. Thereby a number of new algorithms and methods are introduced to satisfy the human need of information and knowledge and enable a usable and attractive way of information acquisition. Each method and algorithm is illustrated in a replicable way to enable the reproduction of the entire “SemaVis” system or parts of it. The introduced evaluation is scientifically well-designed and performed with more than enough participants to validate the benefits of the methods. Beside the introduced new approaches and algorithms, readers may find a sophisticated literature review in Information Visualization and Visual Analytics, Semantics and information extraction, and intelligent and adaptive systems. This book is based on an awarded and distinguished doctoral thesis in computer science.

  7. Designing Adaptive Web Applications

    DEFF Research Database (Denmark)

    Dolog, Peter

    2008-01-01

    Learning system to study a discipline. In business to business interaction, different requirements and parameters of exchanged business requests might be served by different services from third parties. Such applications require certain intelligence and a slightly different approach to design. Adpative web...... adaptation to the changed parameters of environments, user or context. Adaptation can be seen as an orthogonal concern or viewpoint in a design process. In this paper I will discuss design abstractions which are employed in current design methods for web applications. I will exemplify the use......The unique characteristic of web applications is that they are supposed to be used by much bigger and diverse set of users and stakeholders. An example application area is e-Learning or business to business interaction. In eLearning environment, various users with different background use the e...

  8. Improved Adaptive Fingerprint Binarization

    OpenAIRE

    Bartunek, Josef Ström; Nilsson, Mikael; Nordberg, Jörgen; Claesson, Ingvar

    2008-01-01

    In this paper improvements to a previous work are presented. Removing the redundant artifacts in the fingerprint mask is introduced enhancing the final result. The proposed method is entirely adaptive process adjusting to each fingerprint without any further supervision of the user. Hence, the algorithm is insensitive to the characteristics of the fingerprint sensor and the various physical appearances of the fingerprints. Further, a detailed description of fingerprint mask generation not ful...

  9. Adaptable positioner; Posicionador adaptativo

    Energy Technology Data Exchange (ETDEWEB)

    Labrador Pavon, I.

    1993-12-31

    This paper describes the circuits and programs in assembly language, developed to control the two DC motors that give mobility to a mechanical arm with two degrees of freedom. As a whole, the system is based in a adaptable regulator designed around a 8 bit microprocessor that, starting from a mode of regulation based in the successive approximation method, evolve to another mode through which, only one approximation is sufficient to get the right position of each motor. (Author) 22 fig. 6 ref.

  10. Adaptive positioner; Posicionador adaptativo

    Energy Technology Data Exchange (ETDEWEB)

    Labrador Pavon, I.

    1993-07-01

    This paper describes the circuits and programs in assembly language, developed to control the two DC motors that give mobility to a mechanical arm with two degrees of freedom. As a whole, the system is based in a adaptable regulator designed around a 8 bit microprocessor that, starting from a mode of regulation based in the successive approximation method, evolve to another mode through which, only one approximation is sufficient to get the right position of each motor. (Author) 6 refs.

  11. Reconfigurable environmentally adaptive computing

    Science.gov (United States)

    Coxe, Robin L. (Inventor); Galica, Gary E. (Inventor)

    2008-01-01

    Described are methods and apparatus, including computer program products, for reconfigurable environmentally adaptive computing technology. An environmental signal representative of an external environmental condition is received. A processing configuration is automatically selected, based on the environmental signal, from a plurality of processing configurations. A reconfigurable processing element is reconfigured to operate according to the selected processing configuration. In some examples, the environmental condition is detected and the environmental signal is generated based on the detected condition.

  12. Robust Adaptive Control.

    Science.gov (United States)

    1985-09-19

    13.2 3.6. 14.0. 1.8. 11111.52 *.6 L 3 n1 i erated ~~~m nc. AFOSR-TR- 798 s AD-A 161 349 ROBUST ADAPTIVE CONTROL * FINAL REPORT PREPARED BY: R~ OBERT L... Centre Block Computes the Norm of the [1I] Solo, V., "Time Series Recursions and Stochastc Regressors. The Rematning Elemerts Imple- Approximation

  13. Stylistic Adaptation in Translation

    Institute of Scientific and Technical Information of China (English)

    孙芳

    2011-01-01

    <正>A translation criteria universally accepted is faithfulness, which can be examined from different dimensions of content, form and style.Among these three dimensions,faithfulness in content and form is easier to be noted,while the faithfulness in style is harder to judge.This paper will mainly focus on the study of stylistic features for the purpose of language providing methods to achieve stylistic adaptation in translation.

  14. Adaptive Biomedical Innovation.

    Science.gov (United States)

    Honig, P K; Hirsch, G

    2016-12-01

    Adaptive Biomedical Innovation (ABI) is a multistakeholder approach to product and process innovation aimed at accelerating the delivery of clinical value to patients and society. ABI offers the opportunity to transcend the fragmentation and linearity of decision-making in our current model and create a common collaborative framework that optimizes the benefit and access of new medicines for patients as well as creating a more sustainable innovation ecosystem.

  15. Adaptation to High Altitude

    OpenAIRE

    1984-01-01

    Hypoxia is inconsequential for physiologically fit persons below an effective altitude of 2640 metres. At higher altitudes, the adaptation is brought about by four main factors, viz., hyperventilation, increased diffusion of oxygen across alveolar membrane, erythrocythemia and maintenance of body hydration. Carbon dioxide sensitivity is markedly elevated at high altitude, both in sojourners and acclimatized low-landers. The greater pulmonary diffusing capacity observed in high altitude native...

  16. Adaptive colouration in amphibians.

    Science.gov (United States)

    Rudh, Andreas; Qvarnström, Anna

    2013-01-01

    Amphibians, i.e. salamanders, frogs and caecilians show a wide range of bright colours in combination with contrasting patterns. There is variation among species, populations and also within species and populations. Furthermore, individuals often change colours during developmental stages or in response to environmental factors. This extraordinary variation means that there are excellent opportunities to test hypotheses of the adaptive significance of colours using amphibian species as models. We review the present view of functions of colouration in amphibians with the main focus on relatively unexplored topics. Variation in colouration has been found to play a role in thermoregulation, UV protection, predator avoidance and sexual signalling. However, many proposed cases of adaptive functions of colouration in amphibians remain virtually scientifically unexplored and surprisingly few genes influencing pigmentation or patterning have been detected. We would like to especially encourage more studies that take advantage of recent developments in measurement of visual properties of several possible signalling receivers (e.g. predators, competitors or mates). Future investigations on interactions between behaviour, ecology and vision have the potential to challenge our current view of the adaptive function of colouration in amphibians.

  17. Adaptive Signal Processing Testbed

    Science.gov (United States)

    Parliament, Hugh A.

    1991-09-01

    The design and implementation of a system for the acquisition, processing, and analysis of signal data is described. The initial application for the system is the development and analysis of algorithms for excision of interfering tones from direct sequence spread spectrum communication systems. The system is called the Adaptive Signal Processing Testbed (ASPT) and is an integrated hardware and software system built around the TMS320C30 chip. The hardware consists of a radio frequency data source, digital receiver, and an adaptive signal processor implemented on a Sun workstation. The software components of the ASPT consists of a number of packages including the Sun driver package; UNIX programs that support software development on the TMS320C30 boards; UNIX programs that provide the control, user interaction, and display capabilities for the data acquisition, processing, and analysis components of the ASPT; and programs that perform the ASPT functions including data acquisition, despreading, and adaptive filtering. The performance of the ASPT system is evaluated by comparing actual data rates against their desired values. A number of system limitations are identified and recommendations are made for improvements.

  18. Adaptation to High Altitude

    Directory of Open Access Journals (Sweden)

    H. S. Nayar

    1984-10-01

    Full Text Available Hypoxia is inconsequential for physiologically fit persons below an effective altitude of 2640 metres. At higher altitudes, the adaptation is brought about by four main factors, viz., hyperventilation, increased diffusion of oxygen across alveolar membrane, erythrocythemia and maintenance of body hydration. Carbon dioxide sensitivity is markedly elevated at high altitude, both in sojourners and acclimatized low-landers. The greater pulmonary diffusing capacity observed in high altitude natives is well documented. RBC count, haemoglobin and haematocrit increase whereas arterial oxyhaemoglobin saturation percentage decreases at high altitude. Diuretics (Furosemide have no role in adaptation to high altitude and adequate body hydration must be maintained.The ultimate adaptive mechanisms occur at tissue level which facilitate the diffusion of oxygen from blood to tissue and its utilization. The work capacity decreases at high altitude and a relationship between load carried and speed of marching has been determined at various altitudes. Although altitude has an adverse effect on process of cold acclimatization, yet it is possible to induce cold acclimatization by exposing subjects to a temperature of 0° to -5°C for a period of three hours daily for three weeks. The caloric requirements increase at high altitudes and are 4,286 K Cal and 4,380 K Cal at 13000 feet (3950 m and 17000 feet (5170 m, respectively.

  19. Adaptive Structural Mode Control Project

    Data.gov (United States)

    National Aeronautics and Space Administration — M4 Engineering proposes the development of an adaptive structural mode control system. The adaptive control system will begin from a "baseline" dynamic model of the...

  20. The bacterial pathogen Listeria monocytogenes and the interferon family: type I, type II and type III interferons.

    Science.gov (United States)

    Dussurget, Olivier; Bierne, Hélène; Cossart, Pascale

    2014-01-01

    Interferons (IFNs) are secreted proteins of the cytokine family that regulate innate and adaptive immune responses to infection. Although the importance of IFNs in the antiviral response has long been appreciated, their role in bacterial infections is more complex and is currently a major focus of investigation. This review summarizes our current knowledge of the role of these cytokines in host defense against the bacterial pathogen Listeria monocytogenes and highlights recent discoveries on the molecular mechanisms evolved by this intracellular bacterium to subvert IFN responses.