WorldWideScience

Sample records for bacterial population dynamics

  1. Dynamics of genome rearrangement in bacterial populations.

    Directory of Open Access Journals (Sweden)

    Aaron E Darling

    2008-07-01

    represent the first characterization of genome arrangement evolution in a bacterial population evolving outside laboratory conditions. Insight into the process of genomic rearrangement may further the understanding of pathogen population dynamics and selection on the architecture of circular bacterial chromosomes.

  2. Exploring bacterial infections: theoretical and experimental studies of the bacterial population dynamics and antibiotic treatment

    Science.gov (United States)

    Shao, Xinxian

    Bacterial infections are very common in human society. Thus extensive research has been conducted to reveal the molecular mechanisms of the pathogenesis and to evaluate the antibiotics' efficacy against bacteria. Little is known, however, about the population dynamics of bacterial populations and their interactions with the host's immune system. In this dissertation, a stochatic model is developed featuring stochastic phenotypic switching of bacterial individuals to explain the single-variant bottleneck discovered in multi strain bacterial infections. I explored early events in a bacterial infection establishment using classical experiments of Moxon and Murphy on neonatal rats. I showed that the minimal model and its simple variants do not work. I proposed modifications to the model that could explain the data quantitatively. The bacterial infections are also commonly established in physical structures, as biofilms or 3-d colonies. In contrast, most research on antibiotic treatment of bacterial infections has been conducted in well-mixed liquid cultures. I explored the efficacy of antibiotics to treat such bacterial colonies, a broadly applicable method is designed and evaluated where discrete bacterial colonies on 2-d surfaces were exposed to antibiotics. I discuss possible explanations and hypotheses for the experimental results. To verify these hypotheses, we investigated the dynamics of bacterial population as 3-d colonies. We showed that a minimal mathematical model of bacterial colony growth in 3-d was able to account for the experimentally observed presence of a diffusion-limited regime. The model further revealed highly loose packing of the cells in 3-d colonies and smaller cell sizes in colonies than plancktonic cells in corresponding liquid culture. Further experimental tests of the model predictions have revealed that the ratio of the cell size in liquid culture to that in colony cultures was consistent with the model prediction, that the dead cells

  3. Population Dynamics of Patients with Bacterial Resistance in Hospital Environment

    Directory of Open Access Journals (Sweden)

    Leilei Qu

    2016-01-01

    Full Text Available During the past decades, the increase of antibiotic resistance has become a major concern worldwide. The researchers found that superbugs with new type of resistance genes (NDM-1 have two aspects of transmission characteristics; the first is that the antibiotic resistance genes can horizontally transfer among bacteria, and the other is that the superbugs can spread between humans through direct contact. Based on these two transmission mechanisms, we study the dynamics of population in hospital environment where superbugs exist. In this paper, we build three mathematic models to illustrate the dynamics of patients with bacterial resistance in hospital environment. The models are analyzed using stability theory of differential equations. Positive equilibrium points of the system are investigated and their stability analysis is carried out. Moreover, the numerical simulation of the proposed model is also performed which supports the theoretical findings.

  4. Modeling bacterial population growth from stochastic single-cell dynamics.

    Science.gov (United States)

    Alonso, Antonio A; Molina, Ignacio; Theodoropoulos, Constantinos

    2014-09-01

    A few bacterial cells may be sufficient to produce a food-borne illness outbreak, provided that they are capable of adapting and proliferating on a food matrix. This is why any quantitative health risk assessment policy must incorporate methods to accurately predict the growth of bacterial populations from a small number of pathogens. In this aim, mathematical models have become a powerful tool. Unfortunately, at low cell concentrations, standard deterministic models fail to predict the fate of the population, essentially because the heterogeneity between individuals becomes relevant. In this work, a stochastic differential equation (SDE) model is proposed to describe variability within single-cell growth and division and to simulate population growth from a given initial number of individuals. We provide evidence of the model ability to explain the observed distributions of times to division, including the lag time produced by the adaptation to the environment, by comparing model predictions with experiments from the literature for Escherichia coli, Listeria innocua, and Salmonella enterica. The model is shown to accurately predict experimental growth population dynamics for both small and large microbial populations. The use of stochastic models for the estimation of parameters to successfully fit experimental data is a particularly challenging problem. For instance, if Monte Carlo methods are employed to model the required distributions of times to division, the parameter estimation problem can become numerically intractable. We overcame this limitation by converting the stochastic description to a partial differential equation (backward Kolmogorov) instead, which relates to the distribution of division times. Contrary to previous stochastic formulations based on random parameters, the present model is capable of explaining the variability observed in populations that result from the growth of a small number of initial cells as well as the lack of it compared to

  5. Dynamics of adaptive immunity against phage in bacterial populations

    Science.gov (United States)

    Bradde, Serena; Vucelja, Marija; Tesileanu, Tiberiu; Balasubramanian, Vijay

    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 distribution. Bacteria can interpolate between these limiting behaviors by actively tuning their overall acquisition rate.

  6. Bacterial population dynamics during the ensiling of Medicago sativa (alfalfa) and subsequent exposure to air

    Science.gov (United States)

    Aims: To describe, at high resolution, the bacterial population dynamics and chemical transformations during the ensiling of alfalfa and subsequent exposure to air. Methods and Results: Samples of alfalfa, ensiled alfalfa, and silage exposed to air were collected and their bacterial population stru...

  7. Bacterial population dynamics during the ensiling of Medicago sativa (alfalfa) and subsequent exposure to air.

    Science.gov (United States)

    McGarvey, J A; Franco, R B; Palumbo, J D; Hnasko, R; Stanker, L; Mitloehner, F M

    2013-06-01

    To describe, at high resolution, the bacterial population dynamics and chemical transformations during the ensiling of alfalfa and subsequent exposure to air. Samples of alfalfa, ensiled alfalfa and silage exposed to air were collected and their bacterial population structures compared using 16S rRNA gene libraries containing approximately 1900 sequences each. Cultural and chemical analyses were also performed to complement the 16S gene sequence data. Sequence analysis revealed significant differences (P alfalfa-derived library contained mostly sequences associated with the Gammaproteobacteria (including the genera: Enterobacter, Erwinia and Pantoea); the ensiled material contained mostly sequences associated with the lactic acid bacteria (LAB) (including the genera: Lactobacillus, Pediococcus and Lactococcus). Exposure to air resulted in even greater percentages of LAB, especially among the genus Lactobacillus, and a significant drop in bacterial diversity. In-depth 16S rRNA gene sequence analysis revealed significant bacterial population structure changes during ensiling and again during exposure to air. This in-depth description of the bacterial population dynamics that occurred during ensiling and simulated feed out expands our knowledge of these processes. © 2013 The Society for Applied Microbiology No claim to US Government works.

  8. The population and evolutionary dynamics of homologous gene recombination in bacterial populations.

    Directory of Open Access Journals (Sweden)

    Bruce R Levin

    2009-08-01

    Full Text Available In bacteria, recombination is a rare event, not a part of the reproductive process. Nevertheless, recombination -- broadly defined to include the acquisition of genes from external sources, i.e., horizontal gene transfer (HGT -- plays a central role as a source of variation for adaptive evolution in many species of bacteria. Much of niche expansion, resistance to antibiotics and other environmental stresses, virulence, and other characteristics that make bacteria interesting and problematic, is achieved through the expression of genes and genetic elements obtained from other populations of bacteria of the same and different species, as well as from eukaryotes and archaea. While recombination of homologous genes among members of the same species has played a central role in the development of the genetics and molecular biology of bacteria, the contribution of homologous gene recombination (HGR to bacterial evolution is not at all clear. Also, not so clear are the selective pressures responsible for the evolution and maintenance of transformation, the only bacteria-encoded form of HGR. Using a semi-stochastic simulation of mutation, recombination, and selection within bacterial populations and competition between populations, we explore (1 the contribution of HGR to the rate of adaptive evolution in these populations and (2 the conditions under which HGR will provide a bacterial population a selective advantage over non-recombining or more slowly recombining populations. The results of our simulation indicate that, under broad conditions: (1 HGR occurring at rates in the range anticipated for bacteria like Streptococcus pneumoniae, Escherichia coli, Haemophilus influenzae, and Bacillus subtilis will accelerate the rate at which a population adapts to environmental conditions; (2 once established in a population, selection for this capacity to increase rates of adaptive evolution can maintain bacteria-encoded mechanisms of recombination and prevent

  9. Population-Dynamic Modeling of Bacterial Horizontal Gene Transfer by Natural Transformation.

    Science.gov (United States)

    Mao, Junwen; Lu, Ting

    2016-01-05

    Natural transformation is a major mechanism of horizontal gene transfer (HGT) and plays an essential role in bacterial adaptation, evolution, and speciation. Although its molecular underpinnings have been increasingly revealed, natural transformation is not well characterized in terms of its quantitative ecological roles. Here, by using Neisseria gonorrhoeae as an example, we developed a population-dynamic model for natural transformation and analyzed its dynamic characteristics with nonlinear tools and simulations. Our study showed that bacteria capable of natural transformation can display distinct population behaviors ranging from extinction to coexistence and to bistability, depending on their HGT rate and selection coefficient. With the model, we also illustrated the roles of environmental DNA sources-active secretion and passive release-in impacting population dynamics. Additionally, by constructing and utilizing a stochastic version of the model, we examined how noise shapes the steady and dynamic behaviors of the system. Notably, we found that distinct waiting time statistics for HGT events, namely a power-law distribution, an exponential distribution, and a mix of the both, are associated with the dynamics in the regimes of extinction, coexistence, and bistability accordingly. This work offers a quantitative illustration of natural transformation by revealing its complex population dynamics and associated characteristics, therefore advancing our ecological understanding of natural transformation as well as HGT in general. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  10. Imaging the Population Dynamics of Bacterial Communities in the Zebrafish Gut

    Science.gov (United States)

    Jemielita, Matthew; Taormina, Michael; Burns, Adam; Zac Stephens, W.; Hampton, Jennifer; Guillemin, Karen; Parthasarathy, Raghuveer

    2013-03-01

    The vertebrate gut is home to a diverse microbial ecosystem whose composition has a strong influence on the development and health of the host organism. While researchers are increasingly able to identify the constituent members of the microbiome, very little is known about the spatial and temporal dynamics of commensal microbial communities, including the mechanisms by which communities nucleate, grow, and interact. We address these issues using a model organism: the larval zebrafish (Danio rerio) prepared microbe-free and inoculated with controlled compositions of fluorophore-expressing bacteria. Live imaging with light sheet fluorescence microscopy enables visualization of individual bacterial cells as well as growing colonies over the entire volume of the gut over periods up to 24 hours. We analyze the structure and dynamics of imaged bacterial communities, uncovering correlations between population size, growth rates, and the timing of inoculations that suggest the existence of active changes in the host environment induced by early bacterial exposure. Our data provide the first visualizations of gut microbiota development over an extended period of time in a vertebrate.

  11. The type VI secretion system impacts bacterial invasion and population dynamics in a model intestinal microbiota

    Science.gov (United States)

    Logan, Savannah L.; Shields, Drew S.; Hammer, Brian K.; Xavier, Joao B.; Parthasarathy, Raghuveer

    Animal gastrointestinal tracts are home to a diverse community of microbes. The mechanisms by which microbial species interact and compete in this dense, physically dynamic space are poorly understood, limiting our understanding of how natural communities are assembled and how different communities could be engineered. Here, we focus on a physical mechanism for competition: the type VI secretion system (T6SS). The T6SS is a syringe-like organelle used by certain bacteria to translocate effector proteins across the cell membranes of target bacterial cells, killing them. Here, we use T6SS+ and T6SS- strains of V. cholerae, the pathogen that causes cholera in humans, and light sheet fluorescence microscopy for in vivo imaging to show that the T6SS provides an advantage to strains colonizing the larval zebrafish gut. Furthermore, we show that T6SS+ bacteria can invade and alter an existing population of a different species in the zebrafish gut, reducing its abundance and changing the form of its population dynamics. This work both demonstrates a mechanism for altering the gut microbiota with an invasive species and explores the processes controlling the stability and dynamics of the gut ecosystem. Research Corporation, Gordon and Betty Moore Foundation, and the Simons Foundation.

  12. BACTERIAL POPULATION DYNAMICS IN WASTE OILY EMULSIONS FROM THE METAL-PROCESSING INDUSTRY

    Directory of Open Access Journals (Sweden)

    Paweł Kaszycki

    2014-07-01

    Full Text Available Oil-containing wastewaters are regarded as main industrial pollutants of soil and water environments. They can occur as free-floating oil, unstable or stable oil-in-water (O/W emulsions, and in the case of extreme organic load, as water-in-oil (W/O emulsions. In this study two types of oily effluents, a typical O/W emulsion marked as E1 and a W/O emulsion E2, both discharged by local metal processing plants were examined to test their toxicity to microbial communities and the ability to serve as nutrient sources for bacterial growth. The organic contaminant load of the samples was evaluated on the basis of chemical oxygen demand (COD parameter values and was equal to 48 200 mg O2·dm-3 and >300 000 mg O2·dm-3 for E1 and E2, respectively.Both emulsions proved to be non toxic to bacterial communities and were shown to contain biodiverse autochthonous microflora consisting of several bacterial strains adapted to the presence of xenobiotics (the total of 1.36 · 106 CFU·cm-3 and 1.72 · 105 CFU·cm-3 was determined for E1 and E2, respectively. These indigenous bacteria as well as exogenously inoculated specialized allochthonous microorganisms were biostimulated so as to proliferate within the wastewater environment whose organic content served as the only source of carbon. The most favorable cultivation conditions were determined as fully aerobic growth at the temperature of 25 ºC. In 9 to 18 day-tests, autochthonous as well as bioaugmented allochthonous bacterial population dynamics were monitored. For both emulsions tested there was a dramatic increase (up to three orders of magnitude in bacterial frequency, as compared to the respective initial values. The resultant high biomass densities suggest that the effluents are susceptible to bioremediation. A preliminary xenobiotic biodegradation test confirmed that mixed auto- and allochthonous bacterial consortia obtained upon inoculation of the samples with microbiocenoses preselected for efficient

  13. Red Sea Acropora hemprichii Bacterial Population Dynamics under Adverse Anthropogenic Conditions

    KAUST Repository

    Lizcano, Javier

    2012-08-01

    Reef-building corals are cornerstones of life in the oceans. Understanding their interactions with microorganisms and their surrounding physicochemical conditions is important to comprehend reef functioning and ultimately protect coral reef ecosystems. Corals associate with a complex and specific array of microorganisms that supposedly affect their physiology and therefore can significantly determine the condition of a coral ecosystem. As environmental conditions may shape bacterial diversity and ecology in the coral symbiosis, ecosystem changes might have unfavorable consequences for the holobiont, to date poorly understood. Here, we were studying microbial community changes in A. hemprichii as a consequence of simulated eutrophication and overfishing over a period of 16 weeks by using in situ caging and slow release fertilizer treatments in an undisturbed Red Sea reef (22.18ºN, 38.57ºW). We used 16S rDNA amplicon sequencing to evaluate the individual and combined effects of overnutrification and fishing pressure, two of the most common local threats to coral reefs. With our data we hope to better understand bacterial population dynamics under anthropogenic influences and its role in coral resilience. Projecting further, this data will be useful to better predict the consequences of human activity on reef ecosystems.

  14. An obligatory bacterial mutualism in a multi-drug environment exhibits strong oscillatory population dynamics

    Science.gov (United States)

    Conwill, Arolyn; Yurtsev, Eugene; Gore, Jeff

    2014-03-01

    A common mechanism of antibiotic resistance in bacteria involves the production of an enzyme that inactivates the antibiotic. By inactivating the antibiotic, resistant cells can protect other cells in the population that would otherwise be sensitive to the drug. In a multidrug environment, an obligatory mutualism arises because populations of different strains rely on each other to breakdown antibiotics in the environment. Here, we experimentally track the population dynamics of two E. coli strains in the presence of two different antibiotics: ampicillin and chloramphenicol. Together the strains are able to grow in antibiotic concentrations that inhibit growth of either one of the strains alone. Although mutualisms are often thought to stabilize population dynamics, we observe strong oscillatory dynamics even when there is long-term coexistence between the two strains. We expect that our results will provide insight into the evolution of antibiotic resistance and, more generally, the evolutionary origin of phenotypic diversity, cooperation, and ecological stability.

  15. Effect of bacterial population density on germination wheat seeds and dynamics of simple artificial ecosystems

    Science.gov (United States)

    Somova, L. A.; Pechurkin, N. S.; Sarangova, A. B.; Pisman, T. I.

    Effect of the size of rhizospheric bacterial populations on germination of seeds and development of simple terrestrial "wheat plants - rhizospheric microorganisms - artificial soil" and "wheat plants - artificial soil" systems has been studied. Experiments demonstrated that within specify ranges in the inoculate, the rhizospheric bacteria are capable of increasing the yield of germinated seeds and stimulate the growth of plantlets. Germination of seeds inoculated with bacteria was either stimulated, or inhibited or remained at control levels depending on the amount of bacteria. Plant biomass growth and total photoassimilation has been found to depend on the amount of bacteria on the plant roots: the higher the amount of bacteria on plant roots, the smaller is the biomass of plants but the total photoassimilation is, higher. Thus, depending on the amount of bacteria on the roots of plants the system either increases the biomass of plants or increases the total photoassimilation, i.e. "pumps" carbon through itself involving bacteria.

  16. Monitoring the bacterial population dynamics during the ripening of Galician chorizo, a traditional dry fermented Spanish sausage.

    Science.gov (United States)

    Fonseca, Sonia; Cachaldora, Aida; Gómez, María; Franco, Inmaculada; Carballo, Javier

    2013-02-01

    The dynamics of the bacterial population throughout the ripening of Galician chorizo, a traditional dry fermented sausage produced in the north-west of Spain, were investigated by using classical and molecular approaches. Fermented sausages are certainly complex matrices with PCR inhibitors and background microbiota. Therefore, two different DNA preparation methods were performed to elaborate each standard curve and no significant differences were found, showing a very good correlation between both methods (R(2)>0.994). The combination of the results obtained from microbial counts, species and genus-specific PCR as well as real-time quantitative PCR (qPCR) allowed the identification for the dominant bacterial species and the study of the variation in the community composition over the ripening period. According to the data obtained both by identification of plate isolates and by real-time PCR, the dominant species among staphylococci and lactobacilli were Staphylococcus equorum and Lactobacillus sakei, respectively. However, only real-time PCR assay showed enough sensitivity to detect and quantify staphylococci in meat batter before stuffing, showing values of 5.28logCFU/g when quantifying Staphylococcus spp. and 2.87logCFU/g when quantifying S. equorum. In conclusion, real-time PCR was shown to be an efficient tool for the study of the complex associations developed in meat fermentations and for the characterization of dominant populations. Copyright © 2012. Published by Elsevier Ltd.

  17. Evaluation of the dynamics of microalgae population structure and process performance during piggery wastewater treatment in algal-bacterial photobioreactors.

    Science.gov (United States)

    García, Dimas; Posadas, Esther; Blanco, Saúl; Acién, Gabriel; García-Encina, Pedro; Bolado, Silvia; Muñoz, Raúl

    2018-01-01

    The dynamics of microalgae population during piggery wastewater (PWW) treatment in four open photobioreactors operated at 27days of hydraulic retention time, and inoculated with Chlorella sp. (R1), Acutodesmus obliquus (R2), Oscillatoria sp. (R3) and in the absence of inoculum (R4), were evaluated for 6months. In addition, the algal-bacterial biomass concentration, removal of organic matter, nutrients and heavy metals were also assessed. The results revealed a high diversity and rapid variations in the structure of microalgae populations, Chlorella sp. being dominant in R4 throughout most of the operational period. Steady state average biomass concentration ranged from 2445-2610mg/L in R1-R3 to 3265mg/L in R4. No significant differences were recorded in the removal efficiencies (REs) of total organic carbon (86-87%), inorganic carbon (62-71%), total nitrogen (82-85%) and total phosphorous (90-92%). Finally, Zn-REs accounted for 26% in R3, 37% in R2, and 49% in R1 and R4. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Dynamic Changes in Bacterial Population and Corresponding Exoenzyme Activity in Response to a Tropical Phytoplankton Bloom Chattonella marina

    Directory of Open Access Journals (Sweden)

    Anit M. Thomas

    2014-01-01

    Full Text Available The raphidophyte Chattonella marina (Subrahmanyan Hara & Chihara bloom which causes lethal effects on marine ecosystem has been reported intermittently from Indian waters. In the present study, periodic samplings were made in a Chattonella marina bloom area, off Mahe, on 27 and 29 October and 1 November 2011 (in different phases of the bloom to assess the associated bacterial population and their exoenzyme activity. Microbial community composition of Chattonella marina bloom revealed a twentyfold increase in bacterial load over the nonbloom area. The bacterial genera, Micrococcus, Flavobacterium, Vibrio, and Pseudomonas, increased significantly during the declining phase of the bloom. An assessment of the extracellular enzyme production also showed a marked increase in percentage of bacterial strains, potent in protease production, suggesting the possible role of proteolytic bacteria in bloom crash. This study reveals the bacterial community succession during the bloom and indicates that bacteria play an important role in bloom regulation.

  19. Population dynamics

    Directory of Open Access Journals (Sweden)

    Cooch, E. G.

    2004-06-01

    Full Text Available Increases or decreases in the size of populations over space and time are, arguably, the motivation for much of pure and applied ecological research. The fundamental model for the dynamics of any population is straightforward: the net change over time in the abundance of some population is the simple difference between the number of additions (individuals entering the population minus the number of subtractions (individuals leaving the population. Of course, the precise nature of the pattern and process of these additions and subtractions is often complex, and population biology is often replete with fairly dense mathematical representations of both processes. While there is no doubt that analysis of such abstract descriptions of populations has been of considerable value in advancing our, there has often existed a palpable discomfort when the ‘beautiful math’ is faced with the often ‘ugly realities’ of empirical data. In some cases, this attempted merger is abandoned altogether, because of the paucity of ‘good empirical data’ with which the theoretician can modify and evaluate more conceptually–based models. In some cases, the lack of ‘data’ is more accurately represented as a lack of robust estimates of one or more parameters. It is in this arena that methods developed to analyze multiple encounter data from individually marked organisms has seen perhaps the greatest advances. These methods have rapidly evolved to facilitate not only estimation of one or more vital rates, critical to population modeling and analysis, but also to allow for direct estimation of both the dynamics of populations (e.g., Pradel, 1996, and factors influencing those dynamics (e.g., Nichols et al., 2000. The interconnections between the various vital rates, their estimation, and incorporation into models, was the general subject of our plenary presentation by Hal Caswell (Caswell & Fujiwara, 2004. Caswell notes that although interest has traditionally

  20. Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load

    Science.gov (United States)

    Wielgoss, Sébastien; Barrick, Jeffrey E.; Tenaillon, Olivier; Wiser, Michael J.; Dittmar, W. James; Cruveiller, Stéphane; Chane-Woon-Ming, Béatrice; Médigue, Claudine; Lenski, Richard E.; Schneider, Dominique

    2013-01-01

    Mutations are the ultimate source of heritable variation for evolution. Understanding how mutation rates themselves evolve is thus essential for quantitatively understanding many evolutionary processes. According to theory, mutation rates should be minimized for well-adapted populations living in stable environments, whereas hypermutators may evolve if conditions change. However, the long-term fate of hypermutators is unknown. Using a phylogenomic approach, we found that an adapting Escherichia coli population that first evolved a mutT hypermutator phenotype was later invaded by two independent lineages with mutY mutations that reduced genome-wide mutation rates. Applying neutral theory to synonymous substitutions, we dated the emergence of these mutations and inferred that the mutT mutation increased the point-mutation rate by ∼150-fold, whereas the mutY mutations reduced the rate by ∼40–60%, with a corresponding decrease in the genetic load. Thus, the long-term fate of the hypermutators was governed by the selective advantage arising from a reduced mutation rate as the potential for further adaptation declined. PMID:23248287

  1. Dynamics of bacterial populations during bench-scale bioremediation of oily seawater and desert soil bioaugmented with coastal microbial mats.

    Science.gov (United States)

    Ali, Nidaa; Dashti, Narjes; Salamah, Samar; Sorkhoh, Naser; Al-Awadhi, Husain; Radwan, Samir

    2016-03-01

    This study describes a bench-scale attempt to bioremediate Kuwaiti, oily water and soil samples through bioaugmentation with coastal microbial mats rich in hydrocarbonoclastic bacterioflora. Seawater and desert soil samples were artificially polluted with 1% weathered oil, and bioaugmented with microbial mat suspensions. Oil removal and microbial community dynamics were monitored. In batch cultures, oil removal was more effective in soil than in seawater. Hydrocarbonoclastic bacteria associated with mat samples colonized soil more readily than seawater. The predominant oil degrading bacterium in seawater batches was the autochthonous seawater species Marinobacter hydrocarbonoclasticus. The main oil degraders in the inoculated soil samples, on the other hand, were a mixture of the autochthonous mat and desert soil bacteria; Xanthobacter tagetidis, Pseudomonas geniculata, Olivibacter ginsengisoli and others. More bacterial diversity prevailed in seawater during continuous than batch bioremediation. Out of seven hydrocarbonoclastic bacterial species isolated from those cultures, only one, Mycobacterium chlorophenolicum, was of mat origin. This result too confirms that most of the autochthonous mat bacteria failed to colonize seawater. Also culture-independent analysis of seawater from continuous cultures revealed high-bacterial diversity. Many of the bacteria belonged to the Alphaproteobacteria, Flavobacteria and Gammaproteobacteria, and were hydrocarbonoclastic. Optimal biostimulation practices for continuous culture bioremediation of seawater via mat bioaugmentation were adding the highest possible oil concentration as one lot in the beginning of bioremediation, addition of vitamins, and slowing down the seawater flow rate. © 2016 The Author. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  2. Bacterial computing with engineered populations.

    Science.gov (United States)

    Amos, Martyn; Axmann, Ilka Maria; Blüthgen, Nils; de la Cruz, Fernando; Jaramillo, Alfonso; Rodriguez-Paton, Alfonso; Simmel, Friedrich

    2015-07-28

    We describe strategies for the construction of bacterial computing platforms by describing a number of results from the recently completed bacterial computing with engineered populations project. In general, the implementation of such systems requires a framework containing various components such as intracellular circuits, single cell input/output and cell-cell interfacing, as well as extensive analysis. In this overview paper, we describe our approach to each of these, and suggest possible areas for future research. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  3. Diversity of aquatic bacterial populations

    International Nuclear Information System (INIS)

    Teska, J.D.

    1988-01-01

    A study was designed to evaluate the feasibility of adapting the automated Quantum II for the identification of bacterial fish pathogens. Optimal incubation conditions were determined for each of the species used, and, by using a Chi-square goodness of fit test, it was shown that isolates could be sorted into like-species groups with a Ward's hierarchical cluster analysis technique. In a second study, population profiles, growth kinetics, and transformation kinetics were evaluated for bacteria isolated from 4 aquatic environments located in the southeastern United States. Gradual long-term accumulation of organic acids in the waters of the Okefenokee Swamp, located in southeast Georgia and northeast Florida, has resulted in acidic water ranging from pH 3.5 to 4.5. A study was designed to evaluate the metabolic efficiency of surface-water gram-negative nonfermentative bacteria and ascertain whether aquatic bacterial populations exhibit adaptation to the low pH conditions. Using the computerized AMBIS the uptake and incorporation of 35 S-methionine into bacterial proteins under 5 levels of pH was quantitated for each of the test organisms

  4. Effects of photoperiod on nutrient removal, biomass production, and algal-bacterial population dynamics in lab-scale photobioreactors treating municipal wastewater.

    Science.gov (United States)

    Lee, Chang Soo; Lee, Sang-Ah; Ko, So-Ra; Oh, Hee-Mock; Ahn, Chi-Yong

    2015-01-01

    Effects of photoperiod were investigated in lab-scale photobioreactors containing algal-bacterial consortia to reduce organic nutrients from municipal wastewater. Under three photoperiod conditions (12 h:12 h, 36 h:12 h, and 60 h:12 h dark–light cycles), nutrient removals and biomass productions were measured along with monitoring microbial population dynamics. After a batch operation for 12 days, 59–80% carbon, 35–88% nitrogen, and 43–89% phosphorus were removed from influents, respectively. In this study, carbon removal was related positively to the length of dark cycles, while nitrogen and phosphorus removals inversely. On the contrast, the highest microbial biomass in terms of chlorophyll a, dry cell weight, and algal/bacterial rRNA gene markers was produced under the 12 h:12 h dark–light cycle among the three photoperiods. The results showed 1) simultaneous growths between algae and bacteria in the microbial consortia and 2) efficient nitrogen and phosphorus removals along with high microbial biomass production under prolonged light conditions. Statistical analyses indicated that carbon removal was significantly related to the ratio of bacteria to algae in the microbial consortia along with prolonged dark conditions (p < 0.05). In addition, the ratio of nitrogen removal to phosphorus removal decreased significantly under prolonged dark conditions (p < 0.001). These results indicated that the photoperiod condition has remarkable impacts on adjusting nutrient removal, producing microbial biomass, and altering algal-bacterial population dynamics. Therefore, the control of photoperiod was suggested as an important operating parameter in the algal wastewater treatment.

  5. Oscillating dynamics of bacterial populations and their predators in response to fresh organic matter added to soil: The simulation model 'BACWAVE-WEB'

    NARCIS (Netherlands)

    Zelenev, V.V.; Bruggen, van A.H.C.; Leffelaar, P.A.; Bloem, J.; Semenov, A.M.

    2006-01-01

    Recently, regular oscillations in bacterial populations and growth rates of bacterial feeding nematodes (BFN) were shown to occur after addition of fresh organic matter to soil. This paper presents a model developed to investigate potential mechanisms of those oscillations, and whether they were

  6. Heterotrophic bacterial populations in tropical sandy beaches

    Digital Repository Service at National Institute of Oceanography (India)

    Nair, S.; LokaBharathi, P.A.

    Distribution pattern of heterotrophic bacterial flora of three sandy beaches of the west coast of India was studied. The population in these beaches was microbiologically different. Population peaks of halotolerant and limnotolerant forms were...

  7. Population dynamics of toxic phytoplankton and bacterial flora in the waters of the low Adriatic sea; Dinamica di popolazione di fitoplancton tossico e flora batterica nel basso Adriatico

    Energy Technology Data Exchange (ETDEWEB)

    Caroppo, C.; Stabili, L.; Cavallo, R.A.; Pastore, M. [CNR, Ist. Sperimentale Talassografico Attlio Cerruti, Taranto (Italy); Marchiori, E. [Rome Univ., Rome (Italy). Dipt. di Chimica Organica; Bruno, M. [Istituto Superiore di Sanita' , Laboratorio di Igiene Ambientale, Rome (Italy)

    2000-07-01

    The coastal areas of the Southern Adriatic Sea, in particular the Apulian ones, may be considered an example of intact ecosystem and represent an ideal term of comparison to other marine ecosystems having higher levels of pollution (Northern Adriatic Sea). In order to evaluate the sanitary levels of this environment, four transect were investigated during two years monitoring (April 1995-March 1997) along the Otranto Channel coasts, by joint research groups of the Environmental Hygiene Laboratory of the Istituto Superiore di Sanita' and the Istituto Sperimentale Talassografico A. Cerruti of CNR in Taranto. The study underlines the phytoplanktic and bacterial population dynamics, and the detection of the microbiological water quality along the coast tract Brindisi-Lecce-Otranto-S. Maria di Leuca. The results acquired pointed out population dynamics of some potantially toxic species of Dinophysis genus and Pseudo-nitzschia delicatissima. These depended on the winter nutrient loads due to the ASW (Adriatic Superficial Waters) and to the LIW (Levantine Intermediate Waters). The bacterial community was mainly constituted by genera Aeromonas, Photobacterium, Cytophaga and Pseudomonas. Also the presence of Enterobacteriaceae family was relevant. Among the pathogenic vibrios the most frequently isolated species were Vibrio alginolyticus and Vibrio vulnificus. [Italian] Considerando che le zone del basso Adriatico, in particolare quelle pugliesi, costituiscono un biotopo ancora relativamente inalterato, esse sono state oggetto di un'indagine sperimentale condotta in 24 mesi di attivita' (aprile 1995-marzo 1997) lungo le coste del Canale di Otranto, ad opera di un gruppo congiunto del Laboratorio di Igiene Ambientale dell'Istituto Superiore di Sanita' e dei laboratori dell'Istituto Sperimentale Talassografico A. Cerruti del CNR di Taranto, ai fini di valutare lo stato di salute di questo ambiente, che fornisce, con buona probabilita', un

  8. Fish population dynamics

    National Research Council Canada - National Science Library

    Gulland, J. A

    1977-01-01

    This book describes how the dynamics of fish populations can be analysed in terms of the factors affecting their rates of growth, mortality and reproduction, with particular emphasis on the effects of fishing...

  9. Market Squid Population Dynamics

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset contains population dynamics data on paralarvae, juvenile and adult market squid collected off California and the US Pacific Northwest. These data were...

  10. Regional Population Dynamics

    Science.gov (United States)

    Andrew Birt

    2011-01-01

    The population dynamics of the southern pine beetle (SPB) exhibit characteristic fluctuations between relatively long endemic and shorter outbreak periods. Populations exhibit complex and hierarchical spatial structure with beetles and larvae aggregating within individual trees, infestations with multiple infested trees, and regional outbreaks that comprise a large...

  11. 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.

  12. Population bottlenecks promote cooperation in bacterial biofilms.

    Directory of Open Access Journals (Sweden)

    Michael A Brockhurst

    2007-07-01

    Full Text Available Population bottlenecks are assumed to play a key role in the maintenance of social traits in microbes. Ecological parameters such as colonisation or disturbances can favour cooperation through causing population bottlenecks that enhance genetic structuring (relatedness. However, the size of the population bottleneck is likely to play a crucial role in determining the success of cooperation. Relatedness is likely to increase with decreasing bottleneck size thus favouring the evolution of cooperation. I used an experimental evolution approach to test this prediction with biofilm formation by the bacterium Pseudomonas fluorescens as the cooperative trait. Replicate populations were exposed to disturbance events every four days under one of six population bottleneck treatments (from 10(3 to 10(8 bacterial cells. In line with predictions, the frequency of evolved cheats within the populations increased with increasing bottleneck size. This result highlights the importance of ecologically mediated population bottlenecks in the maintenance of social traits in microbes.

  13. Population dynamics and distribution of hydrocarbon utilizing ...

    African Journals Online (AJOL)

    Laboratory studies were carried out to assess the bacterial population dynamics and distribution in composite soil samples collected from five (5) different automobile workshops at various locations (Ikpa road, Nwaniba road, Udi street, Idakokpo lane and Mechanic village) within Uyo metropolis. The hydrocarbon utilizing ...

  14. Dinâmica das populações bacterianas em solos de Cerrados Dynamic of bacterial populations from Cerrado soils

    Directory of Open Access Journals (Sweden)

    João Carlos Pereira

    1999-05-01

    Full Text Available Nos ambientes tropicais, os Cerrados destacam-se pelo seu potencial agrícola. Apesar das funções dos microrganismos no crescimento das plantas e na produtividade das culturas, existem poucas informações dos efeitos resultantes do manejo do solo, na ecologia microbiana. Neste estudo, foram avaliados os efeitos das condições ambientais e das práticas agrícolas sobre as populações bacterianas. As densidades das populações em solos com vegetação nativa foram variáveis e diferenciadas. Em Sete Lagoas, MG, as populações de actinomicetos variaram de 1,7 a 50 X 10(4 UFC/g de solo seco, enquanto em Planaltina as densidades das populações bacterianas em solo com primeiro e segundo ano de cultivo de soja foram semelhantes, mas superiores ao solo com vegetação nativa. A utilização agrícola deste solo não resultou em desequilíbrios acentuados das populações de actinomicetos provenientes de esporos e hifas. As relações esporos/hifas variaram de 1,1 a 5,8. Na rizosfera da soja, os coeficientes de correlação entre as populações de actinomicetos com as demais populações bacterianas foram significativos. Os resultados evidenciam que as práticas agrícolas utilizadas na introdução da cultura da soja em solos de Cerrados pode influenciar o equilíbrio das populações na comunidade bacteriana.Among tropical environments, Cerrados stand out because of its agriculture potencial. Although microorganisms play an important role on soil sustainability and crop production, few information is available on the effects of soil management systems on Cerrado's microbial ecology. In this study the effects of environmental conditions and soil management practices on bacterial populations were evaluated. Bacterial population densities in soil under native vegetation were variable and diferentiated. Actinomycetes densities varied from 1.7 to 50 X 10(4 CFU/g dry soil in Sete Lagoas region, Brazil, whereas bacterial populations in both the

  15. Intrinsically dynamic population models

    Directory of Open Access Journals (Sweden)

    Robert Schoen

    2005-03-01

    Full Text Available Intrinsically dynamic models (IDMs depict populations whose cumulative growth rate over a number of intervals equals the product of the long term growth rates (that is the dominant roots or dominant eigenvalues associated with each of those intervals. Here the focus is on the birth trajectory produced by a sequence of population projection (Leslie matrices. The elements of a Leslie matrix are represented as straightforward functions of the roots of the matrix, and new relationships are presented linking the roots of a matrix to its Net Reproduction Rate and stable mean age of childbearing. Incorporating mortality changes in the rates of reproduction yields an IDM when the subordinate roots are held constant over time. In IDMs, the birth trajectory generated by any specified sequence of Leslie matrices can be found analytically. In the Leslie model with 15 year age groups, the constant subordinate root assumption leads to reasonable changes in the age pattern of fertility, and equations (27 and (30 provide the population size and structure that result from changing levels of net reproduction. IDMs generalize the fixed rate stable population model. They can characterize any observed population, and can provide new insights into dynamic demographic behavior, including the momentum associated with gradual or irregular paths to zero growth.

  16. Bacterial fitness shapes the population dynamics of antibiotic-resistant and -susceptible bacteria in a model of combined antibiotic and anti-virulence treatment

    Science.gov (United States)

    Ternent, Lucy; Dyson, Rosemary J.; Krachler, Anne-Marie; Jabbari, Sara

    2015-01-01

    Bacterial resistance to antibiotic treatment is a huge concern: introduction of any new antibiotic is shortly followed by the emergence of resistant bacterial isolates in the clinic. This issue is compounded by a severe lack of new antibiotics reaching the market. The significant rise in clinical resistance to antibiotics is especially problematic in nosocomial infections, where already vulnerable patients may fail to respond to treatment, causing even greater health concern. A recent focus has been on the development of anti-virulence drugs as a second line of defence in the treatment of antibiotic-resistant infections. This treatment, which weakens bacteria by reducing their virulence rather than killing them, should allow infections to be cleared through the body׳s natural defence mechanisms. In this way there should be little to no selective pressure exerted on the organism and, as such, a predominantly resistant population should be less likely to emerge. However, before the likelihood of resistance to these novel drugs emerging can be predicted, we must first establish whether such drugs can actually be effective. Many believe that anti-virulence drugs would not be powerful enough to clear existing infections, restricting their potential application to prophylaxis. We have developed a mathematical model that provides a theoretical framework to reveal the circumstances under which anti-virulence drugs may or may not be successful. We demonstrate that by harnessing and combining the advantages of antibiotics with those provided by anti-virulence drugs, given infection-specific parameters, it is possible to identify treatment strategies that would efficiently clear bacterial infections, while preventing the emergence of antibiotic-resistant subpopulations. Our findings strongly support the continuation of research into anti-virulence drugs and demonstrate that their applicability may reach beyond infection prevention. PMID:25701634

  17. Bacterial fitness shapes the population dynamics of antibiotic-resistant and -susceptible bacteria in a model of combined antibiotic and anti-virulence treatment.

    Science.gov (United States)

    Ternent, Lucy; Dyson, Rosemary J; Krachler, Anne-Marie; Jabbari, Sara

    2015-05-07

    Bacterial resistance to antibiotic treatment is a huge concern: introduction of any new antibiotic is shortly followed by the emergence of resistant bacterial isolates in the clinic. This issue is compounded by a severe lack of new antibiotics reaching the market. The significant rise in clinical resistance to antibiotics is especially problematic in nosocomial infections, where already vulnerable patients may fail to respond to treatment, causing even greater health concern. A recent focus has been on the development of anti-virulence drugs as a second line of defence in the treatment of antibiotic-resistant infections. This treatment, which weakens bacteria by reducing their virulence rather than killing them, should allow infections to be cleared through the body׳s natural defence mechanisms. In this way there should be little to no selective pressure exerted on the organism and, as such, a predominantly resistant population should be less likely to emerge. However, before the likelihood of resistance to these novel drugs emerging can be predicted, we must first establish whether such drugs can actually be effective. Many believe that anti-virulence drugs would not be powerful enough to clear existing infections, restricting their potential application to prophylaxis. We have developed a mathematical model that provides a theoretical framework to reveal the circumstances under which anti-virulence drugs may or may not be successful. We demonstrate that by harnessing and combining the advantages of antibiotics with those provided by anti-virulence drugs, given infection-specific parameters, it is possible to identify treatment strategies that would efficiently clear bacterial infections, while preventing the emergence of antibiotic-resistant subpopulations. Our findings strongly support the continuation of research into anti-virulence drugs and demonstrate that their applicability may reach beyond infection prevention. Copyright © 2015 The Authors. Published by

  18. Nonlinear Stochastic Modelling of Antimicrobial resistance in Bacterial Populations

    DEFF Research Database (Denmark)

    Philipsen, Kirsten Riber

    an important role for the evolution of resistance. When growing under stressed conditions, such as in the presence of antibiotics, mutators are considered to have an advantages in comparison to non-mutators. This has been supported by a mathematical model for competing growth between a mutator and a non......This thesis applies mathematical modelling and statistical methods to investigate the dynamics and mechanisms of bacterial evolution. More specifically it is concerned with the evolution of antibiotic resistance in bacteria populations, which is an increasing problem for the treatment of infections...... in humans and animals. To prevent the evolution and spread of resistance, there is a need for further understanding of its dynamics. A grey-box modelling approach based on stochastic differential equations is the main and innovative method applied to study bacterial systems in this thesis. Through...

  19. Synchronization and survival of connected bacterial populations

    Science.gov (United States)

    Gokhale, Shreyas; Conwill, Arolyn; Ranjan, Tanvi; Gore, Jeff

    Migration plays a vital role in controlling population dynamics of species occupying distinct habitat patches. While local populations are vulnerable to extinction due to demographic or environmental stochasticity, migration from neighboring habitat patches can rescue these populations through colonization of uninhabited regions. However, a large migratory flux can synchronize the population dynamics in connected patches, thereby enhancing the risk of global extinction during periods of depression in population size. Here, we investigate this trade-off between local rescue and global extinction experimentally using laboratory populations of E. coli bacteria. Our model system consists of co-cultures of ampicillin resistant and chloramphenicol resistant strains that form a cross-protection mutualism and exhibit period-3 oscillations in the relative population density in the presence of both antibiotics. We quantify the onset of synchronization of oscillations in a pair of co-cultures connected by migration and demonstrate that period-3 oscillations can be disturbed for moderate rates of migration. These features are consistent with simulations of a mechanistic model of antibiotic deactivation in our system. The simulations further predict that the probability of survival of connected populations in high concentrations of antibiotics is maximized at intermediate migration rates. We verify this prediction experimentally and show that survival is enhanced through a combination of disturbance of period-3 oscillations and stochastic re-colonization events.

  20. The impact of natural transformation on adaptation in spatially structured bacterial populations

    OpenAIRE

    Moradigaravand, Danesh; Engelstädter, Jan

    2014-01-01

    Background Recent studies have demonstrated that natural transformation and the formation of highly structured populations in bacteria are interconnected. In spite of growing evidence about this connection, little is known about the dynamics of natural transformation in spatially structured bacterial populations. Results In this work, we model the interdependency between the dynamics of the bacterial gene pool and those of environmental DNA in space to dissect the effect of transformation on ...

  1. Efeito do cultivo da soja na dinâmica da população bacteriana, em solos de cerrado Effects of soybean cultivation on the bacterial population dynamics in cerrado soils

    Directory of Open Access Journals (Sweden)

    JOÃO CARLOS PEREIRA

    2000-06-01

    Full Text Available Este trabalho teve por objetivo avaliar a influência do cultivo da soja sobre a dinâmica da população bacteriana, em dois solos de Cerrado do Estado de São Paulo, originalmente cobertos com Paspalum notatum (em Barretos e Brachiaria decumbens (em S��o Carlos. Nesses solos, a densidade da população de bactérias em geral variou de 398,1 x 10³ a 467,7 x 10³ e de 123 x 10³ a 218,8 x 10³ ufc (unidades formadoras de colônias/g de solo seco, respectivamente. O cultivo da soja, em ambos os solos, resultou em incrementos variados nos números de ufc/g de solo seco da população de bactérias em geral, das resistentes aos antibióticos estreptomicina e cloranfenicol, e de actinomicetos. A população de actinomicetos ocorreu no solo principalmente como esporos, e as variações das relações esporos/hifas entre os solos não-rizosférico e rizosférico não foram significativas. Os resultados evidenciam que o cultivo da soja influenciou de forma diferenciada a população desses solos.The effect of soybean cultivation on the population dynamics of the bacterial community was evaluated in two "Cerrado" soils of São Paulo State, Brazil. The experimental areas, in the vicinities of the cities of São Carlos and Barretos, were previously cultivated, respectively, with Paspalum notatum and Brachiaria decumbens. The bacterial population densities in these soils varied from 398.1 x 10³ to 467.7 x 10³ cfu (colony forming units and from 123 x 10³ to 218.8 x 10³ cfu/g of dried soil, respectively, in São Carlos and Barretos soils. Soybean cultivation in both soils resulted in increments in the total bacterial population density, in the actinomycetes population, and in the bacterial population resistant to the antibiotics streptomycin and chloramphenicol. Actinomycetes were present in these soils mainly as spores. Soybean cultivation did not alter the actinomycetes spores/hyphae ratio when comparing rhizospheric and non-rhizospheric soils

  2. 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

  3. Bacterial Pneumonia in Elderly Japanese Populations

    Directory of Open Access Journals (Sweden)

    Naoya Miyashita

    2018-01-01

    Full Text Available Bacterial pneumonia is one of the most important infectious diseases in terms of incidence, effect on quality of life, mortality, and impact on society. Pneumonia was the third leading cause of death in Japan in 2011. In 2016, 119 650 Japanese people died of pneumonia, 96% of whom were aged 65 years and above. The symptoms of pneumonia in elderly people are often atypical. Aspiration pneumonia is seen more frequently than in young people because of swallowing dysfunction in the elderly. The mortality rate is also higher in the elderly than in young people. In Japan, the population is aging at an unprecedented rate, and pneumonia in the elderly will be increasingly important in medicine and medical economics in the future. To manage pneumonia in the elderly, it is important to accurately evaluate its severity, administer appropriate antibiotic treatment, and implement effective preventive measures.

  4. Detecting rare gene transfer events in bacterial populations

    Directory of Open Access Journals (Sweden)

    Kaare Magne Nielsen

    2014-01-01

    Full Text Available Horizontal gene transfer (HGT enables bacteria to access, share, and recombine genetic variation, resulting in genetic diversity that cannot be obtained through mutational processes alone. In most cases, the observation of evolutionary successful HGT events relies on the outcome of initially rare events that lead to novel functions in the new host, and that exhibit a positive effect on host fitness. Conversely, the large majority of HGT events occurring in bacterial populations will go undetected due to lack of replication success of transformants. Moreover, other HGT events that would be highly beneficial to new hosts can fail to ensue due to lack of physical proximity to the donor organism, lack of a suitable gene transfer mechanism, genetic compatibility, and stochasticity in tempo-spatial occurrence. Experimental attempts to detect HGT events in bacterial populations have typically focused on the transformed cells or their immediate offspring. However, rare HGT events occurring in large and structured populations are unlikely to reach relative population sizes that will allow their immediate identification; the exception being the unusually strong positive selection conferred by antibiotics. Most HGT events are not expected to alter the likelihood of host survival to such an extreme extent, and will confer only minor changes in host fitness. Due to the large population sizes of bacteria and the time scales involved, the process and outcome of HGT are often not amenable to experimental investigation. Population genetic modeling of the growth dynamics of bacteria with differing HGT rates and resulting fitness changes is therefore necessary to guide sampling design and predict realistic time frames for detection of HGT, as it occurs in laboratory or natural settings. Here we review the key population genetic parameters, consider their complexity and highlight knowledge gaps for further research.

  5. Evolutionary dynamics of diploid populations

    Science.gov (United States)

    Desimone, Ralph; Newman, Timothy

    2003-10-01

    There has been much recent interest in constructing computer models of evolutionary dynamics. Typically these models focus on asexual population dynamics, which are appropriate for haploid organsims such as bacteria. Using a recently developed ``genome template'' model, we extend the algorithm to a sexual population of diploid organisms. We will present some early results showing the temporal evolution of mean fitness and genetic variation, and compare this to typical results from haploid populations.

  6. Bacterial populations and the volatilome associated to meat spoilage.

    Science.gov (United States)

    Casaburi, Annalisa; Piombino, Paola; Nychas, George-John; Villani, Francesco; Ercolini, Danilo

    2015-02-01

    Microbial spoilage of meat is a complex event to which many different bacterial populations can contribute depending on the temperature of storage and packaging conditions. The spoilage can derive from microbial development and consumption of meat nutrients by bacteria with a consequent release of undesired metabolites. The volatile organic compounds (VOCs) that are generated during meat storage can have an olfactory impact and can lead to rejection of the product when their concentration increase significantly as a result of microbial development. The VOCs most commonly identified in meat during storage include alcohols, aldehydes, ketones, fatty acids, esters and sulfur compounds. In this review, the VOCs found in fresh meat during storage in specific conditions are described together with the possible bacterial populations responsible of their production. In addition, on the basis of the data available in the literature, the sensory impact of the VOCs and their dynamics during storage is discussed to highlight their possible contribution to the spoilage of meat. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. The impact of natural transformation on adaptation in spatially structured bacterial populations.

    Science.gov (United States)

    Moradigaravand, Danesh; Engelstädter, Jan

    2014-06-20

    Recent studies have demonstrated that natural transformation and the formation of highly structured populations in bacteria are interconnected. In spite of growing evidence about this connection, little is known about the dynamics of natural transformation in spatially structured bacterial populations. In this work, we model the interdependency between the dynamics of the bacterial gene pool and those of environmental DNA in space to dissect the effect of transformation on adaptation. Our model reveals that even with only a single locus under consideration, transformation with a free DNA fragment pool results in complex adaptation dynamics that do not emerge in previous models focusing only on the gene shuffling effect of transformation at multiple loci. We demonstrate how spatial restriction on population growth and DNA diffusion in the environment affect the impact of transformation on adaptation. We found that in structured bacterial populations intermediate DNA diffusion rates predominantly cause transformation to impede adaptation by spreading deleterious alleles in the population. Overall, our model highlights distinctive evolutionary consequences of bacterial transformation in spatially restricted compared to planktonic bacterial populations.

  8. Dynamic Viscoelasticity of Individual Bacterial Cells

    Science.gov (United States)

    Vadillo-Rodriguez, Virginia; Dutcher, John

    2009-03-01

    We have used an AFM-based approach to probe the mechanical properties of single bacterial cells (gram-negative Escherichia coli K12) by applying a constant compressive force to the cell under fluid conditions while measuring the time-dependent displacement (creep) of a colloidal AFM tip due to the viscoelastic properties of the cell. We observed that the cells exhibited a viscoelastic solid-like behavior with retarded elasticity, i.e. both an instantaneous and a delayed elastic deformation, which is well described by a three-parameter mechanical model. Using the best fit parameter values, we have calculated the dynamic viscoelastic behavior of the cells over a wide range of frequencies based on a numerical time-frequency transform technique and we have compared the calculated behavior with that measured experimentally. Comparison of the results obtained for E. coli with previously reported data on the mechanical properties of others gram-negative cells and their isolated surface layers suggests that the elastic component of the cell viscoelastic response is dominated by the properties of the peptidoglycan layer, whereas the viscous component likely arises from the liquid-like character of the cell membranes.

  9. Africa population dynamics

    OpenAIRE

    Akinyoade, A.; Damen, J.C.M.; Dietz, A.J.; Kilama, B.B.; Omme, van, G.

    2014-01-01

    Africa's population has grown extremely rapidly over the last fifty years from 289 million inhabitants in 1961 to more than 1 billion today. This is a growth rate of 350% in just half a century and the number of urban residents has increased even more quickly: from 65 million in 1960 to 460 million today, or from 20% to 46% of the population as a whole. Demographers predict that soon more than 50% of all Africans will be living in cities. The average life expectancy, literacy rates and primar...

  10. Africa population dynamics

    NARCIS (Netherlands)

    Akinyoade, A.; Damen, J.C.M.; Dietz, A.J.; Kilama, B.B.; Omme, van G.

    2014-01-01

    Africa's population has grown extremely rapidly over the last fifty years from 289 million inhabitants in 1961 to more than 1 billion today. This is a growth rate of 350% in just half a century and the number of urban residents has increased even more quickly: from 65 million in 1960 to 460 million

  11. Dynamical systems in population biology

    CERN Document Server

    Zhao, Xiao-Qiang

    2017-01-01

    This research monograph provides an introduction to the theory of nonautonomous semiflows with applications to population dynamics. It develops dynamical system approaches to various evolutionary equations such as difference, ordinary, functional, and partial differential equations, and pays more attention to periodic and almost periodic phenomena. The presentation includes persistence theory, monotone dynamics, periodic and almost periodic semiflows, basic reproduction ratios, traveling waves, and global analysis of prototypical population models in ecology and epidemiology. Research mathematicians working with nonlinear dynamics, particularly those interested in applications to biology, will find this book useful. It may also be used as a textbook or as supplementary reading for a graduate special topics course on the theory and applications of dynamical systems. Dr. Xiao-Qiang Zhao is a University Research Professor at Memorial University of Newfoundland, Canada. His main research interests involve applied...

  12. Mathematical Modelling of Bacterial Meningitis Transmission Dynamics with Control Measures

    Directory of Open Access Journals (Sweden)

    Joshua Kiddy K. Asamoah

    2018-01-01

    Full Text Available Vaccination and treatment are the most effective ways of controlling the transmission of most infectious diseases. While vaccination helps susceptible individuals to build either a long-term immunity or short-term immunity, treatment reduces the number of disease-induced deaths and the number of infectious individuals in a community/nation. In this paper, a nonlinear deterministic model with time-dependent controls has been proposed to describe the dynamics of bacterial meningitis in a population. The model is shown to exhibit a unique globally asymptotically stable disease-free equilibrium E0, when the effective reproduction number RVT≤1, and a globally asymptotically stable endemic equilibrium E1, when RVT>1; and it exhibits a transcritical bifurcation at RVT=1. Carriers have been shown (by Tornado plot to have a higher chance of spreading the infection than those with clinical symptoms who will sometimes be bound to bed during the acute phase of the infection. In order to find the best strategy for minimizing the number of carriers and ill individuals and the cost of control implementation, an optimal control problem is set up by defining a Lagrangian function L to be minimized subject to the proposed model. Numerical simulation of the optimal problem demonstrates that the best strategy to control bacterial meningitis is to combine vaccination with other interventions (such as treatment and public health education. Additionally, this research suggests that stakeholders should press hard for the production of existing/new vaccines and antibiotics and their disbursement to areas that are most affected by bacterial meningitis, especially Sub-Saharan Africa; furthermore, individuals who live in communities where the environment is relatively warm (hot/moisture are advised to go for vaccination against bacterial meningitis.

  13. Population Bottlenecks Promote Cooperation in Bacterial Biofilms

    OpenAIRE

    Brockhurst, Michael A.

    2007-01-01

    Population bottlenecks are assumed to play a key role in the maintenance of social traits in microbes. Ecological parameters such as colonisation or disturbances can favour cooperation through causing population bottlenecks that enhance genetic structuring (relatedness). However, the size of the population bottleneck is likely to play a crucial role in determining the success of cooperation. Relatedness is likely to increase with decreasing bottleneck size thus favouring the evolution of coop...

  14. Measurement of Behavioral Evolution in Bacterial Populations

    Science.gov (United States)

    Austin, Robert

    2013-03-01

    A curious aspect of bacterial behavior under stress is the induction of filamentation: the anomalous growth of certain bacteria in which cells continue to elongate but do not divide into progeny. We show that E.coli under the influence of the genotoxic antibiotic ciprofloxacin have robust filamentous growth, which provides individual bacteria a mesoscopic niche for evolution until resistant progeny can bud off and propagate. Hence, filamentation is a form of genomic amplification where even a single, isolated bacteria can have access to multiple genomes. We propose a model that predicts that the first arrival time of the normal sized progeny should follow a Gompertz distribution with the mean first arrival time proportional to the elongation rate of filament. These predictions agree with our experimental measurements. Finally, we suggest bacterial filament growth and budding has many similarities to tumor growth and metastasis and can serve as a simpler model to study those complicated processes. Sponsored by the NCI/NIH Physical Sciences Oncology Centers

  15. Abundance of three bacterial populations in selected streams

    Science.gov (United States)

    O.A. Olapade; X. Gao; L.G. LEff

    2005-01-01

    The population sizes of three bacterial species, Acinetobacter calcoaceticw, Burkholderia cepacia, and Pseudomonas putida, were examined in water and sediment from nine streams in different parts of the United States using fluorescent in situ hybridization (FISH). Population sizes were determined from three sites (upstream,...

  16. Evolutionary dynamics in structured populations

    Science.gov (United States)

    Nowak, Martin A.; Tarnita, Corina E.; Antal, Tibor

    2010-01-01

    Evolutionary dynamics shape the living world around us. At the centre of every evolutionary process is a population of reproducing individuals. The structure of that population affects evolutionary dynamics. The individuals can be molecules, cells, viruses, multicellular organisms or humans. Whenever the fitness of individuals depends on the relative abundance of phenotypes in the population, we are in the realm of evolutionary game theory. Evolutionary game theory is a general approach that can describe the competition of species in an ecosystem, the interaction between hosts and parasites, between viruses and cells, and also the spread of ideas and behaviours in the human population. In this perspective, we review the recent advances in evolutionary game dynamics with a particular emphasis on stochastic approaches in finite sized and structured populations. We give simple, fundamental laws that determine how natural selection chooses between competing strategies. We study the well-mixed population, evolutionary graph theory, games in phenotype space and evolutionary set theory. We apply these results to the evolution of cooperation. The mechanism that leads to the evolution of cooperation in these settings could be called ‘spatial selection’: cooperators prevail against defectors by clustering in physical or other spaces. PMID:20008382

  17. Bayesian modeling of bacterial growth for multiple populations

    OpenAIRE

    Palacios, Ana Paula; Marín, J. Miguel; Quinto, Emiliano J.; Wiper, Michael P.

    2014-01-01

    Bacterial growth models are commonly used for the prediction of microbial safety and the shelf life of perishable foods. Growth is affected by several environmental factors such as temperature, acidity level and salt concentration. In this study, we develop two models to describe bacterial growth for multiple populations under both equal and different environmental conditions. Firstly, a semi-parametric model based on the Gompertz equation is proposed. Assuming that the parameters of the Gomp...

  18. Bayesian modelling of bacterial growth for multiple populations

    OpenAIRE

    Palacios, Ana Paula; Marín Díazaraque, Juan Miguel; Quinto, Emiliano; Wiper, Michael Peter

    2012-01-01

    Bacterial growth models are commonly used for the prediction of microbial safety and the shelf life of perishable foods. Growth is affected by several environmental factors such as temperature, acidity level and salt concentration. In this study, we develop two models to describe bacterial growth for multiple populations under both equal and different environmental conditions. Firstly, a semi-parametric model based on the Gompertz equation is proposed. Assuming that the parameters of the Gomp...

  19. Population dynamics in variable environments

    CERN Document Server

    Tuljapurkar, Shripad

    1990-01-01

    Demography relates observable facts about individuals to the dynamics of populations. If the dynamics are linear and do not change over time, the classical theory of Lotka (1907) and Leslie (1945) is the central tool of demography. This book addresses the situation when the assumption of constancy is dropped. In many practical situations, a population will display unpredictable variation over time in its vital rates, which must then be described in statistical terms. Most of this book is concerned with the theory of populations which are subject to random temporal changes in their vital rates, although other kinds of variation (e. g. , cyclical) are also dealt with. The central questions are: how does temporal variation work its way into a population's future, and how does it affect our interpretation of a population's past. The results here are directed at demographers of humans and at popula­ tion biologists. The uneven mathematical level is dictated by the material, but the book should be accessible to re...

  20. The population dynamics of bacteria, phage and RM Systems

    Science.gov (United States)

    Guet, Calin; Levin, Bruce; Pleska, Maros

    Viruses drive and mediate bacterial evolution as parasites and vectors of horizontal gene transfer, respectively. Temperate bacteriophages, defined by the ability to lysogenize a fraction of hosts and to transmit horizontally as well as vertically in the form of prophages, frequently carry genes that increase fitness or contribute to bacterial pathogenicity. Restriction-modification (RM) systems, which are widely diverse and ubiquitous among bacteria, can prevent infections leading to lysis, but their effect on lysogeny is not clear. We show that RM systems prevent lytic and lysogenic infections to the same extent and therefore represent a molecular barrier to prophage acquisition. Surprisingly, we find that this negative effect can be overcome and even reversed at the population level, as a consequence of dynamic interactions between viruses, hosts and RM systems. Thus the population dynamics of bacteria carrying RM systems impacts bacterial genome-wide evolution. .

  1. BSim: an agent-based tool for modeling bacterial populations in systems and synthetic biology.

    Directory of Open Access Journals (Sweden)

    Thomas E Gorochowski

    Full Text Available Large-scale collective behaviors such as synchronization and coordination spontaneously arise in many bacterial populations. With systems biology attempting to understand these phenomena, and synthetic biology opening up the possibility of engineering them for our own benefit, there is growing interest in how bacterial populations are best modeled. Here we introduce BSim, a highly flexible agent-based computational tool for analyzing the relationships between single-cell dynamics and population level features. BSim includes reference implementations of many bacterial traits to enable the quick development of new models partially built from existing ones. Unlike existing modeling tools, BSim fully considers spatial aspects of a model allowing for the description of intricate micro-scale structures, enabling the modeling of bacterial behavior in more realistic three-dimensional, complex environments. The new opportunities that BSim opens are illustrated through several diverse examples covering: spatial multicellular computing, modeling complex environments, population dynamics of the lac operon, and the synchronization of genetic oscillators. BSim is open source software that is freely available from http://bsim-bccs.sf.net and distributed under the Open Source Initiative (OSI recognized MIT license. Developer documentation and a wide range of example simulations are also available from the website. BSim requires Java version 1.6 or higher.

  2. Mucin dynamics in intestinal bacterial infection.

    Directory of Open Access Journals (Sweden)

    Sara K Lindén

    Full Text Available Bacterial gastroenteritis causes morbidity and mortality in humans worldwide. Murine Citrobacter rodentium infection is a model for gastroenteritis caused by the human pathogens enteropathogenic Escherichia coli and enterohaemorrhagic E. coli. Mucin glycoproteins are the main component of the first barrier that bacteria encounter in the intestinal tract.Using Immunohistochemistry, we investigated intestinal expression of mucins (Alcian blue/PAS, Muc1, Muc2, Muc4, Muc5AC, Muc13 and Muc3/17 in healthy and C. rodentium infected mice. The majority of the C. rodentium infected mice developed systemic infection and colitis in the mid and distal colon by day 12. C. rodentium bound to the major secreted mucin, Muc2, in vitro, and high numbers of bacteria were found in secreted MUC2 in infected animals in vivo, indicating that mucins may limit bacterial access to the epithelial surface. In the small intestine, caecum and proximal colon, the mucin expression was similar in infected and non-infected animals. In the distal colonic epithelium, all secreted and cell surface mucins decreased with the exception of the Muc1 cell surface mucin which increased after infection (p<0.05. Similarly, during human infection Salmonella St Paul, Campylobacter jejuni and Clostridium difficile induced MUC1 in the colon.Major changes in both the cell-surface and secreted mucins occur in response to intestinal infection.

  3. Metabolic competition as a driver of bacterial population structure.

    Science.gov (United States)

    Watkins, Eleanor R; Maiden, Martin Cj; Gupta, Sunetra

    2016-10-01

    Understanding the processes whereby diversity arises and is maintained in pathogen populations is pivotal for designing disease control interventions. A particular problem is the maintenance of strain structure in bacterial pathogen populations despite frequent genetic exchange. Although several theoretical frameworks have been put forward to explain this widespread phenomenon, few have focused on the role of genes encoding metabolic functions, despite an increasing recognition of their importance in pathogenesis and transmission. In this article, we review the literature for evidence of metabolic niches within the host and discuss theoretical frameworks which examine ecological interactions between metabolic genes. We contend that metabolic competition is an important phenomenon which contributes to the maintenance of population structure and diversity of many bacterial pathogens.

  4. In Situ Hydrocarbon Degradation by Indigenous Nearshore Bacterial Populations

    International Nuclear Information System (INIS)

    Cherrier, J.

    2005-01-01

    Potential episodic hydrocarbon inputs associated with oil mining and transportation together with chronic introduction of hydrocarbons via urban runoff into the relatively pristine coastal Florida waters poses a significant threat to Florida's fragile marine environment. It is therefore important to understand the extent to which indigenous bacterial populations are able to degrade hydrocarbon compounds and also determine factors that could potentially control and promote the rate at which these compounds are broken down in situ. Previous controlled laboratory experiments carried out by our research group demonstrated that separately both photo-oxidation and cometabolism stimulate bacterial hydrocarbon degradation by natural bacterial assemblages collected from a chronically petroleum contaminated site in Bayboro Bay, Florida. Additionally, we also demonstrated that stable carbon and radiocarbon abundances of respired CO 2 could be used to trace in situ hydrocarbon degradation by indigenous bacterial populations at this same site. This current proposal had two main objectives: (a) to evaluate the cumulative impact of cometabolism and photo-oxidation on hydrocarbon degradation by natural bacterial assemblages collected the same site in Bayboro Bay, Florida and (b) to determine if in situ hydrocarbon degradation by indigenous bacterial populations this site could be traced using natural radiocarbon and stable carbon abundances of assimilated bacterial carbon. Funds were used for 2 years of full support for one ESI Ph.D. student, April Croxton. To address our first objective a series of closed system bacterial incubations were carried out using photo-oxidized petroleum and pinfish (i.e. cometabolite). Bacterial production of CO 2 was used as the indicator of hydrocarbon degradation and (delta) 13 C analysis of the resultant CO 2 was used to evaluate the source of the respired CO 2 (i.e. petroleum hydrocarbons or the pinfish cometabolite). Results from these time

  5. Nonlinear dynamics of interacting populations

    CERN Document Server

    Bazykin, Alexander D

    1998-01-01

    This book contains a systematic study of ecological communities of two or three interacting populations. Starting from the Lotka-Volterra system, various regulating factors are considered, such as rates of birth and death, predation and competition. The different factors can have a stabilizing or a destabilizing effect on the community, and their interplay leads to increasingly complicated behavior. Studying and understanding this path to greater dynamical complexity of ecological systems constitutes the backbone of this book. On the mathematical side, the tool of choice is the qualitative the

  6. Flood trends and population dynamics

    Science.gov (United States)

    Di Baldassarre, G.

    2012-04-01

    Since the earliest recorded civilizations, such as those in Mesopotamia and Egypt that developed in the fertile floodplains of the Tigris and Euphrates and Nile rivers, humans tend to settle in flood prone areas as they offer favorable conditions for economic development. However, floodplains are also exposed to flood disasters that might cause severe socio-economic and environmental damages not to mention losses of human lives. A flood event turns to be a disaster when it coincides with a vulnerable environment exceeding society's capacity to manage the adverse consequences. This presentation discusses the link between hydrological risk and population change by referring to the outcomes of scientific works recently carried out in Africa and Europe. More specifically, it is shown that the severity of flood disasters, currently affecting more than 100 million people a year, might be seriously exacerbated because of population change. In fact, flood exposure and/or vulnerability might increase because of rapid population growth (and its spatial and temporal dynamics, e.g. urbanization) in the African continent and because of population ageing in many European countries. Lastly, timely and economically sustainable actions to mitigate this increasing hydrological risk are critically evaluated.

  7. Bacterial dynamics in a microphytobenthic biofilm: A tidal mesocosm approach

    Science.gov (United States)

    Agogué, Hélène; Mallet, Clarisse; Orvain, Francis; De Crignis, Margot; Mornet, Françoise; Dupuy, Christine

    2014-09-01

    In intertidal mudflats, during low tide exposure, microphytobenthos (MPB) migrate vertically through the surface sediment and form, with the heterotrophic bacteria, a transient biofilm. Inside this biofilm, multiple interactions exist between MPB and bacteria. These micro-organisms secrete a wide range of extracellular polymeric substances (EPS), which are major components of the biofilm matrix. In this study, we used a tidal mesocosm experiment in order to decipher the interactions of the MPB-EPS-bacteria complex within the biofilm. We tried to determine if the EPS could control bacterial activities and/or production and/or richness according to the age of the biofilm and to the immersion/emersion period. The dynamics of biomasses of MPB and prokaryotes, the bacterial production, the hydrolysis of predominating organic constituents in the dissolved organic carbon (DOC) pool (i.e., carbohydrates and polypeptides), and the bacterial structure were studied in relation to the different EPS fractions (carbohydrates and proteins: colloidal and bound) dynamics during 8 days. Our experiment had emphasized the influence of the environmental conditions (light, immersion/emersion) on the interactions within the biofilm and also on the effects on biofilm aging. Bacterial production was always inhibited by the bound EPS-carbohydrate, especially during low tide. Our results suggest that the concentration and composition of EPS had a major role in the bacterial/MPB interactions: these interactions can be either positive or negative in order to regulate the productive phases of MPB and bacteria.

  8. Atypical bacterial pneumonia in the HIV-infected population.

    Science.gov (United States)

    Head, Breanne M; Trajtman, Adriana; Rueda, Zulma V; Vélez, Lázaro; Keynan, Yoav

    2017-01-01

    Human immunodeficiency virus (HIV)-infected individuals are more susceptible to respiratory tract infections by other infectious agents (viruses, bacteria, parasites, and fungi) as their disease progresses to acquired immunodeficiency syndrome. Despite effective antiretroviral therapy, bacterial pneumonia (the most frequently occurring HIV-associated pulmonary illness) remains a common cause of morbidity and mortality in the HIV-infected population. Over the last few decades, studies have looked at the role of atypical bacterial pneumonia (i.e. pneumonia that causes an atypical clinical presentation or responds differently to typical therapeutics) in association with HIV infection. Due to the lack of available diagnostic strategies, the lack of consideration, and the declining immunity of the patient, HIV co-infections with atypical bacteria are currently believed to be underreported. Thus, following an extensive database search, this review aimed to highlight the current knowledge and gaps regarding atypical bacterial pneumonia in HIV. The authors discuss the prevalence of Chlamydophila pneumoniae , Mycoplasma pneumoniae , Coxiella burnetii , Legionella species and others in the HIV-infected population as well as their clinical presentation, methods of detection, and treatment. Further studies looking at the role of these microbes in association with HIV are required. Increased knowledge of these atypical bacteria will lead to a more rapid diagnosis of these infections, resulting in an improved quality of life for the HIV-infected population.

  9. Assessment of bacterial and structural dynamics in aerobic granular biofilms

    Directory of Open Access Journals (Sweden)

    David G. Weissbrodt

    2013-07-01

    Full Text Available Aerobic granular sludge is based on self-granulated flocs forming mobile biofilms with a gel-like consistence. Bacterial and structural dynamics from flocs to granules were followed in anaerobic-aerobic sequencing batch reactors fed with synthetic wastewater, namely a bubble column (BC-SBR operated under wash-out conditions for fast granulation, and two stirred-tank enrichments of Accumulibacter (PAO-SBR and Competibacter (GAO-SBR operated at steady-state. In the BC-SBR, granules formed within two weeks by swelling of Zoogloea colonies around flocs, developing subsequently smooth zoogloeal biofilms. However, Zoogloea predominance (37-79% led to deteriorated nutrient removal during the first months of reactor operation. Upon maturation, improved nitrification (80-100%, nitrogen removal (43-83%, and high but unstable dephosphatation (75-100% were obtained. Proliferation of dense clusters of nitrifiers, Accumulibacter, and Competibacter from granule cores outwards resulted in heterogeneous bioaggregates, inside which only low abundance Zoogloea (<5% were detected in biofilm interstices. The presence of different extracellular glycoconjugates detected by fluorescence lectin-binding analysis showed the complex nature of the intracellular matrix of these granules. In the PAO-SBR, granulation occurred within two months with abundant and active Accumulibacter populations (56±10% that were selected under full anaerobic uptake of volatile fatty acids and that aggregated as dense clusters within heterogeneous granules. Flocs self-granulated in the GAO-SBR after 480 days during a period of over-aeration caused by biofilm growth on the oxygen sensor. Granules were dominated by heterogeneous clusters of Competibacter (37±11%. Zoogloea were never abundant in biomass of both PAO- and GAO-SBRs. This study showed that Zoogloea, Accumulibacter, and Competibacter affiliates can form granules, and that the granulation mechanisms rely on the dominant population

  10. Effect of isolate of ruminal fibrolytic bacterial culture supplementation on fibrolytic bacterial population and survivability of inoculated bacterial strain in lactating Murrah buffaloes

    Directory of Open Access Journals (Sweden)

    Brishketu Kumar

    2013-02-01

    Full Text Available Aim: The present study was conducted to evaluate the effect of bacterial culture supplementation on ruminal fibrolytic bacterial population as well as on survivability of inoculated bacterial strain in lactating Murrah buffaloes kept on high fibre diet. Materials and Methods: Fibrolytic bacterial strains were isolated from rumen liquor of fistulated Murrah buffaloes and live bacterial culture were supplemented orally in treatment group of lactating Murrah buffaloes fed on high fibre diet to see it's effect on ruminal fibrolytic bacterial population as well as to see the effect of survivability of the inoculated bacterial strain at three different time interval in comparison to control group. Results: It has been shown by real time quantification study that supplementation of bacterial culture orally increases the population of major fibre degrading bacteria i.e. Ruminococcus flavefaciens, Ruminococcus albus as well as Fibrobacter succinogenes whereas there was decrease in secondary fibre degrading bacterial population i.e. Butyrivibrio fibrisolvens over the different time periods. However, the inoculated strain of Ruminococcus flavefaciens survived significantly over the period of time, which was shown in stability of increased inoculated bacterial population. Conclusion: The isolates of fibrolytic bacterial strains are found to be useful in increasing the number of major ruminal fibre degrading bacteria in lactating buffaloes and may act as probiotic in large ruminants on fibre-based diets. [Vet World 2013; 6(1.000: 14-17

  11. Population dynamics and biology of an invasive population of ...

    African Journals Online (AJOL)

    Population dynamics and biology of an invasive population of mosquitofish Gambusia affinis in a temperate estuarine lake system. Hans Sloterdijk, Nicola C. James, M Kyle S. Smith, Werner Ekau, Olaf L.F. Weyl ...

  12. Analysis of Population Dynamics in World Economy

    OpenAIRE

    Martin, Gress

    2011-01-01

    Population dynamics is an important topic in current world economy. The size and growth of population have an impact on economic growth and development of individual countries and vice versa, economic development influences demographic variables in a country. The aim of the article is to analyze historical development of world population, population stock change and relations between population stock change and economic development.

  13. Bacterial Associates Modify Growth Dynamics of the Dinoflagellate Gymnodinium catenatum.

    Science.gov (United States)

    Bolch, Christopher J S; Bejoy, Thaila A; Green, David H

    2017-01-01

    Marine phytoplankton cells grow in close association with a complex microbial associate community known to affect the growth, behavior, and physiology of the algal host. The relative scale and importance these effects compared to other major factors governing algal cell growth remain unclear. Using algal-bacteria co-culture models based on the toxic dinoflagellate Gymnodinium catenatum , we tested the hypothesis that associate bacteria exert an independent effect on host algal cell growth. Batch co-cultures of G. catenatum were grown under identical environmental conditions with simplified bacterial communities composed of one-, two-, or three-bacterial associates. Modification of the associate community membership and complexity induced up to four-fold changes in dinoflagellate growth rate, equivalent to the effect of a 5°C change in temperature or an almost six-fold change in light intensity (20-115 moles photons PAR m -2 s -1 ). Almost three-fold changes in both stationary phase cell concentration and death rate were also observed. Co-culture with Roseobacter sp. DG874 reduced dinoflagellate exponential growth rate and led to a more rapid death rate compared with mixed associate community controls or co-culture with either Marinobacter sp. DG879, Alcanivorax sp. DG881. In contrast, associate bacteria concentration was positively correlated with dinoflagellate cell concentration during the exponential growth phase, indicating growth was limited by supply of dinoflagellate-derived carbon. Bacterial growth increased rapidly at the onset of declining and stationary phases due to either increasing availability of algal-derived carbon induced by nutrient stress and autolysis, or at mid-log phase in Roseobacter co-cultures potentially due to the onset of bacterial-mediated cell lysis. Co-cultures with the three bacterial associates resulted in dinoflagellate and bacterial growth dynamics very similar to more complex mixed bacterial community controls, suggesting that

  14. Disentangling seasonal bacterioplankton population dynamics by high-frequency sampling.

    Science.gov (United States)

    Lindh, Markus V; Sjöstedt, Johanna; Andersson, Anders F; Baltar, Federico; Hugerth, Luisa W; Lundin, Daniel; Muthusamy, Saraladevi; Legrand, Catherine; Pinhassi, Jarone

    2015-07-01

    Multiyear comparisons of bacterioplankton succession reveal that environmental conditions drive community shifts with repeatable patterns between years. However, corresponding insight into bacterioplankton dynamics at a temporal resolution relevant for detailed examination of variation and characteristics of specific populations within years is essentially lacking. During 1 year, we collected 46 samples in the Baltic Sea for assessing bacterial community composition by 16S rRNA gene pyrosequencing (nearly twice weekly during productive season). Beta-diversity analysis showed distinct clustering of samples, attributable to seemingly synchronous temporal transitions among populations (populations defined by 97% 16S rRNA gene sequence identity). A wide spectrum of bacterioplankton dynamics was evident, where divergent temporal patterns resulted both from pronounced differences in relative abundance and presence/absence of populations. Rates of change in relative abundance calculated for individual populations ranged from 0.23 to 1.79 day(-1) . Populations that were persistently dominant, transiently abundant or generally rare were found in several major bacterial groups, implying evolution has favoured a similar variety of life strategies within these groups. These findings suggest that high temporal resolution sampling allows constraining the timescales and frequencies at which distinct populations transition between being abundant or rare, thus potentially providing clues about physical, chemical or biological forcing on bacterioplankton community structure. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  15. Seasonal dynamics of bacterial meningitis: a time-series analysis.

    Science.gov (United States)

    Paireau, Juliette; Chen, Angelica; Broutin, Helene; Grenfell, Bryan; Basta, Nicole E

    2016-06-01

    Bacterial meningitis, which is caused mainly by Neisseria meningitidis, Haemophilus influenzae, and Streptococcus pneumoniae, inflicts a substantial burden of disease worldwide. Yet, the temporal dynamics of this disease are poorly characterised and many questions remain about the ecology of the disease. We aimed to comprehensively assess seasonal trends in bacterial meningitis on a global scale. We developed the first bacterial meningitis global database by compiling monthly incidence data as reported by country-level surveillance systems. Using country-level wavelet analysis, we identified whether a 12 month periodic component (annual seasonality) was detected in time-series that had at least 5 years of data with at least 40 cases reported per year. We estimated the mean timing of disease activity by computing the centre of gravity of the distribution of cases and investigated whether synchrony exists between the three pathogens responsible for most cases of bacterial meningitis. We used country-level data from 66 countries, including from 47 countries outside the meningitis belt in sub-Saharan Africa. A persistent seasonality was detected in 49 (96%) of the 51 time-series from 38 countries eligible for inclusion in the wavelet analyses. The mean timing of disease activity had a latitudinal trend, with bacterial meningitis seasons peaking during the winter months in countries in both the northern and southern hemispheres. The three pathogens shared similar seasonality, but time-shifts differed slightly by country. Our findings provide key insight into the seasonal dynamics of bacterial meningitis and add to knowledge about the global epidemiology of meningitis and the host, environment, and pathogen characteristics driving these patterns. Comprehensive understanding of global seasonal trends in meningitis could be used to design more effective prevention and control strategies. Princeton University Health Grand Challenge, US National Institutes of Health (NIH

  16. Cooperative Bacterial Growth Dynamics Predict the Evolution of Antibiotic Resistance

    Science.gov (United States)

    Artemova, Tatiana; Gerardin, Ylaine; Hsin-Jung Li, Sophia; Gore, Jeff

    2011-03-01

    Since the discovery of penicillin, antibiotics have been our primary weapon against bacterial infections. Unfortunately, bacteria can gain resistance to penicillin by acquiring the gene that encodes beta-lactamase, which inactivates the antibiotic. However, mutations in this gene are necessary to degrade the modern antibiotic cefotaxime. Understanding the conditions that favor the spread of these mutations is a challenge. Here we show that bacterial growth in beta-lactam antibiotics is cooperative and that the nature of this growth determines the conditions in which resistance evolves. Quantitative analysis of the growth dynamics predicts a peak in selection at very low antibiotic concentrations; competition between strains confirms this prediction. We also find significant selection at higher antibiotic concentrations, close to the minimum inhibitory concentrations of the strains. Our results argue that an understanding of the evolutionary forces that lead to antibiotic resistance requires a quantitative understanding of the evolution of cooperation in bacteria.

  17. Population Dynamics of the Stationary Phase Utilizing the ARGOS Method

    Science.gov (United States)

    Algarni, S.; Charest, A. J.; Iannacchione, G. S.

    2015-03-01

    The Area Recorded Generalized Optical Scattering (ARGOS) approach to light scattering employs large image capture array allowing for a well-defined geometry in which images may be manipulated to extract structure with intensity at a specific scattering wave vector (I(q)) and dynamics with intensity at a specific scattering wave vector over time (I (q,t)). The ARGOS method provides morphological dynamics noninvasively over a long time period and allows for a variety of aqueous conditions. This is important because traditional growth models do not provide for conditions similar to the natural environment. The present study found that the population dynamics of bacteria do not follow a traditional growth model and that the ARGOS method allowed for the observation of bacterial changes in terms of individual particles and population dynamics in real time. The observations of relative total intensity suggest that there is no stationary phase and that the bacterial population demonstrates sinusoidal type patterns consistently subsequent to the log phase growth. These observation were compared to shape changes by modeling fractal dimension and size changes by modeling effective radius.

  18. Design and Evaluation of PCR Primers for Analysis of Bacterial Populations in Wine by Denaturing Gradient Gel Electrophoresis

    Science.gov (United States)

    Lopez, Isabel; Ruiz-Larrea, Fernanda; Cocolin, Luca; Orr, Erica; Phister, Trevor; Marshall, Megan; VanderGheynst, Jean; Mills, David A.

    2003-01-01

    Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified ribosomal DNA (rDNA) is routinely used to compare levels of diversity of microbial communities and to monitor population dynamics. While using PCR-DGGE to examine the bacteria in wine fermentations, we noted that several commonly used PCR primers for amplifying bacterial 16S rDNA also coamplified yeast, fungal, or plant DNA present in samples. Unfortunately, amplification of nonbacterial DNA can result in a masking of bacterial populations in DGGE profiles. To surmount this problem, we developed two new primer sets for specific amplification of bacterial 16S rDNA in wine fermentation samples without amplification of eukaryotic DNA. One primer set, termed WLAB1 and WLAB2, amplified lactic acid bacteria, while another, termed WBAC1 and WBAC2, amplified both lactic acid bacterial and acetic acid bacterial populations found in wine. Primer specificity and efficacy were examined with DNA isolated from numerous bacterial, yeast, and fungal species commonly found in wine and must samples. Importantly, both primer sets effectively distinguished bacterial species in wine containing mixtures of yeast and bacteria. PMID:14602643

  19. Leading edge gypsy moth population dynamics

    Science.gov (United States)

    M. R. Carter; F. W. Ravlin; M. L. McManus

    1991-01-01

    Leading edge gypsy moth populations have been the focus of several intervention programs (MDIPM, AIPM). Knowledge of gypsy moth population dynamics in leading edge area is crucial for effective management. Populations in these areas tend to reach outbreak levels (noticeable defoliation) within three to four years after egg masses are first detected. Pheromone traps...

  20. Bacterial population solitary waves can defeat rings of funnels

    International Nuclear Information System (INIS)

    Morris, Ryan J; Phan, Trung V; Austin, Robert H; Black, Matthew; Bos, Julia A; Lin, Ke-Chih; Kevrekidis, Ioannis G

    2017-01-01

    We have constructed a microfabricated circular corral for bacteria made of rings of concentric funnels which channel motile bacteria outwards via non-hydrodynamic interactions with the funnel walls. Initially bacteria do move rapidly outwards to the periphery of the corral. At the edge, nano-slits allow for the transport of nutrients into the device while keeping the bacteria from escaping. After a period of time in which the bacteria increase their cell density in this perimeter region, they are then able to defeat the physical constrains of the funnels by launching back-propagating collective waves. We present the basic data and some nonlinear modeling which can explain how bacterial population waves propagate through a physical funnel, and discuss possible biological implications. (paper)

  1. Bistable responses in bacterial genetic networks: Designs and dynamical consequences

    Science.gov (United States)

    Tiwari, Abhinav; Ray, J. Christian J.; Narula, Jatin; Igoshin, Oleg A.

    2011-01-01

    A key property of living cells is their ability to react to stimuli with specific biochemical responses. These responses can be understood through the dynamics of underlying biochemical and genetic networks. Evolutionary design principles have been well studied in networks that display graded responses, with a continuous relationship between input signal and system output. Alternatively, biochemical networks can exhibit bistable responses so that over a range of signals the network possesses two stable steady states. In this review, we discuss several conceptual examples illustrating network designs that can result in a bistable response of the biochemical network. Next, we examine manifestations of these designs in bacterial master-regulatory genetic circuits. In particular, we discuss mechanisms and dynamic consequences of bistability in three circuits: two-component systems, sigma-factor networks, and a multistep phosphorelay. Analyzing these examples allows us to expand our knowledge of evolutionary design principles for networks with bistable responses. PMID:21385588

  2. Comparing models of Red Knot population dynamics

    Science.gov (United States)

    McGowan, Conor P.

    2015-01-01

    Predictive population modeling contributes to our basic scientific understanding of population dynamics, but can also inform management decisions by evaluating alternative actions in virtual environments. Quantitative models mathematically reflect scientific hypotheses about how a system functions. In Delaware Bay, mid-Atlantic Coast, USA, to more effectively manage horseshoe crab (Limulus polyphemus) harvests and protect Red Knot (Calidris canutus rufa) populations, models are used to compare harvest actions and predict the impacts on crab and knot populations. Management has been chiefly driven by the core hypothesis that horseshoe crab egg abundance governs the survival and reproduction of migrating Red Knots that stopover in the Bay during spring migration. However, recently, hypotheses proposing that knot dynamics are governed by cyclical lemming dynamics garnered some support in data analyses. In this paper, I present alternative models of Red Knot population dynamics to reflect alternative hypotheses. Using 2 models with different lemming population cycle lengths and 2 models with different horseshoe crab effects, I project the knot population into the future under environmental stochasticity and parametric uncertainty with each model. I then compare each model's predictions to 10 yr of population monitoring from Delaware Bay. Using Bayes' theorem and model weight updating, models can accrue weight or support for one or another hypothesis of population dynamics. With 4 models of Red Knot population dynamics and only 10 yr of data, no hypothesis clearly predicted population count data better than another. The collapsed lemming cycle model performed best, accruing ~35% of the model weight, followed closely by the horseshoe crab egg abundance model, which accrued ~30% of the weight. The models that predicted no decline or stable populations (i.e. the 4-yr lemming cycle model and the weak horseshoe crab effect model) were the most weakly supported.

  3. Population dynamics and population control of Galium aparine L.

    NARCIS (Netherlands)

    Weide, van der R.Y.

    1993-01-01

    The population biology of Galium aparine L. needs to be better understood, in order to be able to rationalize decisions about the short- and long-term control of this weed species for different cropping practices.

    A population dynamics model was developed to

  4. Dynamics of bacterial community in the gut of Cornu aspersum

    Directory of Open Access Journals (Sweden)

    ZDRAVKA KOLEVA

    2015-12-01

    Full Text Available The dynamics of the bacterial community in the intestinal tract of Cornu aspersum was investigated during different states of its life cycle. Two approaches were applied – culture and non-culture. The non-culture approach was performed by ARDRA of 16S rDNA using two of the six tested endonucleases. Data were analyzed by hierarchical cluster analysis. The restriction of 16S rDNA samples from the snail of different physiological states with endonucleases HinfI and Csp6I resulted in generation of different profiles depending on the snail states. By the culture approach we found that the total number of cultivable bacteria, representatives of Enterobacteriaceae, lactic acid bacteria, amylolitic and cellulolytic bacteria were the most abundant in active state of the snails. Cellulolytic bacteria were not detected in juveniles of C. aspersum. Escherichia coli, Clostridium perfringens as well as bacteria from the genus Salmonella, Shigella and Pseudomonas were not detected. Bacteria of the genus Aeromonas were found in juveniles of C. aspersum, after that their number decrease and were not found in hibernating snails. On the base of the two applied approaches this study shows that the bacterial flora in the intestinal tract of C. aspersum is affected by the seasonal and environmental variations and undergoes quantitative and qualitative changes during the different states of the life cycle. The snails harbor in their gut intestinal bacteria, which possess biochemical potentiality to degrade the plant components.

  5. Visualization of bacterial flagella dynamics in a viscous shear flow

    Science.gov (United States)

    Ali, Jamel; Kim, Minjun

    2016-11-01

    We report on the dynamics of tethered bacterial flagella in an applied viscous shear flow and analyze their behavior using image processing. Flagellin proteins were repolymerized into flagellar filaments functionalized with biotin at their proximal end, and allowed to self-assemble within a micro channel coated with streptavidin. It was observed that all attached flagellar filaments aligned with the steady shear flow of various polymeric solutions. Furthermore it was observed that many of the filaments were stretched, and at elevated flow rates began to undergo polymorphic transformations, which were initiated at one end of the flagellum. When undergoing a change to a different helical form the flagellum was observed to transform to an oppositely handed helix, as to counteract the viscous torque imparted by the shear flow. It was also observed that some flagellar filaments did not undergo polymorphic transformations, but rotated about their helical axis. The rate of this rotation appears to be a function of the applied flow rate. These results expand on previous experimental work and aid in the development of a novel platform that harnesses the autonomic response of a 'forest' of bacterial flagella for engineering applications. This work was funded by NSF Grant CMMI-1000255, KEIT MOTIE Grant No. 10052980, and with Government support under and awarded by DoD, Air Force Office of Scientific Research, National Defense Science and Engineering Graduate (NDSEG) Fellowship, 32 CFR 168a.

  6. Evolutionary dynamics of cooperation in neutral populations

    Science.gov (United States)

    Szolnoki, Attila; Perc, Matjaž

    2018-01-01

    Cooperation is a difficult proposition in the face of Darwinian selection. Those that defect have an evolutionary advantage over cooperators who should therefore die out. However, spatial structure enables cooperators to survive through the formation of homogeneous clusters, which is the hallmark of network reciprocity. Here we go beyond this traditional setup and study the spatiotemporal dynamics of cooperation in a population of populations. We use the prisoner's dilemma game as the mathematical model and show that considering several populations simultaneously gives rise to fascinating spatiotemporal dynamics and pattern formation. Even the simplest assumption that strategies between different populations are payoff-neutral with one another results in the spontaneous emergence of cyclic dominance, where defectors of one population become prey of cooperators in the other population, and vice versa. Moreover, if social interactions within different populations are characterized by significantly different temptations to defect, we observe that defectors in the population with the largest temptation counterintuitively vanish the fastest, while cooperators that hang on eventually take over the whole available space. Our results reveal that considering the simultaneous presence of different populations significantly expands the complexity of evolutionary dynamics in structured populations, and it allows us to understand the stability of cooperation under adverse conditions that could never be bridged by network reciprocity alone.

  7. Stochastic population dynamic models as probability networks

    Science.gov (United States)

    M.E. and D.C. Lee. Borsuk

    2009-01-01

    The dynamics of a population and its response to environmental change depend on the balance of birth, death and age-at-maturity, and there have been many attempts to mathematically model populations based on these characteristics. Historically, most of these models were deterministic, meaning that the results were strictly determined by the equations of the model and...

  8. How Resource Phenology Affects Consumer Population Dynamics.

    Science.gov (United States)

    Bewick, Sharon; Cantrell, R Stephen; Cosner, Chris; Fagan, William F

    2016-02-01

    Climate change drives uneven phenology shifts across taxa, and this can result in changes to the phenological match between interacting species. Shifts in the relative phenology of partner species are well documented, but few studies have addressed the effects of such changes on population dynamics. To explore this, we develop a phenologically explicit model describing consumer-resource interactions. Focusing on scenarios for univoltine insects, we show how changes in resource phenology can be reinterpreted as transformations in the year-to-year recursion relationships defining consumer population dynamics. This perspective provides a straightforward path for interpreting the long-term population consequences of phenology change. Specifically, by relating the outcome of phenological shifts to species traits governing recursion relationships (e.g., consumer fecundity or competitive scenario), we demonstrate how changes in relative phenology can force systems into different dynamical regimes, with major implications for resource management, conservation, and other areas of applied dynamics.

  9. Bacterial profile of dentine caries and the impact of pH on bacterial population diversity.

    Directory of Open Access Journals (Sweden)

    Nima Kianoush

    Full Text Available Dental caries is caused by the release of organic acids from fermentative bacteria, which results in the dissolution of hydroxyapatite matrices of enamel and dentine. While low environmental pH is proposed to cause a shift in the consortium of oral bacteria, favouring the development of caries, the impact of this variable has been overlooked in microbial population studies. This study aimed to detail the zonal composition of the microbiota associated with carious dentine lesions with reference to pH. We used 454 sequencing of the 16S rRNA gene (V3-V4 region to compare microbial communities in layers ranging in pH from 4.5-7.8 from 25 teeth with advanced dentine caries. Pyrosequencing of the amplicons yielded 449,762 sequences. Nine phyla, 97 genera and 409 species were identified from the quality-filtered, de-noised and chimera-free sequences. Among the microbiota associated with dentinal caries, the most abundant taxa included Lactobacillus sp., Prevotella sp., Atopobium sp., Olsenella sp. and Actinomyces sp. We found a disparity between microbial communities localised at acidic versus neutral pH strata. Acidic conditions were associated with low diversity microbial populations, with Lactobacillus species including L. fermentum, L. rhamnosus and L. crispatus, being prominent. In comparison, the distinctive species of a more diverse flora associated with neutral pH regions of carious lesions included Alloprevotella tanerrae, Leptothrix sp., Sphingomonas sp. and Streptococcus anginosus. While certain bacteria were affected by the pH gradient, we also found that ∼ 60% of the taxa associated with caries were present across the investigated pH range, representing a substantial core. We demonstrated that some bacterial species implicated in caries progression show selective clustering with respect to pH gradient, providing a basis for specific therapeutic strategies.

  10. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations

    OpenAIRE

    Nikolic, Nela; Schreiber, Frank; Dal Co, Alma; Kiviet, Daniel J.; Bergmiller, Tobias; Littmann, Sten; Kuypers, Marcel M. M.; Ackermann, Martin

    2017-01-01

    Author summary This study addresses a fundamental question in bacterial metabolism: do all individuals in a clonal population express the same metabolic functions, or do individuals specialize on different metabolic functions and assimilate different substrates? Reports about stochastic gene expression in bacterial populations raise the possibility that transcriptional differences between individuals translate into different metabolic behaviors, but the prevalence and magnitude of such effect...

  11. Population dynamics in vasopressin cells.

    Science.gov (United States)

    Leng, Gareth; Brown, Colin; Sabatier, Nancy; Scott, Victoria

    2008-01-01

    Most neurons sense and code change, and when presented with a constant stimulus they adapt, so as to be able to detect a fresh change. However, for some things it is important to know their absolute level; to encode such information, neurons must sustain their response to an unchanging stimulus while remaining able to respond to a change in that stimulus. One system that encodes the absolute level of a stimulus is the vasopressin system, which generates a hormonal signal that is proportional to plasma osmolality. Vasopressin cells sense plasma osmolality and secrete appropriate levels of vasopressin from the neurohypophysis as needed to control water excretion; this requires sustained secretion under basal conditions and the ability to increase (or decrease) secretion should plasma osmolality change. Here we explore the mechanisms that enable vasopressin cells to fulfill this function, and consider how coordination between the cells might distribute the secretory load across the population of vasopressin cells. 2008 S. Karger AG, Basel.

  12. Population Dynamics and Air Pollution

    DEFF Research Database (Denmark)

    Flachs, Esben Meulengracht; Sørensen, Jan; Bønløkke, Jacob

    2013-01-01

    Objective. To explore how three different assumptions on demographics affect the health impact of Danish emitted air pollution in Denmark from 2005 to 2030, with health impact modeled from 2005 to 2050. Methods. Modeled air pollution from Danish sources was used as exposure in a newly developed......) a static year 2005 population, (2) morbidity and mortality fixed at the year 2005 level, or (3) an expected development. Results. The health impact of air pollution was estimated at 672,000, 290,000, and 280,000 lost life years depending on demographic assumptions and the corresponding social costs at 430.......4 M€, 317.5 M€, and 261.6 M€ through the modeled years 2005–2050. Conclusion. The modeled health impact of air pollution differed widely with the demographic assumptions, and thus demographics and assumptions on demographics played a key role in making health impact assessments on air pollution....

  13. Diversity of Hindgut Bacterial Population in Subterranean Termite, Reticulitermes flavipes

    Science.gov (United States)

    Olanrewaju Raji; Dragica Jeremic-Nikolic; Juliet D. Tang

    2017-01-01

    The termite hindgut contains a bacterial community that symbiotically aids in digestion of cellulosic materials. For this paper, a species survey of bacterial hindgut symbionts in termites collected from Saucier, Mississippi was examined. Two methods were tested for optimal genetic material isolation. Genomic DNA was isolated from the hindgut luminal contents of five...

  14. Structural stability of nonlinear population dynamics

    Science.gov (United States)

    Cenci, Simone; Saavedra, Serguei

    2018-01-01

    In population dynamics, the concept of structural stability has been used to quantify the tolerance of a system to environmental perturbations. Yet, measuring the structural stability of nonlinear dynamical systems remains a challenging task. Focusing on the classic Lotka-Volterra dynamics, because of the linearity of the functional response, it has been possible to measure the conditions compatible with a structurally stable system. However, the functional response of biological communities is not always well approximated by deterministic linear functions. Thus, it is unclear the extent to which this linear approach can be generalized to other population dynamics models. Here, we show that the same approach used to investigate the classic Lotka-Volterra dynamics, which is called the structural approach, can be applied to a much larger class of nonlinear models. This class covers a large number of nonlinear functional responses that have been intensively investigated both theoretically and experimentally. We also investigate the applicability of the structural approach to stochastic dynamical systems and we provide a measure of structural stability for finite populations. Overall, we show that the structural approach can provide reliable and tractable information about the qualitative behavior of many nonlinear dynamical systems.

  15. Population dynamical responses to climate change

    DEFF Research Database (Denmark)

    Forchhammer, Mads; Schmidt, Niels Martin; Høye, Toke Thomas

    2008-01-01

    , the effects of climate change may potentially extend through any of these interactions. In this chapter, we focus on the extent to which evolutionarily distinct species at different trophic levels respond to similar changes in climate. By using a broad spectrum of statistically and ecologically founded...... and migrating species, respectively. The dynamics of all four resident species were significantly affected by variations in snow-cover and explained up to 65% of their inter-annual dynamics. The three predators differed in their numerical response to changes in prey densities. Whereas the population dynamics...... a bewildering number of interactions. For example, individuals within a population may compete for space and other resources and, being embedded in an ecosystem, individuals in any population may also interact with individuals of competing species as well as those from adjacent trophic levels. In principal...

  16. Harvest and dynamics of duck populations

    Science.gov (United States)

    Sedinger, James S.; Herzog, Mark P.

    2012-01-01

    The role of harvest in the dynamics of waterfowl populations continues to be debated among scientists and managers. Our perception is that interested members of the public and some managers believe that harvest influences North American duck populations based on calls for more conservative harvest regulations. A recent review of harvest and population dynamics of North American mallard (Anas platyrhynchos) populations (Pöysä et al. 2004) reached similar conclusions. Because of the importance of this issue, we reviewed the evidence for an impact of harvest on duck populations. Our understanding of the effects of harvest is limited because harvest effects are typically confounded with those of population density; regulations are typically most liberal when populations are greatest. This problem also exists in the current Adaptive Harvest Management Program (Conn and Kendall 2004). Consequently, even where harvest appears additive to other mortality, this may be an artifact of ignoring effects of population density. Overall, we found no compelling evidence for strong additive effects of harvest on survival in duck populations that could not be explained by other factors.

  17. Stable Regulation of Cell Cycle Events in Mycobacteria: Insights From Inherently Heterogeneous Bacterial Populations

    Science.gov (United States)

    Logsdon, Michelle M.; Aldridge, Bree B.

    2018-01-01

    Model bacteria, such as E. coli and B. subtilis, tightly regulate cell cycle progression to achieve consistent cell size distributions and replication dynamics. Many of the hallmark features of these model bacteria, including lateral cell wall elongation and symmetric growth and division, do not occur in mycobacteria. Instead, mycobacterial growth is characterized by asymmetric polar growth and division. This innate asymmetry creates unequal birth sizes and growth rates for daughter cells with each division, generating a phenotypically heterogeneous population. Although the asymmetric growth patterns of mycobacteria lead to a larger variation in birth size than typically seen in model bacterial populations, the cell size distribution is stable over time. Here, we review the cellular mechanisms of growth, division, and cell cycle progression in mycobacteria in the face of asymmetry and inherent heterogeneity. These processes coalesce to control cell size. Although Mycobacterium smegmatis and Mycobacterium bovis Bacillus Calmette-Guérin (BCG) utilize a novel model of cell size control, they are similar to previously studied bacteria in that initiation of DNA replication is a key checkpoint for cell division. We compare the regulation of DNA replication initiation and strategies used for cell size homeostasis in mycobacteria and model bacteria. Finally, we review the importance of cellular organization and chromosome segregation relating to the physiology of mycobacteria and consider how new frameworks could be applied across the wide spectrum of bacterial diversity. PMID:29619019

  18. Rates, intrinsic linkages, and multistate population dynamics.

    Science.gov (United States)

    Schoen, Robert

    2017-01-01

    Demographic analyses of multistate populations are commonplace, as are situations where population stocks are known but population flows are not. Still, demographic models for multistate populations with changing rates remain at an early stage of development, limiting dynamic analyses and analytical projections. Here, a new approach, the Intrinsic Linkage-Rate Ratio (IL-RR) model, is presented and explored. The key IL parameter, w , is a simple weight for projecting populations. Using the ultimate state composition implied by the prevailing rates, the IL-RR model provides new relationships that connect multistate populations over time and allow analytical population projections. Parameter w reflects population metabolism and scales the level of the transfer rates. Compositional change is driven by the sequence of implicit stable population compositions. The IL-RR approach also provides a new method for estimating transfer rates within an interval from population numbers at the beginning and end of the interval. The new relationships developed advance the ability of demographers to model multistate populations with changing rates and to relate population stocks and flows.

  19. Compositional stability of a salivary bacterial population against supragingival microbiota shift following periodontal therapy.

    Directory of Open Access Journals (Sweden)

    Wataru Yamanaka

    Full Text Available Supragingival plaque is permanently in contact with saliva. However, the extent to which the microbiota contributes to the salivary bacterial population remains unclear. We compared the compositional shift in the salivary bacterial population with that in supragingival plaque following periodontal therapy. Samples were collected from 19 patients with periodontitis before and after periodontal therapy (mean sample collection interval, 25.8 ± 2.6 months, and their bacterial composition was investigated using barcoded pyrosequencing analysis of the 16S rRNA gene. Phylogenetic community analysis using the UniFrac distance metric revealed that the overall bacterial community composition of saliva is distinct from that of supragingival plaque, both pre- and post-therapy. Temporal variation following therapy in the salivary bacterial population was significantly smaller than in the plaque microbiota, and the post-therapy saliva sample was significantly more similar to that pre-therapy from the same individual than to those from other subjects. Following periodontal therapy, microbial richness and biodiversity were significantly decreased in the plaque microbiota, but not in the salivary bacterial population. The operational taxonomic units whose relative abundances changed significantly after therapy were not common to the two microbiotae. These results reveal the compositional stability of salivary bacterial populations against shifts in the supragingival microbiota, suggesting that the effect of the supragingival plaque microbiota on salivary bacterial population composition is limited.

  20. Conspecific brood parasitism and population dynamics.

    Science.gov (United States)

    de Valpine, Perry; Eadie, John M

    2008-10-01

    Conspecific brood parasitism (CBP), defined as parasitic laying of eggs in a conspecific nest without providing parental care, occurs in insects, fishes, amphibians, and many birds. Numerous factors have been proposed to influence the evolution of CBP, including nest site limitation; effects of brood size, laying order, or parasitic status on offspring survival; randomness of parasitic egg distribution; adult life-history trade-offs; and variation in parental female quality or risk of nest predation. However, few theoretical studies consider multiple possible types of parasitism or the interplay between evolution of parasitism and population dynamics. We review existing theory of CBP and develop a synthetic modeling approach to ask how best-of-a-bad job parasitism, separate-strategies parasitism (in which females either nest or parasitize), and joint-strategies parasitism (in which females can both nest and parasitize) differ in their evolutionary conditions and impacts on population dynamics using an adaptive dynamics framework including multivariate traits. CBP can either stabilize or destabilize population dynamics in different scenarios, and the role of comparable parameters on evolutionarily stable strategy parasitism rate, equilibrium population size, and population stability can differ for the different modes of parasitism.

  1. Connecting micro dynamics and population distributions in system dynamics models.

    Science.gov (United States)

    Fallah-Fini, Saeideh; Rahmandad, Hazhir; Chen, Hsin-Jen; Xue, Hong; Wang, Youfa

    2013-01-01

    Researchers use system dynamics models to capture the mean behavior of groups of indistinguishable population elements (e.g., people) aggregated in stock variables. Yet, many modeling problems require capturing the heterogeneity across elements with respect to some attribute(s) (e.g., body weight). This paper presents a new method to connect the micro-level dynamics associated with elements in a population with the macro-level population distribution along an attribute of interest without the need to explicitly model every element. We apply the proposed method to model the distribution of Body Mass Index and its changes over time in a sample population of American women obtained from the U.S. National Health and Nutrition Examination Survey. Comparing the results with those obtained from an individual-based model that captures the same phenomena shows that our proposed method delivers accurate results with less computation than the individual-based model.

  2. Connecting micro dynamics and population distributions in system dynamics models

    Science.gov (United States)

    Rahmandad, Hazhir; Chen, Hsin-Jen; Xue, Hong; Wang, Youfa

    2014-01-01

    Researchers use system dynamics models to capture the mean behavior of groups of indistinguishable population elements (e.g., people) aggregated in stock variables. Yet, many modeling problems require capturing the heterogeneity across elements with respect to some attribute(s) (e.g., body weight). This paper presents a new method to connect the micro-level dynamics associated with elements in a population with the macro-level population distribution along an attribute of interest without the need to explicitly model every element. We apply the proposed method to model the distribution of Body Mass Index and its changes over time in a sample population of American women obtained from the U.S. National Health and Nutrition Examination Survey. Comparing the results with those obtained from an individual-based model that captures the same phenomena shows that our proposed method delivers accurate results with less computation than the individual-based model. PMID:25620842

  3. Genomics reveals historic and contemporary transmission dynamics of a bacterial disease among wildlife and livestock

    Science.gov (United States)

    Kamath, Pauline L.; Foster, Jeffrey T.; Drees, Kevin P.; Luikart, Gordon; Quance, Christine; Anderson, Neil J.; Clarke, P. Ryan; Cole, Eric K.; Drew, Mark L.; Edwards, William H.; Rhyan, Jack C.; Treanor, John J.; Wallen, Rick L.; White, Patrick J.; Robbe-Austerman, Suelee; Cross, Paul C.

    2016-01-01

    Whole-genome sequencing has provided fundamental insights into infectious disease epidemiology, but has rarely been used for examining transmission dynamics of a bacterial pathogen in wildlife. In the Greater Yellowstone Ecosystem (GYE), outbreaks of brucellosis have increased in cattle along with rising seroprevalence in elk. Here we use a genomic approach to examine Brucella abortus evolution, cross-species transmission and spatial spread in the GYE. We find that brucellosis was introduced into wildlife in this region at least five times. The diffusion rate varies among Brucella lineages (B3 to 8 km per year) and over time. We also estimate 12 host transitions from bison to elk, and 5 from elk to bison. Our results support the notion that free-ranging elk are currently a self-sustaining brucellosis reservoir and the source of livestock infections, and that control measures in bison are unlikely to affect the dynamics of unrelated strains circulating in nearby elk populations.

  4. Model Studies of the Dynamics of Bacterial Flagellar Motors

    Science.gov (United States)

    Bai, Fan; Lo, Chien-Jung; Berry, Richard M.; Xing, Jianhua

    2009-01-01

    Abstract The bacterial flagellar motor is a rotary molecular machine that rotates the helical filaments that propel swimming bacteria. Extensive experimental and theoretical studies exist on the structure, assembly, energy input, power generation, and switching mechanism of the motor. In a previous article, we explained the general physics underneath the observed torque-speed curves with a simple two-state Fokker-Planck model. Here, we further analyze that model, showing that 1), the model predicts that the two components of the ion motive force can affect the motor dynamics differently, in agreement with latest experiments; 2), with explicit consideration of the stator spring, the model also explains the lack of dependence of the zero-load speed on stator number in the proton motor, as recently observed; and 3), the model reproduces the stepping behavior of the motor even with the existence of the stator springs and predicts the dwell-time distribution. The predicted stepping behavior of motors with two stators is discussed, and we suggest future experimental procedures for verification. PMID:19383460

  5. Model Studies of the Dynamics of Bacterial Flagellar Motors

    Energy Technology Data Exchange (ETDEWEB)

    Bai, F; Lo, C; Berry, R; Xing, J

    2009-03-19

    The Bacterial Flagellar Motor is a rotary molecular machine that rotates the helical filaments which propel swimming bacteria. Extensive experimental and theoretical studies exist on the structure, assembly, energy input, power generation and switching mechanism of the motor. In our previous paper, we explained the general physics underneath the observed torque-speed curves with a simple two-state Fokker-Planck model. Here we further analyze this model. In this paper we show (1) the model predicts that the two components of the ion motive force can affect the motor dynamics differently, in agreement with the latest experiment by Lo et al.; (2) with explicit consideration of the stator spring, the model also explains the lack of dependence of the zero-load speed on stator number in the proton motor, recently observed by Yuan and Berg; (3) the model reproduces the stepping behavior of the motor even with the existence of the stator springs and predicts the dwelling time distribution. Predicted stepping behavior of motors with two stators is discussed, and we suggest future experimental verification.

  6. Model Studies of the Dynamics of Bacterial Flagellar Motors

    International Nuclear Information System (INIS)

    Bai, F.; Lo, C.; Berry, R.; Xing, J.

    2009-01-01

    The Bacterial Flagellar Motor is a rotary molecular machine that rotates the helical filaments which propel swimming bacteria. Extensive experimental and theoretical studies exist on the structure, assembly, energy input, power generation and switching mechanism of the motor. In our previous paper, we explained the general physics underneath the observed torque-speed curves with a simple two-state Fokker-Planck model. Here we further analyze this model. In this paper we show (1) the model predicts that the two components of the ion motive force can affect the motor dynamics differently, in agreement with the latest experiment by Lo et al.; (2) with explicit consideration of the stator spring, the model also explains the lack of dependence of the zero-load speed on stator number in the proton motor, recently observed by Yuan and Berg; (3) the model reproduces the stepping behavior of the motor even with the existence of the stator springs and predicts the dwelling time distribution. Predicted stepping behavior of motors with two stators is discussed, and we suggest future experimental verification.

  7. POPULATION DYNAMICS OF PSEUDO-NITZSCHIA SPECIES ...

    African Journals Online (AJOL)

    nb

    ABSTRACT. The genus Pseudo-nitzschia is a chain-forming diatom comprising about 30 species some of which are known to produce domoic acid (DA) that causes amnesic shellfish poisoning (ASP). The current study aimed at assessing the population dynamics of Pseudo-nitzschia in the near shore waters of Dar es ...

  8. Population dynamics of Pseudo-nitzschia species ...

    African Journals Online (AJOL)

    The genus Pseudo-nitzschia is a chain-forming diatom comprising about 30 species some of which are known to produce domoic acid (DA) that causes amnesic shellfish poisoning (ASP). The current study aimed at assessing the population dynamics of Pseudo-nitzschia in the near shore waters of Dar es Salaam. Samples ...

  9. Population dynamics of Prostephanus truncatus (Horn) and ...

    African Journals Online (AJOL)

    The effects of three maize varieties and two storage seasons on the population dynamics of Prostephanus truncates (Horn) and Sitophilus zeamais Motschulsky were observed in the traditional `Ewe' barn in the field. Two local varieties, Dzolokpuita and Abutia and an improved variety, Abeleehi, were stored with the husk on ...

  10. POPULATION DYNAMICS AND SPAWNING OF THE FLATFISH ...

    African Journals Online (AJOL)

    The population dynamics of flatfish Solea bleekeri and Pseudorhombus arsius within the intertidal area of Inhaca Island, Moçambique, was investigated using bottom trawl data collected during summer (December 1996–March 1997) and winter (June 1997–August 1997). The endemic S. bleekeri is a small, relatively ...

  11. The population dynamics of the Prorocentraceae, Gonyaulacaceae ...

    African Journals Online (AJOL)

    An investigation into the dynamics of Protozoan populations in Ologe lagoon was carried out for a period of 24 months. It covered identification, diversity and elucidating the influence of some physical and chemical parameters on temporal abundance and spatial distribution of the Protozoa. Four villages around the lagoon ...

  12. PCR-DGGE analysis of bacterial community dynamics in kava beverages during refrigeration.

    Science.gov (United States)

    Dong, J; Kandukuru, P; Huang, A S; Li, Y

    2011-07-01

    Kava beverages are highly perishable even under refrigerated conditions. This study aimed to investigate the bacterial community dynamics in kava beverages during refrigeration.  Four freshly made kava beverages were obtained from kava bars and stored at 4°C. On days 0, 3 and 6, the aerobic plate count (APC), lactic acid bacteria (LAB) count and yeast and mould count (YMC) of the samples were determined. Meanwhile, bacterial DNA was extracted from each sample and subjected to the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Moreover, species-specific PCR assays were employed to identify predominant Pseudomonas spp. involved in kava spoilage. Over the storage period, the APC, LAB count and YMC of the four kava beverages all increased, whereas their pH values decreased. The DGGE profile revealed diverse bacterial populations in the samples. LAB, such as Weissella soli, Lactobacillus spp. and Lactococcus lactis, were found in the kava beverages. Species-specific PCR assays detected Pseudomonas putida and Pseudomonas fluorescens in the samples; Ps. fluorescens became dominant during refrigeration. LAB and Pseudomonas may play a significant role in the spoilage of kava beverages. This study provides important information that may be used to extend the shelf life of kava beverages. © 2011 The Authors. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

  13. Population-based surveillance for bacterial meningitis in China, September 2006-December 2009.

    Science.gov (United States)

    Li, Yixing; Yin, Zundong; Shao, Zhujun; Li, Manshi; Liang, Xiaofeng; Sandhu, Hardeep S; Hadler, Stephen C; Li, Junhong; Sun, Yinqi; Li, Jing; Zou, Wenjing; Lin, Mei; Zuo, Shuyan; Mayer, Leonard W; Novak, Ryan T; Zhu, Bingqing; Xu, Li; Luo, Huiming

    2014-01-01

    During September 2006-December 2009, we conducted active population and sentinel laboratory-based surveillance for bacterial meningitis pathogens, including Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae type b, in 4 China prefectures. We identified 7,876 acute meningitis and encephalitis syndrome cases, including 6,388 among prefecture residents. A total of 833 resident cases from sentinel hospitals met the World Health Organization case definition for probable bacterial meningitis; 339 of these cases were among children bacterial meningitis in 74 of 3,391 tested cases. The estimated annual incidence (per 100,000 population) of probable bacterial meningitis ranged from 1.84 to 2.93 for the entire population and from 6.95 to 22.30 for children bacterial meningitis cases in China, but more complete laboratory testing is needed to better define the epidemiology of the disease in this country.

  14. Population-based Surveillance for Bacterial Meningitis in China, September 2006–December 2009

    Science.gov (United States)

    Li, Yixing; Yin, Zundong; Shao, Zhujun; Li, Manshi; Liang, Xiaofeng; Sandhu, Hardeep S.; Hadler, Stephen C.; Li, Junhong; Sun, Yinqi; Li, Jing; Zou, Wenjing; Lin, Mei; Zuo, Shuyan; Mayer, Leonard W.; Novak, Ryan T.; Zhu, Bingqing; Xu, Li

    2014-01-01

    During September 2006–December 2009, we conducted active population and sentinel laboratory–based surveillance for bacterial meningitis pathogens, including Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae type b, in 4 China prefectures. We identified 7,876 acute meningitis and encephalitis syndrome cases, including 6,388 among prefecture residents. A total of 833 resident cases from sentinel hospitals met the World Health Organization case definition for probable bacterial meningitis; 339 of these cases were among children bacterial meningitis in 74 of 3,391 tested cases. The estimated annual incidence (per 100,000 population) of probable bacterial meningitis ranged from 1.84 to 2.93 for the entire population and from 6.95 to 22.30 for children bacterial meningitis cases in China, but more complete laboratory testing is needed to better define the epidemiology of the disease in this country. PMID:24377388

  15. Seasonal effect on the bacterial and fungal population of an oilfield ...

    African Journals Online (AJOL)

    Seasonal effect on the bacterial and fungal populations of an oilfield wastewater – polluted soil was investigated for a period of 12 months. Many bacterial and fungal species were present in the soil and the wastewater of the area investigated. Some of the organisms occurred in both the soil and oilfield wastewater while ...

  16. Bacterial populations concomitant with Sclerotium rolfsii sclerotia in ...

    African Journals Online (AJOL)

    SARAH

    2015-09-30

    Sep 30, 2015 ... J. Appl. Biosci. Bacterial communities concomitant with sclerotia. 8708. Table 4 : Soil chemical characteristics before and after flooding in the greenhouse and fielda. Redox potential Eh (mV)b,c. Electrical conductivity (µS m-1)c. Treatments. 1 DAF. 15 DAF. 30 DAF before after. Greenhouse experiment.

  17. Petroleum-hydrocarbon utilization by native bacterial population ...

    African Journals Online (AJOL)

    Two Nigerian crude oils (Bonny light and Escravos blend) were exposed to the wastewater canal via oil impregnated membrane filters (0.45 μm diameter) for 21 days in a microcosm experiment. Bacterial petroleum-hydrocarbon utilizers were later harvested from both the millipore membrane filters and laboratory ...

  18. Visualizing the response of a gut bacterial population to antibiotic perturbations

    Science.gov (United States)

    Schlomann, Brandon; Wiles, Travis; Guillemin, Karen; Parthasarathy, Raghuveer

    Each of our intestines is home to a vast ecosystem composed of trillions of bacteria in a dynamic environment. Bacterial communities face fluctuations in nutrient influx, invasions by new microbes, physical disturbances from peristalsis, and, perhaps, the arrival of antibiotic drugs. Metagenomic profiling has shown that antibiotic treatments can cause major changes in the composition of species present in the gut, at timescales shorter than a day. How this happens is unknown, as these dynamics have never been observed directly. I'll present recent work that addresses this by using well-defined microbial communities in a model organism, the zebrafish. Light Sheet Fluorescence Microscopy is used to image a commensal species of Vibrioresponding to antibiotic perturbations in the guts of live, larval fish. We find that sub-lethal concentrations of different classes of antibiotics induce similar physical responses in Vibrio, namely filamentation and reduction of motility. The arrested bacteria then aggregate and can be ejected via peristalsis, resulting in large population collapses. These observations suggest that antibiotics can cause large disruptions to gut ecosystems even in low concentrations, and that physical processes may be important drivers of response dynamics.

  19. Characterization of bacterial community dynamics in a full-scale drinking water treatment plant.

    Science.gov (United States)

    Li, Cuiping; Ling, Fangqiong; Zhang, Minglu; Liu, Wen-Tso; Li, Yuxian; Liu, Wenjun

    2017-01-01

    Understanding the spatial and temporal dynamics of microbial communities in drinking water systems is vital to securing the microbial safety of drinking water. The objective of this study was to comprehensively characterize the dynamics of microbial biomass and bacterial communities at each step of a full-scale drinking water treatment plant in Beijing, China. Both bulk water and biofilm samples on granular activated carbon (GAC) were collected over 9months. The proportion of cultivable cells decreased during the treatment processes, and this proportion was higher in warm season than cool season, suggesting that treatment processes and water temperature probably had considerable impact on the R2A cultivability of total bacteria. 16s rRNA gene based 454 pyrosequencing analysis of the bacterial community revealed that Proteobacteria predominated in all samples. The GAC biofilm harbored a distinct population with a much higher relative abundance of Acidobacteria than water samples. Principle coordinate analysis and one-way analysis of similarity indicated that the dynamics of the microbial communities in bulk water and biofilm samples were better explained by the treatment processes rather than by sampling time, and distinctive changes of the microbial communities in water occurred after GAC filtration. Furthermore, 20 distinct OTUs contributing most to the dissimilarity among samples of different sampling locations and 6 persistent OTUs present in the entire treatment process flow were identified. Overall, our findings demonstrate the significant effects that treatment processes have on the microbial biomass and community fluctuation and provide implications for further targeted investigation on particular bacteria populations. Copyright © 2016. Published by Elsevier B.V.

  20. The failure rate dynamics in heterogeneous populations

    International Nuclear Information System (INIS)

    Cha, Ji Hwan; Finkelstein, Maxim

    2013-01-01

    Most populations encountered in real world are heterogeneous. In reliability applications, the mixture (observed) failure rate, obviously, can be considered as a measure of ‘average’ quality in these populations. However, in addition to this average measure, some variability characteristics for failure rates can be very helpful in describing the time-dependent changes in quality of heterogeneous populations. In this paper, we discuss variance and the coefficient of variation of the corresponding random failure rate as variability measures for items in heterogeneous populations. Furthermore, there is often a risk that items of poor quality are selected for important missions. Therefore, along with the ‘average quality’ of a population, more ‘conservative’ quality measures should be also defined and studied. For this purpose, we propose the percentile and the tail-mixture of the failure rates as the corresponding conservative measures. Some illustrative examples are given. -- Highlights: ► This paper provides the insight on the variability measures in heterogeneous populations. ► The conservative quality measures in heterogeneous populations are defined. ► The utility of these measures is illustrated by meaningful examples. ► This paper provides a better understanding of the dynamics in heterogeneous populations

  1. Daily variations in pathogenic bacterial populations in a monsoon influenced tropical environment

    Digital Repository Service at National Institute of Oceanography (India)

    Khandeparker, L.; Anil, A; Naik, S.D.; Gaonkar, C.C.

    Changing climatic conditions have influenced the monsoon pattern in recent years. Variations in bacterial population in one such tropical environment were observed everyday over two years and point out intra and inter annual changes driven...

  2. Dynamic light scattering: A fast and reliable method to analyze bacterial growth during the lag phase.

    Science.gov (United States)

    Vargas, Susana; Millán-Chiu, Blanca E; Arvizu-Medrano, Sofía M; Loske, Achim M; Rodríguez, Rogelio

    2017-06-01

    A comparison between plate counting (PC) and dynamic light scattering (DLS) is reported. PC is the standard technique to determine bacterial population as a function of time; however, this method has drawbacks, such as the cumbersome preparation and handling of samples, as well as the long time required to obtain results. Alternative methods based on optical density are faster, but do not distinguish viable from non-viable cells. These inconveniences are overcome by using DLS. Two different bacteria strains were considered: Escherichia coli and Staphylococcus aureus. DLS was performed at two different illuminating conditions: continuous and intermittent. By the increment of particle size as a function of time, it was possible to observe cell division and the formation of aggregates containing very few bacteria. The scattered intensity profiles showed the lag phase and the transition to the exponential phase of growth, providing a quantity proportional to viable bacteria concentration. The results revealed a clear and linear correlation in both lag and exponential phase, between the Log 10 (colony-forming units/mL) from PC and the Log 10 of the scattered intensity I s from DLS. These correlations provide a good support to use DLS as an alternative technique to determine bacterial population. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Population dynamics with symmetric and asymmetric harvesting

    Directory of Open Access Journals (Sweden)

    J. Ali

    2009-10-01

    Here $\\lambda, a, b, c$ and $L$ are positive constants with $0population dynamics with logistic type growth and constant yield harvesting. Here $u$ is the population density, $\\frac{1}{\\lambda}$ is the diffusion coefficient and $c$ is the harvesting effort. In particular, model A corresponds to a symmetric harvesting case and model B to an asymmetric harvesting case. Our objective is to study the existence of positive solutions and also discuss the effects of harvesting. We will develop appropriate quadrature methods via which we will establish our results.

  4. Bacterial incorporation of tritiated thymidine and populations of bacteriophagous fauna in the rhizosphere of wheat

    DEFF Research Database (Denmark)

    Christensen, Henrik; Griffiths, Bryan; Christensen, Søren

    1992-01-01

    Bacterial and microfaunal populations, and bacterial productivity measured by tritiated thymidine (3HTdr) incorporation, in the rhizosphere of wheat seedlings were measured. Soil from planted pots was fractionated into rhizosphere and non-rhizosphere (bulk) soil, while unplanted soil was taken from...... pots without plants. Total bacterial counts and biovolume did not differ between fractions but viable (plate) counts were 8 times higher in the rhizosphere compared to bulk and unplanted soil. 3HTdr was incorporated at a constant rate with low variability in bulk or unplanted soil. In rhizosphere soil...... 3HTdr incorporation was lower than in bulk or unplanted soils and showed high variability. The populations of bacterial-feeding protozoa and nematodes indicated that rhizosphere bacterial activity was actually 3–4 times greater in rhizosphere than bulk soil in accordance with the results...

  5. Worldwide populations of the aphid Aphis craccivora are infected with diverse facultative bacterial symbionts.

    Science.gov (United States)

    Brady, Cristina M; Asplen, Mark K; Desneux, Nicolas; Heimpel, George E; Hopper, Keith R; Linnen, Catherine R; Oliver, Kerry M; Wulff, Jason A; White, Jennifer A

    2014-01-01

    Facultative bacterial endosymbionts can play an important role in the evolutionary trajectory of their hosts. Aphids (Hemiptera: Aphididae) are infected with a wide variety of facultative endosymbionts that can confer ecologically relevant traits, which in turn may drive microevolutionary processes in a dynamic selective environment. However, relatively little is known about how symbiont diversity is structured in most aphid species. Here, we investigate facultative symbiont species richness and prevalence among world-wide populations of the cowpea aphid, Aphis craccivora Koch. We surveyed 44 populations of A. craccivora, and detected 11 strains of facultative symbiotic bacteria, representing six genera. There were two significant associations between facultative symbiont and aphid food plant: the symbiont Arsenophonus was found at high prevalence in A. craccivora populations collected from Robinia sp. (locust), whereas the symbiont Hamiltonella was almost exclusively found in A. craccivora populations from Medicago sativa (alfalfa). Aphids collected from these two food plants also had divergent mitochondrial haplotypes, potentially indicating the formation of specialized aphid lineages associated with food plant (host-associated differentiation). The role of facultative symbionts in this process remains to be determined. Overall, observed facultative symbiont prevalence in A. craccivora was lower than that of some other well-studied aphids (e.g., Aphis fabae and Acyrthosiphon pisum), possibly as a consequence of A. craccivora's almost purely parthenogenetic life history. Finally, most (70 %) of the surveyed populations were polymorphic for facultative symbiont infection, indicating that even when symbiont prevalence is relatively low, symbiont-associated phenotypic variation may allow population-level evolutionary responses to local selection.

  6. Whitefly population dynamics in okra plantations

    OpenAIRE

    Leite,Germano Leão Demolin; Picanço,Marcelo; Jham,Gulab Newandram; Moreira,Márcio Dionízio

    2005-01-01

    The control of whitefly Bemisia tabaci (Gennadius) biotype B (Hemiptera: Aleyrodidae) on okra (Abelmoschus esculentus L.) consists primarily in the use of insecticides, due to the lack of information on other mortality factors. The objective of this study was to evaluate the spatial and temporal population dynamics of the whitefly B. tabaci biotype B on two successive A. esculentus var. "Santa Cruz" plantations. Leaf chemical composition, leaf nitrogen and potassium contents, trichome density...

  7. Particle-associated bacterial dynamics in a tropical tidal plain (Zuari estuary, India)

    Digital Repository Service at National Institute of Oceanography (India)

    DeSouza, M.J.B.D.; Nair, S.; LokaBharathi, P.A.; Chandramohan, D.

    The dynamics of particle-associated bacteria (PAB) in a tropical estuary, Zuari, in Goa on the west coast of India, was studied for a year from September 1997 to October 1998. Bacterial abundance, productivity and enzymatic activities were measured...

  8. Delay differential systems for tick population dynamics.

    Science.gov (United States)

    Fan, Guihong; Thieme, Horst R; Zhu, Huaiping

    2015-11-01

    Ticks play a critical role as vectors in the transmission and spread of Lyme disease, an emerging infectious disease which can cause severe illness in humans or animals. To understand the transmission dynamics of Lyme disease and other tick-borne diseases, it is necessary to investigate the population dynamics of ticks. Here, we formulate a system of delay differential equations which models the stage structure of the tick population. Temperature can alter the length of time delays in each developmental stage, and so the time delays can vary geographically (and seasonally which we do not consider). We define the basic reproduction number [Formula: see text] of stage structured tick populations. The tick population is uniformly persistent if [Formula: see text] and dies out if [Formula: see text]. We present sufficient conditions under which the unique positive equilibrium point is globally asymptotically stable. In general, the positive equilibrium can be unstable and the system show oscillatory behavior. These oscillations are primarily due to negative feedback within the tick system, but can be enhanced by the time delays of the different developmental stages.

  9. Of the Phrensy: an update on the epidemiology and pathogenesis of bacterial meningitis in the pediatric population [version 1; referees: 3 approved

    Directory of Open Access Journals (Sweden)

    Andrew Janowski

    2017-01-01

    Full Text Available In the past century, advances in antibiotics and vaccination have dramatically altered the incidence and clinical outcomes of bacterial meningitis. We review the shifting epidemiology of meningitis in children, including after the implementation of vaccines that target common meningitic pathogens and the introduction of intrapartum antibiotic prophylaxis offered to mothers colonized with Streptococcus agalactiae. We also discuss what is currently known about the pathogenesis of meningitis. Recent studies of the human microbiome have illustrated dynamic relationships of bacterial and viral populations with the host, which may potentiate the risk of bacterial meningitis.

  10. Microbial dynamics during harmful dinoflagellate Ostreopsis cf. ovata growth: Bacterial succession and viral abundance pattern.

    Science.gov (United States)

    Guidi, Flavio; Pezzolesi, Laura; Vanucci, Silvana

    2018-02-27

    Algal-bacterial interactions play a major role in shaping diversity of algal associated bacterial communities. Temporal variation in bacterial phylogenetic composition reflects changes of these complex interactions which occur during the algal growth cycle as well as throughout the lifetime of algal blooms. Viruses are also known to cause shifts in bacterial community diversity which could affect algal bloom phases. This study investigated on changes of bacterial and viral abundances, bacterial physiological status, and on bacterial successional pattern associated with the harmful benthic dinoflagellate Ostreopsis cf. ovata in batch cultures over the algal growth cycle. Bacterial community phylogenetic structure was assessed by 16S rRNA gene ION torrent sequencing. A comparison between bacterial community retrieved in cultures and that one co-occurring in situ during the development of the O. cf. ovata bloom from where the algal strain was isolated was also reported. Bacterial community growth was characterized by a biphasic pattern with the highest contributions (~60%) of highly active bacteria found at the two bacterial exponential growth steps. An alphaproteobacterial consortium composed by the Rhodobacteraceae Dinoroseobacter (22.2%-35.4%) and Roseovarius (5.7%-18.3%), together with Oceanicaulis (14.2-40.3%), was strongly associated with O. cf. ovata over the algal growth. The Rhodobacteraceae members encompassed phylotypes with an assessed mutualistic-pathogenic bimodal behavior. Fabibacter (0.7%-25.2%), Labrenzia (5.6%-24.3%), and Dietzia (0.04%-1.7%) were relevant at the stationary phase. Overall, the successional pattern and the metabolic and functional traits of the bacterial community retrieved in culture mirror those ones underpinning O. cf. ovata bloom dynamics in field. Viral abundances increased synoptically with bacterial abundances during the first bacterial exponential growth step while being stationary during the second step. Microbial trends

  11. Galactic civilizations - Population dynamics and interstellar diffusion

    Science.gov (United States)

    Newman, W. I.; Sagan, C.

    1981-01-01

    A model is developed of the interstellar diffusion of galactic civilizations which takes into account the population dynamics of such civilizations. The problem is formulated in terms of potential theory, with a family of nonlinear partial differential and difference equations specifying population growth and diffusion for an organism with advantageous genes that undergoes random dispersal while increasing in population locally, and a population at zero population growth. In the case of nonlinear diffusion with growth and saturation, it is found that the colonization wavefront from the nearest independently arisen galactic civilization can have reached the earth only if its lifetime exceeds 2.6 million years, or 20 million years if discretization can be neglected. For zero population growth, the corresponding lifetime is 13 billion years. It is concluded that the earth is uncolonized not because interstellar spacefaring civilizations are rare, but because there are too many worlds to be colonized in the plausible colonization lifetime of nearby civilizations, and that there exist no very old galactic civilizations with a consistent policy of the conquest of inhabited worlds.

  12. Source-sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities.

    Science.gov (United States)

    Hall, James P J; Wood, A Jamie; Harrison, Ellie; Brockhurst, Michael A

    2016-07-19

    Horizontal gene transfer is a fundamental process in bacterial evolution that can accelerate adaptation via the sharing of genes between lineages. Conjugative plasmids are the principal genetic elements mediating the horizontal transfer of genes, both within and between bacterial species. In some species, plasmids are unstable and likely to be lost through purifying selection, but when alternative hosts are available, interspecific plasmid transfer could counteract this and maintain access to plasmid-borne genes. To investigate the evolutionary importance of alternative hosts to plasmid population dynamics in an ecologically relevant environment, we established simple soil microcosm communities comprising two species of common soil bacteria, Pseudomonas fluorescens and Pseudomonas putida, and a mercury resistance (Hg(R)) plasmid, pQBR57, both with and without positive selection [i.e., addition of Hg(II)]. In single-species populations, plasmid stability varied between species: although pQBR57 survived both with and without positive selection in P. fluorescens, it was lost or replaced by nontransferable Hg(R) captured to the chromosome in P. putida A simple mathematical model suggests these differences were likely due to pQBR57's lower intraspecific conjugation rate in P. putida By contrast, in two-species communities, both models and experiments show that interspecific conjugation from P. fluorescens allowed pQBR57 to persist in P. putida via source-sink transfer dynamics. Moreover, the replacement of pQBR57 by nontransferable chromosomal Hg(R) in P. putida was slowed in coculture. Interspecific transfer allows plasmid survival in host species unable to sustain the plasmid in monoculture, promoting community-wide access to the plasmid-borne accessory gene pool and thus potentiating future evolvability.

  13. Critical dynamics in population vaccinating behavior.

    Science.gov (United States)

    Pananos, A Demetri; Bury, Thomas M; Wang, Clara; Schonfeld, Justin; Mohanty, Sharada P; Nyhan, Brendan; Salathé, Marcel; Bauch, Chris T

    2017-12-26

    Vaccine refusal can lead to renewed outbreaks of previously eliminated diseases and even delay global eradication. Vaccinating decisions exemplify a complex, coupled system where vaccinating behavior and disease dynamics influence one another. Such systems often exhibit critical phenomena-special dynamics close to a tipping point leading to a new dynamical regime. For instance, critical slowing down (declining rate of recovery from small perturbations) may emerge as a tipping point is approached. Here, we collected and geocoded tweets about measles-mumps-rubella vaccine and classified their sentiment using machine-learning algorithms. We also extracted data on measles-related Google searches. We find critical slowing down in the data at the level of California and the United States in the years before and after the 2014-2015 Disneyland, California measles outbreak. Critical slowing down starts growing appreciably several years before the Disneyland outbreak as vaccine uptake declines and the population approaches the tipping point. However, due to the adaptive nature of coupled behavior-disease systems, the population responds to the outbreak by moving away from the tipping point, causing "critical speeding up" whereby resilience to perturbations increases. A mathematical model of measles transmission and vaccine sentiment predicts the same qualitative patterns in the neighborhood of a tipping point to greatly reduced vaccine uptake and large epidemics. These results support the hypothesis that population vaccinating behavior near the disease elimination threshold is a critical phenomenon. Developing new analytical tools to detect these patterns in digital social data might help us identify populations at heightened risk of widespread vaccine refusal. Copyright © 2017 the Author(s). Published by PNAS.

  14. Characterization by culture-dependent and culture-1 independent methods of the 2 bacterial population of suckling-lamb packaged in different atmospheres

    NARCIS (Netherlands)

    Oses, S.M.; Diez, A.M.; Melero, B.; Luning, P.A.; Jaime, I.; Rovira, J.

    2013-01-01

    This study offers insight into the dynamics of bacterial populations in fresh cuts of suckling lamb under four different atmospheric conditions: air (A), and three Modified Atmosphere Packaging (MAP) environments, 15%O2/30%CO2/55%N2 (C, commercial), 70%O2/30%CO2 (O), and 15%O2/85%CO2 (H) for 18

  15. Seasonal changes in the heavy metal resistant bacterial population ...

    African Journals Online (AJOL)

    Seasonal changes and the contribution of industrial effluent discharges to the population of heavy metal – resistant bacteria (HMRB) in the river water and sediment of the New Calabar River, were examined. On exposure of river water microflora to 2µg of heavy metals, the HMRB population ranged from 55 to 78% in the ...

  16. Detailed analyses of the bacterial populations in processed cocoa beans of different geographic origin, subject to varied fermentation conditions.

    Science.gov (United States)

    Bortolini, Cristian; Patrone, Vania; Puglisi, Edoardo; Morelli, Lorenzo

    2016-11-07

    The quality of chocolate is influenced by several parameters, one of which is bacterial diversity during fermentation and drying; a crucial factor for the generation of the optimal cocoa flavor precursors. Our understanding of the bacterial populations involved in chocolate fermentation can be improved by the use of high-throughput sequencing technologies (HTS), combined with PCR amplification of the 16S rRNA subunit. Here, we have conducted a high-throughput assessment of bacterial diversity in four processed samples of cocoa beans from different geographic origins. As part of this study, we also assessed whether different DNA extraction methods could affect the quality of our data. The dynamics of microbial populations were analyzed postharvest (fermentation and sun drying) and shipment, before entry to the industrial process. A total of 691,867 high quality sequences were obtained by Illumina MiSeq sequencing of the two bacterial 16S rRNA hypervariable regions, V3 and V4, following paired-read assembly of the raw reads. Manual curation of the 16S database allowed us to assign the correct taxonomic classifications, at species level, for 83.8% of those reads. This approach revealed a limited biodiversity and population dynamics for both the lactic acid bacteria (LAB) and acetic acid bacteria (AAB), both of which are key players during the acetification and lactic acid fermentation phases. Among the LAB, the most abundant species were Lactobacillus fermentum, Enterococcus casseliflavus, Weissella paramesenteroides, and Lactobacillus plantarum/paraplantarum. Among the AAB, Acetobacter syzygii, was most abundant, then Acetobacter senegalensis and Acetobacter pasteriuanus. Our results indicate that HTS approach has the ability to provide a comprehensive view of the cocoa bean microbiota at the species level. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Bacterial meningitis in patients with HIV: A population-based prospective study.

    Science.gov (United States)

    van Veen, Kiril E B; Brouwer, Matthijs C; van der Ende, Arie; van de Beek, Diederik

    2016-03-01

    We studied occurrence, disease course, and prognosis of community-acquired bacterial meningitis in HIV-infected adults in the Netherlands. We performed a nationwide, prospective cohort study. Patients over 16 years old with bacterial meningitis were included. Data on patient history, symptoms and signs on admission, laboratory findings, radiologic examination, treatment, and outcome were collected prospectively. For HIV-positive patients additional information was collected retrospectively. From March 2006 to December 2013, 1354 episodes of community-acquired meningitis were included in the cohort. Thirteen patients were HIV-infected (1.0%). The annual incidence of bacterial meningitis was 8.3-fold higher (95%CI 4.6-15.1, P bacterial meningitis as compared to the general population despite cART therapy. Clinical presentation and outcome of patients with acute bacterial meningitis with and without HIV are similar. Copyright © 2016 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

  18. Monitoring microbial population dynamics at low densities

    Science.gov (United States)

    Julou, Thomas; Desprat, Nicolas; Bensimon, David; Croquette, Vincent

    2012-07-01

    We propose a new and simple method for the measurement of microbial concentrations in highly diluted cultures. This method is based on an analysis of the intensity fluctuations of light scattered by microbial cells under laser illumination. Two possible measurement strategies are identified and compared using simulations and measurements of the concentration of gold nanoparticles. Based on this comparison, we show that the concentration of Escherichia coli and Saccharomyces cerevisiae cultures can be easily measured in situ across a concentration range that spans five orders of magnitude. The lowest measurable concentration is three orders of magnitude (1000×) smaller than in current optical density measurements. We show further that this method can also be used to measure the concentration of fluorescent microbial cells. In practice, this new method is well suited to monitor the dynamics of population growth at early colonization of a liquid culture medium. The dynamic data thus obtained are particularly relevant for microbial ecology studies.

  19. Bacterial community dynamics and polycyclic aromatic hydrocarbon degradation during bioremediation of heavily creosote-contaminated soil.

    Science.gov (United States)

    Viñas, Marc; Sabaté, Jordi; Espuny, María José; Solanas, Anna M

    2005-11-01

    Bacterial community dynamics and biodegradation processes were examined in a highly creosote-contaminated soil undergoing a range of laboratory-based bioremediation treatments. The dynamics of the eubacterial community, the number of heterotrophs and polycyclic aromatic hydrocarbon (PAH) degraders, and the total petroleum hydrocarbon (TPH) and PAH concentrations were monitored during the bioremediation process. TPH and PAHs were significantly degraded in all treatments (72 to 79% and 83 to 87%, respectively), and the biodegradation values were higher when nutrients were not added, especially for benzo(a)anthracene and chrysene. The moisture content and aeration were determined to be the key factors associated with PAH bioremediation. Neither biosurfactant addition, bioaugmentation, nor ferric octate addition led to differences in PAH or TPH biodegradation compared to biodegradation with nutrient treatment. All treatments resulted in a high first-order degradation rate during the first 45 days, which was markedly reduced after 90 days. A sharp increase in the size of the heterotrophic and PAH-degrading microbial populations was observed, which coincided with the highest rates of TPH and PAH biodegradation. At the end of the incubation period, PAH degraders were more prevalent in samples to which nutrients had not been added. Denaturing gradient gel electrophoresis analysis and principal-component analysis confirmed that there was a remarkable shift in the composition of the bacterial community due to both the biodegradation process and the addition of nutrients. At early stages of biodegradation, the alpha-Proteobacteria group (genera Sphingomonas and Azospirillum) was the dominant group in all treatments. At later stages, the gamma-Proteobacteria group (genus Xanthomonas), the alpha-Proteobacteria group (genus Sphingomonas), and the Cytophaga-Flexibacter-Bacteroides group (Bacteroidetes) were the dominant groups in the nonnutrient treatment, while the gamma

  20. Bacterial communities differ among Drosophila melanogaster populations and affect host resistance against parasitoids

    NARCIS (Netherlands)

    Chaplinska, Mariia; Gerritsma, Sylvia; Dini-Andreote, Francisco; Falcao Salles, Joana; Wertheim, Bregje

    2016-01-01

    In Drosophila, diet is considered a prominent factor shaping the associated bacterial community. However, the host population background (e.g. genotype, geographical origin and founder effects) is a factor that may also exert a significant influence and is often overlooked. To test for population

  1. Population Model with a Dynamic Food Supply

    Science.gov (United States)

    Dickman, Ronald; da Silva Nascimento, Jonas

    2009-09-01

    We propose a simple population model including the food supply as a dynamic variable. In the model, survival of an organism depends on a certain minimum rate of food consumption; a higher rate of consumption is required for reproduction. We investigate the stationary behavior under steady food input, and the transient behavior of growth and decay when food is present initially but is not replenished. Under a periodic food supply, the system exhibits period-doubling bifurcations and chaos in certain ranges of the reproduction rate. Bifurcations and chaos are favored by a slow reproduction rate and a long period of food-supply oscillation.

  2. Population dynamical responses to climate change

    DEFF Research Database (Denmark)

    Forchhammer, Mads; Schmidt, Niels Martin; Høye, Toke Thomas

    2008-01-01

    , the effects of climate change may potentially extend through any of these interactions. In this chapter, we focus on the extent to which evolutionarily distinct species at different trophic levels respond to similar changes in climate. By using a broad spectrum of statistically and ecologically founded......, is related to differences in the compositions of predator and prey species. The significant inter-trophic interactions are centred on the collared lemming as a result of which there is a significant potential for indirect climate effects mediated across the established consumer-resource interactions......it is well established that climatic as well as biological factors, in concert, form the mechanistic basis for our understanding of how populations develop over time and across space. Although this seemingly suggests simplicity, the climate-biology dichotomy of population dynamics embraces...

  3. Diagnosis and Management of Bacterial Meningitis in the Paediatric Population: A Review

    Directory of Open Access Journals (Sweden)

    Catherine L. Tacon

    2012-01-01

    Full Text Available Paediatric bacterial meningitis is a neurological emergency which, despite advances in medical management, still has a significant morbidity and mortality. Over recent decades new vaccines have led to a change in epidemiology of the disease; however, it remains a condition that requires a high index of suspicion, prompt diagnosis, and early management in the emergency department. New laboratory techniques and clinical tools are aiding the diagnosis of bacterial meningitis, yet some controversies still exist in its management. This paper outlines the changing epidemiology of the disease, current diagnostic techniques as well as controversies and advances in the management of bacterial meningitis in the paediatric population.

  4. 10 original article dynamics of germs responsible for acute bacterial ...

    African Journals Online (AJOL)

    boaz

    The aim of this study was to analyze ten (10) years of epidemiological surveillance data of meningitis in Burkina Faso for high risk germs patterns identification in order to contribute to the strengthening of prevention strategies. A retrospective study of the past decade (2005- 2014) of cases of acute bacterial meningitis ...

  5. Dynamics of germs responsible for acute bacterial meningitis in ...

    African Journals Online (AJOL)

    The aim of this study was to analyze ten (10) years of epidemiological surveillance data of meningitis in Burkina Faso for high risk germs patterns identification in order to contribute to the strengthening of prevention strategies. A retrospective study of the past decade (2005- 2014) of cases of acute bacterial meningitis ...

  6. Bacterial predator–prey dynamics in microscale patchy landscapes

    NARCIS (Netherlands)

    Hol, F.J.H.; Rotem, Or; Jurkevitch, Edouard; Dekker, C.; Koster, D.

    2016-01-01

    Soil is a microenvironment with a fragmented (patchy) spatial structure in which many bacterial species interact. Here, we explore the interaction between the predatory bacterium Bdellovibrio bacteriovorus and its prey Escherichia coli in microfabricated landscapes. We ask how fragmentation

  7. Dynamic Computational Model of Symptomatic Bacteremia to Inform Bacterial Separation Treatment Requirements.

    Directory of Open Access Journals (Sweden)

    Sinead E Miller

    Full Text Available The rise of multi-drug resistance has decreased the effectiveness of antibiotics, which has led to increased mortality rates associated with symptomatic bacteremia, or bacterial sepsis. To combat decreasing antibiotic effectiveness, extracorporeal bacterial separation approaches have been proposed to capture and separate bacteria from blood. However, bacteremia is dynamic and involves host-pathogen interactions across various anatomical sites. We developed a mathematical model that quantitatively describes the kinetics of pathogenesis and progression of symptomatic bacteremia under various conditions, including bacterial separation therapy, to better understand disease mechanisms and quantitatively assess the biological impact of bacterial separation therapy. Model validity was tested against experimental data from published studies. This is the first multi-compartment model of symptomatic bacteremia in mammals that includes extracorporeal bacterial separation and antibiotic treatment, separately and in combination. The addition of an extracorporeal bacterial separation circuit reduced the predicted time of total bacteria clearance from the blood of an immunocompromised rodent by 49%, compared to antibiotic treatment alone. Implementation of bacterial separation therapy resulted in predicted multi-drug resistant bacterial clearance from the blood of a human in 97% less time than antibiotic treatment alone. The model also proposes a quantitative correlation between time-dependent bacterial load among tissues and bacteremia severity, analogous to the well-known 'area under the curve' for characterization of drug efficacy. The engineering-based mathematical model developed may be useful for informing the design of extracorporeal bacterial separation devices. This work enables the quantitative identification of the characteristics required of an extracorporeal bacteria separation device to provide biological benefit. These devices will potentially

  8. Reorganization of the bacterial and archaeal populations associated with organic loading conditions in a thermophilic anaerobic digester.

    Science.gov (United States)

    Hori, Tomoyuki; Haruta, Shin; Sasaki, Daisuke; Hanajima, Dai; Ueno, Yoshiyuki; Ogata, Atsushi; Ishii, Masaharu; Igarashi, Yasuo

    2015-03-01

    Organic loading conditions are an important factor influencing reactor performances in methanogenic bioreactors. Yet the underlying microbiological basis of the process stability, deterioration, and recovery remains to be understood. Here, structural responses of the bacterial and archaeal populations to the change of organic loading conditions in a thermophilic anaerobic digester were investigated by process analyses and 16S rRNA gene-based molecular approaches. The biogas was produced stably without the accumulation of volatile fatty acids (VFAs) at low organic loading rates (OLRs) in the beginning of reactor operation. Increasing OLR in stages disrupted the stable reactor performance, and high OLR conditions continued the deteriorated performance with slight biogas production and high accumulation of VFAs. Thereafter, the gradual decrease of OLR resulted in the recovery from the deterioration, giving rise to the stable performance again. The stable performances before and after the high OLR conditions conducted were associated with compositionally similar but not identical methanogenic consortia. The bacterial and archaeal populations were synchronously changed at both the transient phases toward the deteriorated performance and in recovery process, during which the dynamic shift of aceticlastic and hydrogenotrophic methanogens including the recently identified Methanomassiliicoccus might contribute to the maintenance of the methanogenic activity. The distinctive bacterial population with a high predominance of Methanobacterium formicicum as archaeal member was found for the deteriorated performance. The results in this study indicate the coordinated reorganization of the bacterial and archaeal populations in response to functional states induced by the change of organic loading conditions in the anaerobic digester. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  9. Seasonal Effect on the Bacterial and Fungal Population of an

    African Journals Online (AJOL)

    ... the microbial densities. llowcver, fungal counts l showed somewhat seasonahpollutant effect in two locationsv The chemical constituents of the wastewater are relatively of low toxicity and hence had no toxic effects on the soil microbial population Seasonal variations showed that the drier seasons supported large active ...

  10. Bacterial Contaminants of Poultry Meat: Sources, Species, and Dynamics

    OpenAIRE

    Rouger, Amélie; Tresse, Odile; Zagorec, Monique

    2017-01-01

    With the constant increase in poultry meat consumption worldwide and the large variety of poultry meat products and consumer demand, ensuring the microbial safety of poultry carcasses and cuts is essential. In the present review, we address the bacterial contamination of poultry meat from the slaughtering steps to the use-by-date of the products. The different contamination sources are identified. The contaminants occurring in poultry meat cuts and their behavior toward sanitizing treatments ...

  11. Population Dynamic of Dendronephthya sp.-Associated Bacteria in Natural and Artificial Habitats

    Directory of Open Access Journals (Sweden)

    SUSAN SOKA

    2011-06-01

    Full Text Available Dendronephthya sp. is a soft coral that has huge distribution starting from Indopacific, Tonga, Solomon Islands to Great Barrier Reef in Australia. However, this soft corals survive only in short period after cultivation in artificial habitat (aquarium. Recent study showed that the soft coral Dendronephtya sp. has an association or symbiotic relationship with several bacteria, commonly known as coral associated bacteria (CAB. In this study, we compared the population dynamic of Dendronephthya sp.-associated bacteria in natural and artificial habitat, resulting different bacterial community profiles using terminal restriction fragment length polymorphism (T-RFLP analysis of bacterial community DNA. There were 15 main classes of bacterial population identified along with uncultured microorganism, uncultured organism, uncultured bacteria and unidentified organism. Members of Actinobacteria, Arthrobacteria, Chlorobia, Caldilineae, Δ-proteobacteria and Proteobacteria were predicted to give contributions in the survival ability of both Dendronephthya sp. The cultivation of soft corals after 2 weeks in artificial habitat increases bacterial population similarity on 2 different samples by 10%. Bacterial population similarity in artificial habitat would increase along with the longer cultivation time of soft corals.

  12. Population Dynamic of Dendronephthya sp.-Associated Bacteria in Natural and Artificial Habitats

    Directory of Open Access Journals (Sweden)

    SUSAN SOKA

    2011-06-01

    Full Text Available Dendronephthya sp. is a soft coral that has huge distribution starting from Indopacific, Tonga, Solomon Islands to Great Barrier Reef in Australia. However, this soft corals survive only in short period after cultivation in artificial habitat (aquarium. Recent study showed that the soft coral Dendronephtya sp. has an association or symbiotic relationship with several bacteria, commonly known as coral associated bacteria (CAB. In this study, we compared the population dynamic of Dendronephthya sp.-associated bacteria in natural and artificial habitat, resulting different bacterial community profiles using terminal restriction fragment length polymorphism (T-RFLP analysis of bacterial community DNA. There were 15 main classes of bacterial population identified along with uncultured microorganism, uncultured organism, uncultured bacteria and unidentified organism. Members of Actinobacteria, Arthrobacteria, Chlorobia, Caldilineae, -proteobacteria and Proteobacteria were predicted to give contributions in the survival ability of both Dendronephthya sp. The cultivation of soft corals after 2 weeks in artificial habitat increases bacterial population similarity on 2 different samples by 10%. Bacterial population similarity in artificial habitat would increase along with the longer cultivation time of soft corals.

  13. Bacterial diversity in a nonsaline alkaline environment: heterotrophic aerobic populations.

    Science.gov (United States)

    Tiago, Igor; Chung, Ana Paula; Veríssimo, António

    2004-12-01

    Heterotrophic populations were isolated and characterized from an alkaline groundwater environment generated by active serpentinization, which results in a Ca(OH)2-enriched, extremely diluted groundwater with pH 11.4. One hundred eighty-five strains were isolated in different media at different pH values during two sampling periods. To assess the degree of diversity present in the environment and to select representative strains for further characterization of the populations, we screened the isolates by using random amplified polymorphic DNA-PCR profiles and grouped them based on similarities determined by fatty acid methyl ester analysis. Phenotypic characterization, determinations of G+C content, phylogenetic analyses by direct sequencing of 16S rRNA genes, and determinations of pH tolerance were performed with the selected isolates. Although 38 different populations were identified and characterized, the vast majority of the isolates were gram positive with high G+C contents and were affiliated with three distinct groups, namely, strains closely related to the species Dietzia natrolimnae (32% of the isolates), to Frigoribacterium/Clavibacter lineages (29% of the isolates), and to the type strain of Microbacterium kitamiense (20% of the isolates). Other isolates were phylogenetically related to strains of the genera Agrococcus, Leifsonia, Kytococcus, Janibacter, Kocuria, Rothia, Nesterenkonia, Citrococcus, Micrococcus, Actinomyces, Rhodococcus, Bacillus, and Staphylococcus. Only five isolates were gram negative: one was related to the Sphingobacteria lineage and the other four were related to the alpha-Proteobacteria lineage. Despite the pH of the environment, the vast majority of the populations were alkali tolerant, and only two strains were able to grow at pH 11.

  14. The dynamics and implications of bacterial transmission events arising from the anesthesia work area.

    Science.gov (United States)

    Loftus, Randy W; Koff, Matthew D; Birnbach, David J

    2015-04-01

    Health care-associated infections are a hospital-wide concern associated with a significant increase in patient morbidity, mortality, and health care costs. Bacterial transmission in the anesthesia work area of the operating room environment is a root cause of 30-day postoperative infections affecting as many as 16% of patients undergoing surgery. A better understanding of anesthesia-related bacterial transmission dynamics may help to generate improvements in intraoperative infection control and improve patient safety.

  15. Population pharmacokinetics of ceftaroline in patients with acute bacterial skin and skin structure infections or community-acquired bacterial pneumonia.

    Science.gov (United States)

    Van Wart, Scott A; Forrest, Alan; Khariton, Tatiana; Rubino, Christopher M; Bhavnani, Sujata M; Reynolds, Daniel K; Riccobene, Todd; Ambrose, Paul G

    2013-11-01

    Ceftaroline, the active form of ceftaroline fosamil, is a broad-spectrum cephalosporin antibiotic. A population pharmacokinetic (PPK) model for ceftaroline was developed in NONMEM® using data from 185 healthy subjects and 92 patients with acute bacterial skin and skin structure infection (ABSSSI). Data from 128 patients with community-acquired bacterial pneumonia (CABP) were used for external model validation. Healthy subjects received 50-2,000 mg ceftaroline fosamil via intravenous (IV) infusion over 1 hour or intramuscular (IM) injection q12h or q24h. ABSSSI and CABP patients received 600 mg of ceftaroline fosamil IV over 1 hour q12h. A three-compartment model with zero-order IV or parallel first-order IM input and first-order elimination described ceftaroline fosamil PK. A two-compartment model with first-order conversion of prodrug to ceftaroline and parallel linear and saturable elimination described ceftaroline PK. Creatinine clearance was the primary determinant of ceftaroline exposure. Good agreement between the observed data and both population (r(2)  = 0.93) and individual post-hoc (r(2)  = 0.98) predictions suggests the PPK model can adequately approximate ceftaroline PK using covariate information. Such a PPK model can evaluate dose adjustments for patients with renal impairment and generate ceftaroline exposures for use in pharmacokinetic-pharmacodynamic assessments of efficacy in patients with ABSSSI or CABP. © 2013, The American College of Clinical Pharmacology.

  16. Dynamics of inhomogeneous populations and global demography models

    OpenAIRE

    Karev, Georgy P.

    2005-01-01

    The dynamic theory of inhomogeneous populations developed during the last decade predicts several essential new dynamic regimes applicable even to the well-known, simple population models. We show that, in an inhomogeneous population with a distributed reproduction coefficient, the entire initial distribution of the coefficient should be used to investigate real population dynamics. In the general case, neither the average rate of growth nor the variance or any finite number of moments of the...

  17. On fermionic models of a closed ecosystem with application to bacterial populations

    Directory of Open Access Journals (Sweden)

    Rosa Di Salvo

    2016-09-01

    Full Text Available This paper deals with the application of operatorial techniques of quantum physics to a theoretical model of closed ecosystems. The model is built by using fermionic operators whose evolution is ruled by a self--adjoint Hamiltonian operator. Adopting Heisenberg--like dynamics, we consider either linear or nonlinear models with the aim of describing the long-term survival of bacterial populations; the introduction of effective dissipative mechanisms is also considered. Moreover, a variant of linear models through the introduction of additional rules acting periodically on the system is proposed. Specifically, the evolution in a time interval is obtained by gluing the evolutions in a finite set of adjacent subintervals. In each subinterval the Hamiltonian is time independent, but the values of the parameters entering the Hamiltonian may be changed by the rules at the end of a subinterval on the basis of the actual state of the system. Within this context, a new approach is provided in order to obtain reliable results, without increasing the computational cost of the numerical integration of the differential equations involved.

  18. Bacterial Contaminants of Poultry Meat: Sources, Species, and Dynamics

    Science.gov (United States)

    Rouger, Amélie; Zagorec, Monique

    2017-01-01

    With the constant increase in poultry meat consumption worldwide and the large variety of poultry meat products and consumer demand, ensuring the microbial safety of poultry carcasses and cuts is essential. In the present review, we address the bacterial contamination of poultry meat from the slaughtering steps to the use-by-date of the products. The different contamination sources are identified. The contaminants occurring in poultry meat cuts and their behavior toward sanitizing treatments or various storage conditions are discussed. A list of the main pathogenic bacteria of concern for the consumer and those responsible for spoilage and waste of poultry meat is established. PMID:28841156

  19. Analytic derivation of bacterial growth laws from a simple model of intracellular chemical dynamics.

    Science.gov (United States)

    Pandey, Parth Pratim; Jain, Sanjay

    2016-09-01

    Experiments have found that the growth rate and certain other macroscopic properties of bacterial cells in steady-state cultures depend upon the medium in a surprisingly simple manner; these dependencies are referred to as 'growth laws'. Here we construct a dynamical model of interacting intracellular populations to understand some of the growth laws. The model has only three population variables: an amino acid pool, a pool of enzymes that transport an external nutrient and produce the amino acids, and ribosomes that catalyze their own and the enzymes' production from the amino acids. We assume that the cell allocates its resources between the enzyme sector and the ribosomal sector to maximize its growth rate. We show that the empirical growth laws follow from this assumption and derive analytic expressions for the phenomenological parameters in terms of the more basic model parameters. Interestingly, the maximization of the growth rate of the cell as a whole implies that the cell allocates resources to the enzyme and ribosomal sectors in inverse proportion to their respective 'efficiencies'. The work introduces a mathematical scheme in which the cellular growth rate can be explicitly determined and shows that two large parameters, the number of amino acid residues per enzyme and per ribosome, are useful for making approximations.

  20. Influence of copper on Euplotes sp. and associated bacterial population

    Directory of Open Access Journals (Sweden)

    Guilherme Oliveira Andrade da Silva

    2014-05-01

    Full Text Available The influence of copper on the ciliate Euplotes sp. and associated bacteria isolated from sediment samples of Guanabara Bay were investigated in bioassays. This region is highly affected by heavy metals such as copper, from solid waste constantly dumped in the bay and other sources such as industrial effluents, antifouling paints, atmospheric deposition and urban drainage, and even today there are few data on the metal toxicity to the ecosystem of the Bay of Guanabara. Bioassays were conducted to estimate the LC50-24 h of copper, in order to determine the concentration of metal bearing 50% of the population mortality. The results indicated that the concentrations of 0.05 and 0.009 mg L-1 presented no toxicity to Euplotes sp. The associated bacteria are tolerant to copper concentrations used in bioassays, and suggest that they could be used as a potential agent in the bioremediation of areas affected by copper.

  1. Characteristics of phylogenetic diversity in airborne bacterial populations in China

    Science.gov (United States)

    Chaudhry, Zahra; Santarpia, Joshua L.; Martins, J. V.

    2011-05-01

    Considering their potential implications for human health, agricultural productivity, and ecosystem stability, surprisingly little is known about the composition or dynamics of the atmosphere's biological aerosols. The few studies that have examined phylogenetic diversity in China focused on a single sampling period, whereas this study spans 3 months and includes over 300 samples. The 300+ samples were categorized by month and direction of their back-trajectory. DNA extraction was carried out on the pooled samples in a quantitative manner to allow for comparison between the amount of extracted material and the amount of initial total aerosol mass. Within an individual month, samples originating from similar land types and approximately equidistant to the sampling location exhibited similar diversity, whereas samples originating from much greater distances and from different land types included phyla unique to that location. Phyla from the same origin also varied from one month to the next. The biological diversity found from the Phylochips reinforces the hypothesis that air samples carry a biological record of their history.

  2. Protozoa Drive the Dynamics of Culturable Biocontrol Bacterial Communities.

    Science.gov (United States)

    Müller, Maren Stella; Scheu, Stefan; Jousset, Alexandre

    2013-01-01

    Some soil bacteria protect plants against soil-borne diseases by producing toxic secondary metabolites. Such beneficial biocontrol bacteria can be used in agricultural systems as alternative to agrochemicals. The broad spectrum toxins responsible for plant protection also inhibit predation by protozoa and nematodes, the main consumers of bacteria in soil. Therefore, predation pressure may favour biocontrol bacteria and contribute to plant health. We analyzed the effect of Acanthamoeba castellanii on semi-natural soil bacterial communities in a microcosm experiment. We determined the frequency of culturable bacteria carrying genes responsible for the production of the antifungal compounds 2,4-diacetylphloroglucinol (DAPG), pyrrolnitrin (PRN) and hydrogen cyanide (HCN) in presence and absence of A. castellanii. We then measured if amoebae affected soil suppressiveness in a bioassay with sugar beet seedlings confronted to the fungal pathogen Rhizoctonia solani. Amoebae increased the frequency of both DAPG and HCN positive bacteria in later plant growth phases (2 and 3 weeks), as well as the average number of biocontrol genes per bacterium. The abundance of DAPG positive bacteria correlated with disease suppression, suggesting that their promotion by amoebae may enhance soil health. However, the net effect of amoebae on soil suppressiveness was neutral to slightly negative, possibly because amoebae slow down the establishment of biocontrol bacteria on the recently emerged seedlings used in the assay. The results indicate that microfaunal predators foster biocontrol bacterial communities. Understanding interactions between biocontrol bacteria and their predators may thus help developing environmentally friendly management practices of agricultural systems.

  3. Protozoa Drive the Dynamics of Culturable Biocontrol Bacterial Communities.

    Directory of Open Access Journals (Sweden)

    Maren Stella Müller

    Full Text Available Some soil bacteria protect plants against soil-borne diseases by producing toxic secondary metabolites. Such beneficial biocontrol bacteria can be used in agricultural systems as alternative to agrochemicals. The broad spectrum toxins responsible for plant protection also inhibit predation by protozoa and nematodes, the main consumers of bacteria in soil. Therefore, predation pressure may favour biocontrol bacteria and contribute to plant health. We analyzed the effect of Acanthamoeba castellanii on semi-natural soil bacterial communities in a microcosm experiment. We determined the frequency of culturable bacteria carrying genes responsible for the production of the antifungal compounds 2,4-diacetylphloroglucinol (DAPG, pyrrolnitrin (PRN and hydrogen cyanide (HCN in presence and absence of A. castellanii. We then measured if amoebae affected soil suppressiveness in a bioassay with sugar beet seedlings confronted to the fungal pathogen Rhizoctonia solani. Amoebae increased the frequency of both DAPG and HCN positive bacteria in later plant growth phases (2 and 3 weeks, as well as the average number of biocontrol genes per bacterium. The abundance of DAPG positive bacteria correlated with disease suppression, suggesting that their promotion by amoebae may enhance soil health. However, the net effect of amoebae on soil suppressiveness was neutral to slightly negative, possibly because amoebae slow down the establishment of biocontrol bacteria on the recently emerged seedlings used in the assay. The results indicate that microfaunal predators foster biocontrol bacterial communities. Understanding interactions between biocontrol bacteria and their predators may thus help developing environmentally friendly management practices of agricultural systems.

  4. Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy.

    Science.gov (United States)

    Ulrich, Nikea; Rosenberger, Abigail; Brislawn, Colin; Wright, Justin; Kessler, Collin; Toole, David; Solomon, Caroline; Strutt, Steven; McClure, Erin; Lamendella, Regina

    2016-06-15

    Bacterial community composition and longitudinal fluctuations were monitored in a riverine system during and after Superstorm Sandy to better characterize inter- and intracommunity responses associated with the disturbance associated with a 100-year storm event. High-throughput sequencing of the 16S rRNA gene was used to assess microbial community structure within water samples from Muddy Creek Run, a second-order stream in Huntingdon, PA, at 12 different time points during the storm event (29 October to 3 November 2012) and under seasonally matched baseline conditions. High-throughput sequencing of the 16S rRNA gene was used to track changes in bacterial community structure and divergence during and after Superstorm Sandy. Bacterial community dynamics were correlated to measured physicochemical parameters and fecal indicator bacteria (FIB) concentrations. Bioinformatics analyses of 2.1 million 16S rRNA gene sequences revealed a significant increase in bacterial diversity in samples taken during peak discharge of the storm. Beta-diversity analyses revealed longitudinal shifts in the bacterial community structure. Successional changes were observed, in which Betaproteobacteria and Gammaproteobacteria decreased in 16S rRNA gene relative abundance, while the relative abundance of members of the Firmicutes increased. Furthermore, 16S rRNA gene sequences matching pathogenic bacteria, including strains of Legionella, Campylobacter, Arcobacter, and Helicobacter, as well as bacteria of fecal origin (e.g., Bacteroides), exhibited an increase in abundance after peak discharge of the storm. This study revealed a significant restructuring of in-stream bacterial community structure associated with hydric dynamics of a storm event. In order to better understand the microbial risks associated with freshwater environments during a storm event, a more comprehensive understanding of the variations in aquatic bacterial diversity is warranted. This study investigated the bacterial

  5. Humpback whale populations share a core skin bacterial community: towards a health index for marine mammals?

    Directory of Open Access Journals (Sweden)

    Amy Apprill

    Full Text Available Microbes are now well regarded for their important role in mammalian health. The microbiology of skin--a unique interface between the host and environment--is a major research focus in human health and skin disorders, but is less explored in other mammals. Here, we report on a cross-population study of the skin-associated bacterial community of humpback whales (Megaptera novaeangliae, and examine the potential for a core bacterial community and its variability with host (endogenous or geographic/environmental (exogenous specific factors. Skin biopsies or freshly sloughed skin from 56 individuals were sampled from populations in the North Atlantic, North Pacific and South Pacific oceans and bacteria were characterized using 454 pyrosequencing of SSU rRNA genes. Phylogenetic and statistical analyses revealed the ubiquity and abundance of bacteria belonging to the Flavobacteria genus Tenacibaculum and the Gammaproteobacteria genus Psychrobacter across the whale populations. Scanning electron microscopy of skin indicated that microbial cells colonize the skin surface. Despite the ubiquity of Tenacibaculum and Psychrobater spp., the relative composition of the skin-bacterial community differed significantly by geographic area as well as metabolic state of the animals (feeding versus starving during migration and breeding, suggesting that both exogenous and endogenous factors may play a role in influencing the skin-bacteria. Further, characteristics of the skin bacterial community from these free-swimming individuals were assembled and compared to two entangled and three dead individuals, revealing a decrease in the central or core bacterial community members (Tenacibaculum and Psychrobater spp., as well as the emergence of potential pathogens in the latter cases. This is the first discovery of a cross-population, shared skin bacterial community. This research suggests that the skin bacteria may be connected to humpback health and immunity and could

  6. Humpback whale populations share a core skin bacterial community: towards a health index for marine mammals?

    Science.gov (United States)

    Apprill, Amy; Robbins, Jooke; Eren, A Murat; Pack, Adam A; Reveillaud, Julie; Mattila, David; Moore, Michael; Niemeyer, Misty; Moore, Kathleen M T; Mincer, Tracy J

    2014-01-01

    Microbes are now well regarded for their important role in mammalian health. The microbiology of skin--a unique interface between the host and environment--is a major research focus in human health and skin disorders, but is less explored in other mammals. Here, we report on a cross-population study of the skin-associated bacterial community of humpback whales (Megaptera novaeangliae), and examine the potential for a core bacterial community and its variability with host (endogenous) or geographic/environmental (exogenous) specific factors. Skin biopsies or freshly sloughed skin from 56 individuals were sampled from populations in the North Atlantic, North Pacific and South Pacific oceans and bacteria were characterized using 454 pyrosequencing of SSU rRNA genes. Phylogenetic and statistical analyses revealed the ubiquity and abundance of bacteria belonging to the Flavobacteria genus Tenacibaculum and the Gammaproteobacteria genus Psychrobacter across the whale populations. Scanning electron microscopy of skin indicated that microbial cells colonize the skin surface. Despite the ubiquity of Tenacibaculum and Psychrobater spp., the relative composition of the skin-bacterial community differed significantly by geographic area as well as metabolic state of the animals (feeding versus starving during migration and breeding), suggesting that both exogenous and endogenous factors may play a role in influencing the skin-bacteria. Further, characteristics of the skin bacterial community from these free-swimming individuals were assembled and compared to two entangled and three dead individuals, revealing a decrease in the central or core bacterial community members (Tenacibaculum and Psychrobater spp.), as well as the emergence of potential pathogens in the latter cases. This is the first discovery of a cross-population, shared skin bacterial community. This research suggests that the skin bacteria may be connected to humpback health and immunity and could possibly serve

  7. Genomic evolution of bacterial populations under coselection by antibiotics and phage.

    Science.gov (United States)

    Cairns, Johannes; Frickel, Jens; Jalasvuori, Matti; Hiltunen, Teppo; Becks, Lutz

    2017-04-01

    Bacteria live in dynamic systems where selection pressures can alter rapidly, forcing adaptation to the prevailing conditions. In particular, bacteriophages and antibiotics of anthropogenic origin are major bacterial stressors in many environments. We previously observed that populations of the bacterium Pseudomonas fluorescens SBW25 exposed to the lytic bacteriophage SBW25Φ2 and a noninhibitive concentration of the antibiotic streptomycin (coselection) achieved higher levels of phage resistance compared to populations exposed to the phage alone. In addition, the phage became extinct under coselection while remaining present in the phage alone environment. Further, phenotypic tests indicated that these observations might be associated with increased mutation rate under coselection. In this study, we examined the genetic causes behind these phenotypes by whole-genome sequencing clones isolated from the end of the experiments. We were able to identify genetic factors likely responsible for streptomycin resistance, phage resistance and hypermutable (mutator) phenotypes. This constitutes genomic evidence in support of the observation that while the presence of phage did not affect antibiotic resistance, the presence of antibiotic affected phage resistance. We had previously hypothesized an association between mutators and elevated levels of phage resistance under coselection. However, our evidence regarding the mechanism was inconclusive, as although with phage mutators were only found under coselection, additional genomic evidence was lacking and phage resistance was also observed in nonmutators under coselection. More generally, our study provides novel insights into evolution between univariate and multivariate selection (here two stressors), as well as the potential role of hypermutability in natural communities. © 2016 John Wiley & Sons Ltd.

  8. Effect of dietary monensin on the bacterial population structure of dairy cattle colonic contents.

    Science.gov (United States)

    McGarvey, Jeffery A; Hamilton, Scott W; DePeters, Edward J; Mitloehner, Frank M

    2010-02-01

    To determine the effect of monensin, a carboxylic polyether ionophore antibiotic, on the bacterial population structure of dairy cattle colonic contents, we fed six lactating Holstein cows a diet containing monensin (600 mg day(-1)) or an identical diet without monensin. Fresh waste samples were taken directly from the animals once a month for 3 months and assayed for their bacterial population structure via 16S rRNA gene sequence analysis. In total 6,912 16S rRNA genes were examined, comprising 345 and 315 operational taxonomic units (OTUs) from the monensin fed and control animals, respectively. Coverage estimates of the OTUs identified were 87.6% for the monensin fed and 88.3% for the control colonic content derived library. Despite this high level of coverage, no significant difference was found between the libraries down to the genus level. Thus we concluded that although monensin is believed to increase milk production in dairy cattle by altering the bacterial population structure within the bovine gastrointestinal tract, we were unable to identify any significant difference in the bacterial population structure of the colonic contents of monensin fed vs. the control dairy cattle, down to the genus level.

  9. Allee effects on population dynamics in continuous (overlapping) case

    International Nuclear Information System (INIS)

    Merdan, H.; Duman, O.; Akin, O.; Celik, C.

    2009-01-01

    This paper presents the stability analysis of equilibrium points of a continuous population dynamics with delay under the Allee effect which occurs at low population density. The mathematical results and numerical simulations show the stabilizing role of the Allee effects on the stability of the equilibrium point of this population dynamics.

  10. Population Density Modulates Drug Inhibition and Gives Rise to Potential Bistability of Treatment Outcomes for Bacterial Infections.

    Directory of Open Access Journals (Sweden)

    Jason Karslake

    2016-10-01

    Full Text Available The inoculum effect (IE is an increase in the minimum inhibitory concentration (MIC of an antibiotic as a function of the initial size of a microbial population. The IE has been observed in a wide range of bacteria, implying that antibiotic efficacy may depend on population density. Such density dependence could have dramatic effects on bacterial population dynamics and potential treatment strategies, but explicit measures of per capita growth as a function of density are generally not available. Instead, the IE measures MIC as a function of initial population size, and population density changes by many orders of magnitude on the timescale of the experiment. Therefore, the functional relationship between population density and antibiotic inhibition is generally not known, leaving many questions about the impact of the IE on different treatment strategies unanswered. To address these questions, here we directly measured real-time per capita growth of Enterococcus faecalis populations exposed to antibiotic at fixed population densities using multiplexed computer-automated culture devices. We show that density-dependent growth inhibition is pervasive for commonly used antibiotics, with some drugs showing increased inhibition and others decreased inhibition at high densities. For several drugs, the density dependence is mediated by changes in extracellular pH, a community-level phenomenon not previously linked with the IE. Using a simple mathematical model, we demonstrate how this density dependence can modulate population dynamics in constant drug environments. Then, we illustrate how time-dependent dosing strategies can mitigate the negative effects of density-dependence. Finally, we show that these density effects lead to bistable treatment outcomes for a wide range of antibiotic concentrations in a pharmacological model of antibiotic treatment. As a result, infections exceeding a critical density often survive otherwise effective treatments.

  11. Population dynamics of species-rich ecosystems: the mixture of matrix population models approach

    DEFF Research Database (Denmark)

    Mortier, Frédéric; Rossi, Vivien; Guillot, Gilles

    2013-01-01

    Matrix population models are widely used to predict population dynamics, but when applied to species-rich ecosystems with many rare species, the small population sample sizes hinder a good fit of species-specific models. This issue can be overcome by assigning species to groups to increase the size...... species with similar population dynamics....

  12. Evaluating seasonal dynamics of bacterial communities in marine fish aquaculture: a preliminary study before applying phage therapy.

    Science.gov (United States)

    Pereira, Carla; Salvador, Sara; Arrojado, Cátia; Silva, Yolanda; Santos, Ana L; Cunha, Angela; Gomes, Newton C M; Gomes, Newton; Almeida, Adelaide

    2011-04-01

    The increasing problem of antibiotic resistance in common pathogenic bacteria and the concern about the spreading of antibiotics in the environment bring the need to find new methods to control fish pathogens. Phage therapy represents a potential alternative to antibiotics, but its use in aquaculture requires a detailed understanding of bacterial communities, namely of fish pathogenic bacteria. Therefore, in this study the seasonal dynamics of the overall bacterial communities, microbiological water quality and disease-causing bacteria were followed in a marine aquaculture system of Ria de Aveiro (Portugal). Analysis of the bacterial diversity of the water samples by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments indicates that the bacterial community structure varied seasonally, showing a higher complexity during the warm season. The diversity of the main fish pathogenic bacteria, assessed by DGGE targeting the Vibrio genus, showed lower seasonal variation, with new dominating populations appearing mainly in the spring. Bacterial indicators, faecal coliforms and enterococci, enumerated by the filter-membrane method, also varied seasonally. The fluorescent in situ hybridization (FISH) results showed that the specific groups of bacteria varied during the study period and that the non-indigenous Enterobactereaceae family was the most abundant group followed by Vibrio and Aeromonas. The seasonal variation detected in terms of density and structure of total and pathogenic bacterial communities demonstrates the need for a careful monitoring of water through the year in order to select the suitable phages to inactivate fish pathogenic bacteria. The spring season seems to be the critical time period when phage therapy should be applied.

  13. Paraquat Herbicide in Peat Soil: I. Its Effects on The Dynamics of Microbial Population

    Directory of Open Access Journals (Sweden)

    Sebastian Margino

    2000-12-01

    Full Text Available Paraquat has been used widely and periodically in peat soil. It is stable in acid environments, therefore its application in peat soil which represents an acid environment, might prolong its persistence. Liming treatment has known to reduce peat soil acidity. This research was conducted to study the effect of paraquat and liming treatments on the dynamics of microbial population in peat soil. Unlimed and limed peat soil were treated with paraquat to a final concentration of 20 ppm, and incubated for 2 months. Microbiological analysis, consisting of counting of bacterial, actinomycetes, and fungal population were done weekly. The changes of pH value and paraquat residue were also measured. The results showed that in unlimed peat soil, paraquat treatment did not influence microbial population. However, when paraquat was added into limed peat soil, the number of microbial population decreased; especially the population of bacteria. Liming treatment increased bacterial population and changed the population dynamics of actinomycetes. No significant difference of fungal population in peat soil treated with paraquat and lime. Additionally, there was no significant difference in paraquat resistance between limed and unlimed peat soil.

  14. Phenotypic resistance and the dynamics of bacterial escape from phage control

    DEFF Research Database (Denmark)

    Bull, James J.; Vegge, Christina Skovgaard; Schmerer, Matthew

    2014-01-01

    The canonical view of phage - bacterial interactions in dense, liquid cultures is that the phage will eliminate most of the sensitive cells; genetic resistance will then ascend to restore high bacterial densities. Yet there are various mechanisms by which bacteria may remain sensitive to phages...... be specific to the receptors used by phages, awareness of its mechanisms may identify ways of improving the choice of phages for therapy. Phenotypic resistance can also explain several enigmas in the ecology of phage-bacterial dynamics. Phenotypic resistance does not preclude the evolution of genetic...... but still attain high densities in their presence - because bacteria enter a transient state of reduced adsorption. Importantly, these mechanisms may be cryptic and inapparent prior to the addition of phage yet result in a rapid rebound of bacterial density after phage are introduced. We describe...

  15. Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes.

    Science.gov (United States)

    Zhang, Yuanchen; Kastman, Erik K; Guasto, Jeffrey S; Wolfe, Benjamin E

    2018-01-23

    Most studies of bacterial motility have examined small-scale (micrometer-centimeter) cell dispersal in monocultures. However, bacteria live in multispecies communities, where interactions with other microbes may inhibit or facilitate dispersal. Here, we demonstrate that motile bacteria in cheese rind microbiomes use physical networks created by filamentous fungi for dispersal, and that these interactions can shape microbial community structure. Serratia proteamaculans and other motile cheese rind bacteria disperse on fungal networks by swimming in the liquid layers formed on fungal hyphae. RNA-sequencing, transposon mutagenesis, and comparative genomics identify potential genetic mechanisms, including flagella-mediated motility, that control bacterial dispersal on hyphae. By manipulating fungal networks in experimental communities, we demonstrate that fungal-mediated bacterial dispersal can shift cheese rind microbiome composition by promoting the growth of motile over non-motile community members. Our single-cell to whole-community systems approach highlights the interactive dynamics of bacterial motility in multispecies microbiomes.

  16. Combinations of bacterial species associated with symptomatic endodontic infections in a Chinese population.

    Science.gov (United States)

    Qi, Z; Cao, H; Jiang, H; Zhao, J; Tang, Z

    2016-01-01

    To use microarrays to detect 11 selected bacteria in infected root canals, revealing bacterial combinations that are associated with clinical symptoms and signs of primary endodontic infections in a Chinese population. DNA was extracted from 90 samples collected from the root canals of teeth with primary endodontic infections in a Chinese population, and the 16S rRNA gene was amplified by polymerase chain reaction (PCR). The PCR products were hybridized to microarrays containing specific oligonucleotide probes targeting 11 species, and the arrays were screened with a confocal laser scanner. Pearson's chi-squared test and cluster analysis were performed to investigate the associations between the bacterial combinations and clinical symptoms and signs using SAS 8.02. Seventy-seven samples (86%) yielded at least one of the 11 target species. Parvimonas micra (56%), Porphyromonas endodontalis (51%), Tannerella forsythia (48%), Prevotella intermedia (44%) and Porphyromonas gingivalis (37%) were the most prevalent taxa and were often concomitant. The following positive associations were found between the bacterial combinations and clinical features: P. endodontalis and T. forsythia with abscess; P. gingivalis and P. micra with sinus tract; P. gingivalis and P. endodontalis or P. micra and P. endodontalis with abscess and sinus tract; and the combination of P. endodontalis, P. micra, T. forsythia and P. gingivalis with sinus tract (P endodontic origin with bacterial synergism in a Chinese population. © 2015 International Endodontic Journal. Published by John Wiley & Sons Ltd.

  17. Neural Population Dynamics Underlying Motor Learning Transfer.

    Science.gov (United States)

    Vyas, Saurabh; Even-Chen, Nir; Stavisky, Sergey D; Ryu, Stephen I; Nuyujukian, Paul; Shenoy, Krishna V

    2018-03-07

    Covert motor learning can sometimes transfer to overt behavior. We investigated the neural mechanism underlying transfer by constructing a two-context paradigm. Subjects performed cursor movements either overtly using arm movements, or covertly via a brain-machine interface that moves the cursor based on motor cortical activity (in lieu of arm movement). These tasks helped evaluate whether and how cortical changes resulting from "covert rehearsal" affect overt performance. We found that covert learning indeed transfers to overt performance and is accompanied by systematic population-level changes in motor preparatory activity. Current models of motor cortical function ascribe motor preparation to achieving initial conditions favorable for subsequent movement-period neural dynamics. We found that covert and overt contexts share these initial conditions, and covert rehearsal manipulates them in a manner that persists across context changes, thus facilitating overt motor learning. This transfer learning mechanism might provide new insights into other covert processes like mental rehearsal. Copyright © 2018 Elsevier Inc. All rights reserved.

  18. Long-Term Bacterial Dynamics in a Full-Scale Drinking Water Distribution System

    NARCIS (Netherlands)

    Prest, E.I.E.D.; Weissbrodt, D.G.; Hammes, F; van Loosdrecht, Mark C.M.; Vrouwenvelder, J.S.

    2016-01-01

    Large seasonal variations in microbial drinking water quality can occur in distribution networks, but are often not taken into account when evaluating results from short-term water sampling campaigns. Temporal dynamics in bacterial community characteristics were investigated during a two-year

  19. Dynamics of Bacterial Community Abundance and Structure in Horizontal Subsurface Flow Wetland Mesocosms Treating Municipal Wastewater

    Directory of Open Access Journals (Sweden)

    Kristjan Oopkaup

    2016-10-01

    Full Text Available Dynamics of bacterial community abundance and structure of a newly established horizontal subsurface flow (HSSF pilot-scale wetland were studied using high-throughput sequencing and quantitative polymerase chain reaction (PCR methods. Bacterial community abundance increased rapidly within one month and stabilised thereafter in three replicate HSSF constructed wetland (CW mesocosms. The most dominant phylum was Proteobacteria, followed by Bacteroidetes in wetland media biofilms and Firmicutes in influent wastewater. CW bacterial community diversity increased over time and was positively related to the wastewater treatment efficiency. Increase in the abundance of total bacteria in the community was accompanied with the abundance of denitrifying bacteria that promoted nitrate and nitrite removal from the wastewater. During the 150-day study period, similar patterns of bacterial community successions were observed in replicate HSSF CW mesocosms. The data indicate that successions in the bacterial community in HSSF CW are shaped by biotic interactions, with a significant contribution made by external abiotic factors such as influent chemical parameters. Network analysis of the bacterial community revealed that organic matter and nitrogen removal in HSSF CW could be, in large part, allocated to a small subset of tightly interconnected bacterial species. The diversity of bacterial community and abundance of denitrifiers were good predictors of the removal efficiency of ammonia, nitrate and total organic C in HSSF CW mesocosms, while the removal of the seven-day biochemical oxygen demand (BOD7 was best predicted by the abundance of a small set of bacterial phylotypes. The results suggest that nitrogen removal in HSSF CW consist of two main pathways. The first is heterotrophic nitrification, which is coupled with aerobic denitrification and mediated by mixotrophic nitrite-oxidizers. The second pathway is anaerobic denitrification, which leads to gaseous

  20. Biochemical fingerprinting of water coliform bacteria, a new method for measuring phenotypic diversity and for comparing different bacterial populations.

    Science.gov (United States)

    Kühn, I; Allestam, G; Stenström, T A; Möllby, R

    1991-01-01

    A simple, automated microplate system for biochemical characterization of water isolates can be used to obtain fingerprints of the bacterial flora from various water samples. Mathematical models for calculating the diversities and similarities between bacterial populations are described for such fingerprints. The diversity may give information on whether an indigenous or allochthonous flora is present, and the similarities between bacterial populations, as calculated by using a population similarity coefficient (Sp), may indicate contaminations between different water samples. The system was demonstrated on coliform bacterial populations from various water samples, with or without suspected intercontamination. For unrelated water samples, the Sps were close to 0, whereas repeated samples of the same source showed Sps of 0.64 to 0.74. The Sp values from several water samples were also clustered to form a dendrogram, thus indicating the relative similarities between the bacterial populations to confirm suspected common sources of pollution. PMID:1781680

  1. Microscopic dynamics and velocity profiles of bacterial superfluids under oscillatory shear

    Science.gov (United States)

    Cheng, Xiang; Guo, Shuo; Samanta, Devranjan; Peng, Yi; Xu, Xinliang

    Bacterial suspensions a premier example of active fluids show an unusual response to shear stresses. Rather than increasing the viscosity of the suspending fluid, swimming bacteria can self-organize into collective flows under shear, turning the suspension into a ``superfluid'' with zero apparent viscosity. Although the existence of the bacterial superfluid has been demonstrated in bulk rheology measurements, little is known about the microscopic dynamics of such an exotic phase. Here, by combining sensitive rheology measurements with high-speed confocal microscopy, we study the detailed 3D dynamics of concentrated bacterial suspensions confined in narrow gaps under oscillatory shear. We find that sheared bacterial suspensions in the superfluidic phase exhibit velocity profiles with strong spatial heterogeneity, unexpected from the established hydrodynamic theory of active fluids. We quantitatively explain the observed velocity profiles by considering a balance of active stresses and shear stresses in an ensemble average. Our experiments reveal a profound influence of shear flows on bacterial locomotion and provide new insights to the origin of the unique flow behaviors of active fluids.

  2. Temporal Dynamics of Bacterial and Fungal Community Composition in the Atmospheric Boundary Layer

    Science.gov (United States)

    Emerson, J. B.; Perring, A. E.; Schwarz, J. P.; Fahey, D. W.; Fierer, N.

    2014-12-01

    There is increasing evidence for significant microbial influences on atmospheric chemistry, cloud condensation, and ice nuclei concentrations, with known health impacts, yet we have a limited understanding of the types, abundances, and spatiotemporal dynamics of bacteria and fungi in the atmosphere. Here we use culture-independent molecular approaches, including targeted gene sequencing and quantitative PCR, to characterize bacterial and fungal community composition and abundance in the atmospheric boundary layer. We present results from 32 air samples, collected via vacuum filtration at 10 m and 250 m on the Boulder Atmospheric Observatory tower (Erie, CO) between November 2013 and April 2014. Samples were collected at night, and each sample was integrated over consecutive nights for approximately two weeks. Significant temporal shifts in bacterial and fungal community composition were observed over the course of the study, corresponding to changing bacterial and fungal concentrations. Within the same sampling time periods, bacterial and fungal communities from the near-surface atmosphere (10 m) were generally similar to those aloft (250 m), although coupled temporal and altitudinal effects were observed in some cases, particularly for fungi. Overall, our results indicate that bacterial and fungal communities exhibit minimal vertical stratification throughout the nocturnal atmospheric boundary layer but show a high degree of variability on two-week timescales. This study paves the way for further research into the connections between boundary layer microbiology, atmospheric dynamics, emissions, and local meteorology.

  3. Dynamics of self-organized rotating spiral-coils in bacterial swarms.

    Science.gov (United States)

    Lin, Szu-Ning; Lo, Wei-Chang; Lo, Chien-Jung

    2014-02-07

    Self-propelled particles (SPP) exhibit complex collective motions, mimicking autonomous behaviors that are often seen in the natural world, but essentially are generated by simple mutual interactions. Previous research on SPP systems focuses on collective behaviors of a uniform population. However, very little is known about the evolution of individual particles under the same global influence. Here we show self-organized rotating spiral coils in a two-dimensional (2D) active system. By using swarming bacteria Vibrio alginolyticus as an ideal experimental realization of a well-controlled 2D self-propelled system, we study the interaction between ultra-long cells and short background active cells. The self-propulsion of long cells and their interactions with neighboring short cells leads to a self-organized, stable spiral rotational state in 2D. We find four types of spiral coils with two main features: the rotating direction (clockwise or counter-clockwise) and the central structure (single or double spiral). The body length of the spiral coils falls between 32 and 296 μm and their rotational speed is within a range from 2.22 to 22.96 rad s(-1). The dynamics of these spiral coils involves folding and unfolding processes, which require local velocity changes of the long bacterium. This phenomenon can be qualitatively replicated by a Brownian dynamics simulation using a simple rule of the propulsion thrust, imitating the reorientation of bacterial flagella. Apart from the physical and biological interests in swarming cells, the formation of self-organized spiral coils could be useful for the next generation of microfabrication.

  4. Dynamic Effects of Biochar on the Bacterial Community Structure in Soil Contaminated with Polycyclic Aromatic Hydrocarbons.

    Science.gov (United States)

    Song, Yang; Bian, Yongrong; Wang, Fang; Xu, Min; Ni, Ni; Yang, Xinglun; Gu, Chenggang; Jiang, Xin

    2017-08-16

    Amending soil with biochar is an effective soil remediation strategy for organic contaminants. This study investigated the dynamic effects of wheat straw biochar on the bacterial community structure during remediation by high-throughput sequencing. The wheat straw biochar amended into the soil significantly reduced the bioavailability and toxicity of polycyclic aromatic hydrocarbons (PAHs). Biochar amendment helped to maintain the bacterial diversity in the PAH-contaminated soil. The relationship between the immobilization of PAHs and the soil bacterial diversity fit a quadratic model. Before week 12 of the incubation, the incubation time was the main factor contributing to the changes in the soil bacterial community structure. However, biochar greatly affected the bacterial community structure after 12 weeks of amendment, and the effects were dependent upon the biochar type. Amendment with biochar mainly facilitated the growth of rare bacterial genera (relative abundance of 0.01-1%) in the studied soil. Therefore, the application of wheat straw biochar into PAH-contaminated soil can reduce the environmental risks of PAHs and benefit the soil microbial ecology.

  5. Multiscale modeling of bacterial colonies: how pili mediate the dynamics of single cells and cellular aggregates

    Science.gov (United States)

    Pönisch, Wolfram; Weber, Christoph A.; Juckeland, Guido; Biais, Nicolas; Zaburdaev, Vasily

    2017-01-01

    Neisseria gonorrhoeae is the causative agent of one of the most common sexually transmitted diseases, gonorrhea. Over the past two decades there has been an alarming increase of reported gonorrhea cases where the bacteria were resistant to the most commonly used antibiotics thus prompting for alternative antimicrobial treatment strategies. The crucial step in this and many other bacterial infections is the formation of microcolonies, agglomerates consisting of up to several thousands of cells. The attachment and motility of cells on solid substrates as well as the cell-cell interactions are primarily mediated by type IV pili, long polymeric filaments protruding from the surface of cells. While the crucial role of pili in the assembly of microcolonies has been well recognized, the exact mechanisms of how they govern the formation and dynamics of microcolonies are still poorly understood. Here, we present a computational model of individual cells with explicit pili dynamics, force generation and pili-pili interactions. We employ the model to study a wide range of biological processes, such as the motility of individual cells on a surface, the heterogeneous cell motility within the large cell aggregates, and the merging dynamics and the self-assembly of microcolonies. The results of numerical simulations highlight the central role of pili generated forces in the formation of bacterial colonies and are in agreement with the available experimental observations. The model can quantify the behavior of multicellular bacterial colonies on biologically relevant temporal and spatial scales and can be easily adjusted to include the geometry and pili characteristics of various bacterial species. Ultimately, the combination of the microbiological experimental approach with the in silico model of bacterial colonies might provide new qualitative and quantitative insights on the development of bacterial infections and thus pave the way to new antimicrobial treatments.

  6. Dynamics of highly polydisperse colloidal suspensions as a model system for bacterial cytoplasm.

    Science.gov (United States)

    Hwang, Jiye; Kim, Jeongmin; Sung, Bong June

    2016-08-01

    There are various kinds of macromolecules in bacterial cell cytoplasm. The size polydispersity of the macromolecules is so significant that the crystallization and the phase separation could be suppressed, thus stabilizing the liquid state of bacterial cytoplasm. On the other hand, recent experiments suggested that the macromolecules in bacterial cytoplasm should exhibit glassy dynamics, which should be also affected significantly by the size polydispersity of the macromolecules. In this work, we investigate the anomalous and slow dynamics of highly polydisperse colloidal suspensions, of which size distribution is chosen to mimic Escherichia coli cytoplasm. We find from our Langevin dynamics simulations that the diffusion coefficient (D_{tot}) and the displacement distribution functions (P(r,t)) averaged over all colloids of different sizes do not show anomalous and glassy dynamic behaviors until the system volume fraction ϕ is increased up to 0.82. This indicates that the intrinsic polydispersity of bacterial cytoplasm should suppress the glass transition and help maintain the liquid state of the cytoplasm. On the other hand, colloids of each kind show totally different dynamic behaviors depending on their size. The dynamics of colloids of different size becomes non-Gaussian at a different range of ϕ, which suggests that a multistep glass transition should occur. The largest colloids undergo the glass transition at ϕ=0.65, while the glass transition does not occur for smaller colloids in our simulations even at the highest value of ϕ. We also investigate the distribution (P(θ,t)) of the relative angles of displacement for macromolecules and find that macromolecules undergo directionally correlated motions in a sufficiently dense system.

  7. Archaeal and bacterial community dynamics and bioprocess performance of a bench-scale two-stage anaerobic digester.

    Science.gov (United States)

    Gonzalez-Martinez, Alejandro; Garcia-Ruiz, Maria Jesus; Rodriguez-Sanchez, Alejandro; Osorio, Francisco; Gonzalez-Lopez, Jesus

    2016-07-01

    Two-stage technologies have been developed for anaerobic digestion of waste-activated sludge. In this study, the archaeal and bacterial community structure dynamics and bioprocess performance of a bench-scale two-stage anaerobic digester treating urban sewage sludge have been studied by the means of high-throughput sequencing techniques and physicochemical parameters such as pH, dried sludge, volatile dried sludge, acid concentration, alkalinity, and biogas generation. The coupled analyses of archaeal and bacterial communities and physicochemical parameters showed a direct relationship between archaeal and bacterial populations and bioprocess performance during start-up and working operation of a two-stage anaerobic digester. Moreover, results demonstrated that archaeal and bacterial community structure was affected by changes in the acid/alkalinity ratio in the bioprocess. Thus, a predominance of the acetoclastic methanogen Methanosaeta was observed in the methanogenic bioreactor at high-value acid/alkaline ratio, while a predominance of Methanomassilicoccaeceae archaea and Methanoculleus genus was observed in the methanogenic bioreactor at low-value acid/alkaline ratio. Biodiversity tag-iTag sequencing studies showed that methanogenic archaea can be also detected in the acidogenic bioreactor, although its biological activity was decreased after 4 months of operation as supported by physicochemical analyses. Also, studies of the VFA producers and VFA consumers microbial populations showed as these microbiota were directly affected by the physicochemical parameters generated in the bioreactors. We suggest that the results obtained in our study could be useful for future implementations of two-stage anaerobic digestion processes at both bench- and full-scale.

  8. A comparison of bacterial populations in enhanced biological phosphorus removal processes using membrane filtration or gravity sedimentation for solids-liquid separation.

    Science.gov (United States)

    Hall, Eric R; Monti, Alessandro; Mohn, William W

    2010-05-01

    In an earlier phase of this study, we compared the performances of pilot scale treatment systems operated in either a conventional enhanced biological phosphorus removal (CEBPR) mode, or a membrane enhanced biological phosphorus removal (MEBPR) mode. In the present investigation, we characterized the bacterial community populations in these processes during parallel operation with the same municipal wastewater feed. The objectives of the study were (1) to assess the similarity of the bacterial communities supported in the two systems over time, (2) to determine if distinct bacterial populations are associated with the MEBPR and CEBPR processes, and (3) to relate the dynamics of the community composition to changes in treatment process configuration and to treatment process performance. The characteristics of the bacterial populations were first investigated with ribosomal intergenic spacer analysis, or RISA. To further understand the bacterial population dynamics, important RISA phylotypes were isolated and identified through 16S RNA gene sequencing. The parallel MEBPR and CEBPR systems developed bacterial communities that were distinct. The CEBPR community appeared to exhibit greater diversity, and this may have been the primary reason why the CEBPR treatment train demonstrated superior functional stability relative to the MEBPR counterpart. Moreover, the more diverse bacterial population apparent in the CEBPR system was observed to be more dynamic than that of the MEBPR process. Several RISA bands were found to be characteristic of either the membrane or conventional biological system. In particular, the MEBPR configuration appeared to be selective for the slow-growing organism Magnospira bakii and for the foam-associated Microthrix parvicella and Gordonia sp., while gravity separation led to the washout of M. parvicella. In both pilot trains, sequence analysis confirmed the presence of EBPR-related organisms such as Accumulibacter phosphatis. The survey of the

  9. Evolutionary dynamics with fluctuating population sizes and strong mutualism.

    Science.gov (United States)

    Chotibut, Thiparat; Nelson, David R

    2015-08-01

    Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems.

  10. Evolutionary dynamics with fluctuating population sizes and strong mutualism

    Science.gov (United States)

    Chotibut, Thiparat; Nelson, David R.

    2015-08-01

    Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems.

  11. The habits of highly effective phages: population dynamics as a framework for identifying therapeutic phages

    Directory of Open Access Journals (Sweden)

    James J Bull

    2014-11-01

    Full Text Available The use of bacteriophages as antibacterial agents is being actively researched on a global scale. Typically, the phages used are isolated from the wild by plating on the bacteria of interest, and a far larger set of candidate phages is often available than can be used in any application. When an excess of phages is available, how should the best phages be identified? Here we consider phage-bacterial population dynamics as a basis for evaluating and predicting phage success. A central question is whether the innate dynamical properties of phages are the determinants of success, or instead, whether extrinsic, indirect effects can be responsible. We address the dynamical perspective, motivated in part by the absence of dynamics in previously suggested principles of phage therapy. Current mathematical models of bacterial-phage dynamics do not capture the realities of in vivo dynamics, nor is this likely to change, but they do give insight to qualitative properties that may be generalizable. In particular, phage adsorption rate may be critical to treatment success, so understanding the effects of the in vivo environment on host availability may allow prediction of useful phages prior to in vivo experimentation. Principles for predicting efficacy may be derived by developing a greater understanding of the in vivo system, or such principles could be determined empirically by comparing phages with known differences in their dynamic properties. The comparative approach promises to be a powerful method of discovering the key to phage success. We offer five recommendations for future study: (i compare phages differing in treatment efficacy to identify the phage properties associated with success, (ii assay dynamics in vivo, (iii understand mechanisms of bacterial escape from phages, (iv test phages in model infections that are relevant to the intended clinical applications, and (v develop new classes of models for phage growth in spatially heterogeneous

  12. Supplemental Dietary Inulin of Variable Chain Lengths Alters Intestinal Bacterial Populations in Young Pigs123

    Science.gov (United States)

    Patterson, Jannine K.; Yasuda, Koji; Welch, Ross M.; Miller, Dennis D.; Lei, Xin Gen

    2010-01-01

    Previously, we showed that supplementation of diets with short-chain inulin (P95), long-chain inulin (HP), and a 50:50 mixture of both (Synergy 1) improved body iron status and altered expression of the genes involved in iron homeostasis and inflammation in young pigs. However, the effects of these 3 types of inulin on intestinal bacteria remain unknown. Applying terminal restriction fragment length polymorphism analysis, we determined the abundances of luminal and adherent bacterial populations from 6 segments of the small and large intestines of pigs (n = 4 for each group) fed an iron-deficient basal diet (BD) or the BD supplemented with 4% of P95, Synergy 1, or HP for 5 wk. Compared with BD, all 3 types of inulin enhanced (P inulin on bacterial populations in the lumen contents were found. Meanwhile, all 3 types of inulin suppressed the less desirable bacteria Clostridium spp. and members of the Enterobacteriaceae in the lumen and mucosa of various gut segments. Our findings suggest that the ability of dietary inulin to alter intestinal bacterial populations may partially account for its iron bioavailability-promoting effect and possibly other health benefits. PMID:20980641

  13. Bacterial Communities Differ among Drosophila melanogaster Populations and Affect Host Resistance against Parasitoids.

    Science.gov (United States)

    Chaplinska, Mariia; Gerritsma, Sylvia; Dini-Andreote, Francisco; Falcao Salles, Joana; Wertheim, Bregje

    2016-01-01

    In Drosophila, diet is considered a prominent factor shaping the associated bacterial community. However, the host population background (e.g. genotype, geographical origin and founder effects) is a factor that may also exert a significant influence and is often overlooked. To test for population background effects, we characterized the bacterial communities in larvae of six genetically differentiated and geographically distant D. melanogaster lines collected from natural populations across Europe. The diet for these six lines had been identical for ca. 50 generations, thus any differences in the composition of the microbiome originates from the host populations. We also investigated whether induced shifts in the microbiome-in this case by controlled antibiotic administration-alters the hosts' resistance to parasitism. Our data revealed a clear signature of population background on the diversity and composition of D. melanogaster microbiome that differed across lines, even after hosts had been maintained at the same diet and laboratory conditions for over 4 years. In particular, the number of bacterial OTUs per line ranged from 8 to 39 OTUs. Each line harboured 2 to 28 unique OTUs, and OTUs that were highly abundant in some lines were entirely missing in others. Moreover, we found that the response to antibiotic treatment differed among the lines and significantly altered the host resistance to the parasitoid Asobara tabida in one of the six lines. Wolbachia, a widespread intracellular endosymbiont associated with parasitoid resistance, was lacking in this line, suggesting that other components of the Drosophila microbiome caused a change in host resistance. Collectively, our results revealed that lines that originate from different population backgrounds show significant differences in the established Drosophila microbiome, outpacing the long-term effect of diet. Perturbations on these naturally assembled microbiomes to some degree influenced the hosts' resistance

  14. Biodegradation of polycyclic aromatic hydrocarbons, selection and dynamics of bacterial populations in the rhizosphere in relation with the distance to roots; Biodegradation des Hydrocarbures Aromatiques Polycycliques, selection et dynamique des populations bacteriennes dans la rhizosphere en fonction de la distance aux racines

    Energy Technology Data Exchange (ETDEWEB)

    Corgie, St.

    2004-03-01

    The biodegradation of Polycyclic Aromatic Hydrocarbons (PAH) is mainly performed by microorganisms that can use these compounds as sole source of carbon and energy. Such capacity has been amply studied to use and optimise microbial activity for remediation of contaminated soils. The use of plants has been suggested to increase and accelerate biodegradation rate by improving microbial activity. However, biodegradation mechanisms still remain poorly described as the interactions between plant, pollutant and rhizosphere microflora are often complex. A simplified compartmented device was developed to study rhizospheric processes, especially biodegradation of PAH, as a function of distance to roots, where root exudates and/or PAH were the only carbon sources for microbial growth. The development and use of bio-molecular techniques (nucleic acid isolation, PCR, RT-PCR, TGGE, hybridization with a degradation gene specific probe) permitted to follow the structure of bacterial communities. Gradients of phenanthrene biodegradation were observed as a function of distance to roots, in parallel to spatial and temporal variations in bacterial community structure. These bacterial communities, as well as PAH biodegradation rate, also depended on the aromaticity of PAH and were modified by the symbiosis between plant and an arbuscular mycorrhizal fungus. (author)

  15. Review Of the interplay between population dynamics and

    African Journals Online (AJOL)

    Review Of the interplay between population dynamics and malaria transmission in Ethiopia. Wakgari Deressa, Ahmed Ali, Yemane Berhane. Abstract. Background: The rapid growth of human population in malaria endemic areas has become a threat leading to the resurgence of the disease. Population growth and ...

  16. Leisure Today: Population Dynamics--The Changing Face of America.

    Science.gov (United States)

    Dunn, Diana R., Ed.; And Others

    1981-01-01

    A collection of articles examines the changing character of the American population and the importance of planning new recreation and leisure services to meet changing population needs. Included are discussions on demography and population dynamics; the effects of immigration; changing work and life styles; and changes in family structure and…

  17. [The effect of the new technological revolution on population dynamics].

    Science.gov (United States)

    Wu, K

    1985-01-29

    The impact of modernization on population dynamics in China is examined. The author notes that the industrialization process involves the concentration of the population in urban areas and the mechanization of agriculture. The need to redistribute the urban population from major urban areas to smaller towns is noted.

  18. Population dynamics model for plasmid bearing and plasmid lacking ...

    African Journals Online (AJOL)

    Streptokinase production in bioreactor is well associated to cell population dynamics. It is an established fact that two types of cell populations are found to emerge from the initial pool of recombinant cell population. This phenomenon leads to an undesired loss in yield of the product. Primary metabolites, like acetic acid etc ...

  19. Bacterial meningitis in hematopoietic stem cell transplant recipients: a population-based prospective study.

    Science.gov (United States)

    van Veen, K E B; Brouwer, M C; van der Ende, A; van de Beek, D

    2016-11-01

    We performed a nationwide prospective cohort study on the epidemiology and clinical features of community-acquired bacterial meningitis. Patients with a medical history of autologous or allogeneic hematopoietic stem cell transplantation (HSCT) were identified from the cohort performed from March 2006 to October 2014. Fourteen of 1449 episodes (1.0%) of bacterial meningitis occurred in patients with a history of HSCT. The incidence of bacterial meningitis in HSCT recipients was 40.4 per 100 000 patients per year (95% confidence interval (CI) 23.9-62.2), which is 30-fold (95% CI 18-51; Pmeningitis were infected with a serotype included in the 23-valent pneumococcal polysaccharide vaccine, of whom four developed meningitis despite vaccination. In conclusion, HSCT recipients have a substantially increased risk compared with the general population of acquiring bacterial meningitis, which is mostly due to S. pneumoniae, and disease is associated with high mortality and morbidity. Vaccination is important to prevent disease although vaccine failures did occur.

  20. The dynamic nature and territory of transcriptional machinery in the bacterial chromosome

    Directory of Open Access Journals (Sweden)

    Ding Jun Jin

    2015-05-01

    Full Text Available Our knowledge of the regulation of genes involved in bacterial growth and stress responses is extensive; however, we have only recently begun to understand how environmental cues influence the dynamic, three-dimensional distribution of RNA polymerase (RNAP in Escherichia coli on the level of single cell, using wide-field fluorescence microscopy and state-of-the-art imaging techniques. Live-cell imaging using either an agarose-embedding procedure or a microfluidic system further underscores the dynamic nature of the distribution of RNAP in response to changes in the environment. A general agreement between live-cell and fixed-cell images has validated the formaldehyde-fixing procedure, which is a technical breakthrough in the study of the cell biology of RNAP. In this review we use a systems biology perspective to summarize the advances in the cell biology of RNAP in E. coli, including the discoveries of the bacterial nucleolus, the spatial compartmentalization of the transcription machinery at the periphery of the nucleoid, and the segregation of the chromosome territories for the two major cellular functions of transcription and replication in fast-growing cells. Our understanding of the coupling of transcription and bacterial chromosome (or nucleoid structure is also summarized. Using E. coli as a simple model system, co-imaging of RNAP with DNA and other factors during growth and stress responses will continue to be a useful tool for studying bacterial growth and adaptation in changing environment.

  1. Host-Specificity and Dynamics in Bacterial Communities Associated with Bloom-Forming Freshwater Phytoplankton

    Science.gov (United States)

    Bagatini, Inessa Lacativa; Eiler, Alexander; Bertilsson, Stefan; Klaveness, Dag; Tessarolli, Letícia Piton; Vieira, Armando Augusto Henriques

    2014-01-01

    Many freshwater phytoplankton species have the potential to form transient nuisance blooms that affect water quality and other aquatic biota. Heterotrophic bacteria can influence such blooms via nutrient regeneration but also via antagonism and other biotic interactions. We studied the composition of bacterial communities associated with three bloom-forming freshwater phytoplankton species, the diatom Aulacoseira granulata and the cyanobacteria Microcystis aeruginosa and Cylindrospermopsis raciborskii. Experimental cultures incubated with and without lake bacteria were sampled in three different growth phases and bacterial community composition was assessed by 454-Pyrosequencing of 16S rRNA gene amplicons. Betaproteobacteria were dominant in all cultures inoculated with lake bacteria, but decreased during the experiment. In contrast, Alphaproteobacteria, which made up the second most abundant class of bacteria, increased overall during the course of the experiment. Other bacterial classes responded in contrasting ways to the experimental incubations causing significantly different bacterial communities to develop in response to host phytoplankton species, growth phase and between attached and free-living fractions. Differences in bacterial community composition between cyanobacteria and diatom cultures were greater than between the two cyanobacteria. Despite the significance, major differences between phytoplankton cultures were in the proportion of the OTUs rather than in the absence or presence of specific taxa. Different phytoplankton species favoring different bacterial communities may have important consequences for the fate of organic matter in systems where these bloom forming species occur. The dynamics and development of transient blooms may also be affected as bacterial communities seem to influence phytoplankton species growth in contrasting ways. PMID:24465807

  2. Lateral Gene Transfer Dynamics in the Ancient Bacterial GenusStreptomyces.

    Science.gov (United States)

    McDonald, Bradon R; Currie, Cameron R

    2017-06-06

    Lateral gene transfer (LGT) profoundly shapes the evolution of bacterial lineages. LGT across disparate phylogenetic groups and genome content diversity between related organisms suggest a model of bacterial evolution that views LGT as rampant and promiscuous. It has even driven the argument that species concepts and tree-based phylogenetics cannot be applied to bacteria. Here, we show that acquisition and retention of genes through LGT are surprisingly rare in the ubiquitous and biomedically important bacterial genus Streptomyces Using a molecular clock, we estimate that the Streptomyces bacteria are ~380 million years old, indicating that this bacterial genus is as ancient as land vertebrates. Calibrating LGT rate to this geologic time span, we find that on average only 10 genes per million years were acquired and subsequently maintained. Over that same time span, Streptomyces accumulated thousands of point mutations. By explicitly incorporating evolutionary timescale into our analyses, we provide a dramatically different view on the dynamics of LGT and its impact on bacterial evolution. IMPORTANCE Tree-based phylogenetics and the use of species as units of diversity lie at the foundation of modern biology. In bacteria, these pillars of evolutionary theory have been called into question due to the observation of thousands of lateral gene transfer (LGT) events within and between lineages. Here, we show that acquisition and retention of genes through LGT are exceedingly rare in the bacterial genus Streptomyces , with merely one gene acquired in Streptomyces lineages every 100,000 years. These findings stand in contrast to the current assumption of rampant genetic exchange, which has become the dominant hypothesis used to explain bacterial diversity. Our results support a more nuanced understanding of genetic exchange, with LGT impacting evolution over short timescales but playing a significant role over long timescales. Deeper understanding of LGT provides new

  3. Host-specificity and dynamics in bacterial communities associated with Bloom-forming freshwater phytoplankton.

    Directory of Open Access Journals (Sweden)

    Inessa Lacativa Bagatini

    Full Text Available Many freshwater phytoplankton species have the potential to form transient nuisance blooms that affect water quality and other aquatic biota. Heterotrophic bacteria can influence such blooms via nutrient regeneration but also via antagonism and other biotic interactions. We studied the composition of bacterial communities associated with three bloom-forming freshwater phytoplankton species, the diatom Aulacoseira granulata and the cyanobacteria Microcystis aeruginosa and Cylindrospermopsis raciborskii. Experimental cultures incubated with and without lake bacteria were sampled in three different growth phases and bacterial community composition was assessed by 454-Pyrosequencing of 16S rRNA gene amplicons. Betaproteobacteria were dominant in all cultures inoculated with lake bacteria, but decreased during the experiment. In contrast, Alphaproteobacteria, which made up the second most abundant class of bacteria, increased overall during the course of the experiment. Other bacterial classes responded in contrasting ways to the experimental incubations causing significantly different bacterial communities to develop in response to host phytoplankton species, growth phase and between attached and free-living fractions. Differences in bacterial community composition between cyanobacteria and diatom cultures were greater than between the two cyanobacteria. Despite the significance, major differences between phytoplankton cultures were in the proportion of the OTUs rather than in the absence or presence of specific taxa. Different phytoplankton species favoring different bacterial communities may have important consequences for the fate of organic matter in systems where these bloom forming species occur. The dynamics and development of transient blooms may also be affected as bacterial communities seem to influence phytoplankton species growth in contrasting ways.

  4. Response of single bacterial cells to stress gives rise to complex history dependence at the population level

    Science.gov (United States)

    Mathis, Roland; Ackermann, Martin

    2016-01-01

    Most bacteria live in ever-changing environments where periods of stress are common. One fundamental question is whether individual bacterial cells have an increased tolerance to stress if they recently have been exposed to lower levels of the same stressor. To address this question, we worked with the bacterium Caulobacter crescentus and asked whether exposure to a moderate concentration of sodium chloride would affect survival during later exposure to a higher concentration. We found that the effects measured at the population level depended in a surprising and complex way on the time interval between the two exposure events: The effect of the first exposure on survival of the second exposure was positive for some time intervals but negative for others. We hypothesized that the complex pattern of history dependence at the population level was a consequence of the responses of individual cells to sodium chloride that we observed: (i) exposure to moderate concentrations of sodium chloride caused delays in cell division and led to cell-cycle synchronization, and (ii) whether a bacterium would survive subsequent exposure to higher concentrations was dependent on the cell-cycle state. Using computational modeling, we demonstrated that indeed the combination of these two effects could explain the complex patterns of history dependence observed at the population level. Our insight into how the behavior of single cells scales up to processes at the population level provides a perspective on how organisms operate in dynamic environments with fluctuating stress exposure. PMID:26960998

  5. Bacterial Community Dynamics and Biocement Formation during Stimulation and Augmentation: Implications for Soil Consolidation

    Directory of Open Access Journals (Sweden)

    Navdeep K. Dhami

    2017-07-01

    Full Text Available Microbially-induced CaCO3 precipitation (MICP is a naturally occurring process wherein durable carbonates are formed as a result of microbial metabolic activities. In recent years, MICP technology has been widely harnessed for applications in civil engineering wherein synthesis of calcium carbonate crystals occurs at ambient temperature paving way for low energy biocement. MICP using pure urease (UA and carbonic anhydrase (CA producing bacteria has been promising in laboratory conditions. In the current study we enriched ureolytic and carbonic anhydrase communities in calcareous soil under biostimulation and bioaugmentation conditions and investigated the effect of microbial dynamics on carbonate precipitation, calcium carbonate polymorph selection and consolidation of biological sand column under nutrient limited and rich conditions. All treatments for stimulation and augmentation led to significant changes in the composition of indigenous bacterial population. Biostimulation as well as augmentation through the UA route was found to be faster and more effective compared to the CA route in terms of extracellular enzyme production and carbonate precipitation. Synergistic role of augmented cultures along with indigenous communities was recorded via both the routes of UA and CA as more effective calcification was seen in case of augmentation compared to stimulation. The survival of supplemented isolates in presence of indigenous bacterial communities was confirmed through sequencing of total diversity and it was seen that both UA and CA isolate had the potential to survive along with native communities under high nutrient conditions. Nutrient conditions played significant role in determining calcium carbonate polymorph fate as calcitic crystals dominated under high carbon supplementation. Finally, the consolidation of sand columns via stimulation and augmentation was successfully achieved through both UA and CA route under high nutrient conditions

  6. Population typing of the causal agent of cassava bacterial blight in the Eastern Plains of Colombia using two types of molecular markers.

    Science.gov (United States)

    Trujillo, César A; Arias-Rojas, Nathalia; Poulin, Lucie; Medina, César A; Tapiero, Anibal; Restrepo, Silvia; Koebnik, Ralf; Bernal, Adriana J

    2014-06-19

    Molecular typing of pathogen populations is an important tool for the development of effective strategies for disease control. Diverse molecular markers have been used to characterize populations of Xanthomonas axonopodis pv. manihotis (Xam), the main bacterial pathogen of cassava. Recently, diversity and population dynamics of Xam in the Colombian Caribbean coast were estimated using AFLPs, where populations were found to be dynamic, diverse and with haplotypes unstable across time. Aiming to examine the current state of pathogen populations located in the Colombian Eastern Plains, we also used AFLP markers and we evaluated the usefulness of Variable Number Tandem Repeats (VNTRs) as new molecular markers for the study of Xam populations. The population analyses showed that AFLP and VNTR provide a detailed and congruent description of Xam populations from the Colombian Eastern Plains. These two typing strategies clearly separated strains from the Colombian Eastern Plains into distinct populations probably because of geographical distance. Although the majority of analyses were congruent between typing markers, fewer VNTRs were needed to detect a higher number of genetic populations of the pathogen as well as a higher genetic flow among sampled locations than those detected by AFLPs. This study shows the advantages of VNTRs over AFLPs in the surveillance of pathogen populations and suggests the implementation of VNTRs in studies that involve large numbers of Xam isolates in order to obtain a more detailed overview of the pathogen to improve the strategies for disease control.

  7. Stochastic population dynamics under resource constraints

    Energy Technology Data Exchange (ETDEWEB)

    Gavane, Ajinkya S., E-mail: ajinkyagavane@gmail.com; Nigam, Rahul, E-mail: rahul.nigam@hyderabad.bits-pilani.ac.in [BITS Pilani Hyderabad Campus, Shameerpet, Hyd - 500078 (India)

    2016-06-02

    This paper investigates the population growth of a certain species in which every generation reproduces thrice over a period of predefined time, under certain constraints of resources needed for survival of population. We study the survival period of a species by randomizing the reproduction probabilities within a window at same predefined ages and the resources are being produced by the working force of the population at a variable rate. This randomness in the reproduction rate makes the population growth stochastic in nature and one cannot predict the exact form of evolution. Hence we study the growth by running simulations for such a population and taking an ensemble averaged over 500 to 5000 such simulations as per the need. While the population reproduces in a stochastic manner, we have implemented a constraint on the amount of resources available for the population. This is important to make the simulations more realistic. The rate of resource production then is tuned to find the rate which suits the survival of the species. We also compute the mean life time of the species corresponding to different resource production rate. Study for these outcomes in the parameter space defined by the reproduction probabilities and rate of resource production is carried out.

  8. Stochastic population dynamics under resource constraints

    International Nuclear Information System (INIS)

    Gavane, Ajinkya S.; Nigam, Rahul

    2016-01-01

    This paper investigates the population growth of a certain species in which every generation reproduces thrice over a period of predefined time, under certain constraints of resources needed for survival of population. We study the survival period of a species by randomizing the reproduction probabilities within a window at same predefined ages and the resources are being produced by the working force of the population at a variable rate. This randomness in the reproduction rate makes the population growth stochastic in nature and one cannot predict the exact form of evolution. Hence we study the growth by running simulations for such a population and taking an ensemble averaged over 500 to 5000 such simulations as per the need. While the population reproduces in a stochastic manner, we have implemented a constraint on the amount of resources available for the population. This is important to make the simulations more realistic. The rate of resource production then is tuned to find the rate which suits the survival of the species. We also compute the mean life time of the species corresponding to different resource production rate. Study for these outcomes in the parameter space defined by the reproduction probabilities and rate of resource production is carried out.

  9. Dynamic laser speckle to detect motile bacterial response of Pseudomonas aeruginosa

    International Nuclear Information System (INIS)

    Sendra, H; Murialdo, S; Passoni, L

    2007-01-01

    This proposal deals with the technique for detection of motile response of Pseudomonas aeruginosa using dynamic laser speckle or biospeckle as an alternative method. The study of bacterial displacement plays an essential role in biocatalysts processes and biodegradation. Hence, some biodegrading enzymes are benign catalytic that could be used for the production of industrially useful compounds as well as in wastewater treatments. This work presents an experimental set up and a computational process using frame sequences of dynamic laser speckle as a novel application. The objective was the detection of different levels of motility in bacteria. The encouraging results were achieved through a direct and non invasive observation method of the phenomenon

  10. Dynamic instability in the hook-flagellum system that triggers bacterial flicks

    Science.gov (United States)

    Jabbarzadeh, Mehdi; Fu, Henry Chien

    2018-01-01

    Dynamical bending, buckling, and polymorphic transformations of the flagellum are known to affect bacterial motility, but run-reverse-flick motility of monotrichous bacteria also involves the even more flexible hook connecting the flagellum to its rotary motor. Although flick initiation has been hypothesized to involve either static Euler buckling or dynamic bending of the hook, the precise mechanism of flick initiation remains unknown. Here, we find that flicks initiate via a dynamic instability requiring flexibility in both the hook and flagellum. We obtain accurate estimates of forces and torques on the hook that suggest that flicks occur for stresses below the (static) Euler buckling criterion, then provide a mechanistic model for flick initiation that requires combined bending of the hook and flagellum. We calculate the triggering torque-stiffness ratio and find that our predicted onset of dynamic instability corresponds well with experimental observations.

  11. Galactic civilizations: Population dynamics and interstellar diffusion

    Science.gov (United States)

    Newman, W. I.; Sagan, C.

    1978-01-01

    The interstellar diffusion of galactic civilizations is reexamined by potential theory; both numerical and analytical solutions are derived for the nonlinear partial differential equations which specify a range of relevant models, drawn from blast wave physics, soil science, and, especially, population biology. An essential feature of these models is that, for all civilizations, population growth must be limited by the carrying capacity of the environment. Dispersal is fundamentally a diffusion process; a density-dependent diffusivity describes interstellar emigration. Two models are considered: the first describing zero population growth (ZPG), and the second which also includes local growth and saturation of a planetary population, and for which an asymptotic traveling wave solution is found.

  12. Seasonal population dynamics and energy consumption by ...

    African Journals Online (AJOL)

    Dynamiques saisonnières de population et consommation énergétique par les oiseaux aquatiques d'un petit estuaire tempéré De simples mesures des dynamiques de population et de consommation énergétique peuvent fournir des informations de base sur le rôle des consommateurs au sein des réseaux trophiques, ...

  13. Statistical dynamics of regional populations and economies

    Science.gov (United States)

    Huo, Jie; Wang, Xu-Ming; Hao, Rui; Wang, Peng

    Quantitative analysis of human behavior and social development is becoming a hot spot of some interdisciplinary studies. A statistical analysis on the population and GDP of 150 cities in China from 1990 to 2013 is conducted. The result indicates the cumulative probability distribution of the populations and that of the GDPs obeying the shifted power law, respectively. In order to understand these characteristics, a generalized Langevin equation describing variation of population is proposed, which is based on the correlations between population and GDP as well as the random fluctuations of the related factors. The equation is transformed into the Fokker-Plank equation to express the evolution of population distribution. The general solution demonstrates a transition of the distribution from the normal Gaussian distribution to a shifted power law, which suggests a critical point of time at which the transition takes place. The shifted power law distribution in the supercritical situation is qualitatively in accordance with the practical result. The distribution of the GDPs is derived from the well-known Cobb-Douglas production function. The result presents a change, in supercritical situation, from a shifted power law to the Gaussian distribution. This is a surprising result-the regional GDP distribution of our world will be the Gaussian distribution one day in the future. The discussions based on the changing trend of economic growth suggest it will be true. Therefore, these theoretical attempts may draw a historical picture of our society in the aspects of population and economy.

  14. Bacterial dynamics during yearlong spontaneous fermentation for production of ngari, a dry fermented fish product of Northeast India.

    Science.gov (United States)

    Devi, Khunjamayum Romapati; Deka, Manab; Jeyaram, Kumaraswamy

    2015-04-16

    Ngari is the most popular traditionally processed non-salted fish product, prepared from sun-dried small cyprinid fish Puntius sophore (Ham.) in Manipur state of Northeast India. The microbial involvement in ngari production remained uncertain due to its low moisture content and yearlong incubation in anaerobically sealed earthen pots without any significant change in total microbial count. The culture-independent PCR-DGGE analysis used during this study confirmed a drastic bacterial community structural change in comparison to its raw material. To understand the bacterial dynamics during this dry fermentation, time series samples collected over a period of nine months through destructive sampling from two indigenous ngari production centres were analysed by using both culture-dependent and culture-independent molecular methods. A total of 210 bacteria isolated from the samples were identified by amplified ribosomal DNA restriction analysis (ARDRA) based grouping and 16S rRNA gene sequence similarity analysis. The dominant bacteria were Staphylococcus cohnii subsp. cohnii (38.0%), Tetragenococcus halophilus subsp. flandriensis (16.8%), a novel phylotype related to Lactobacillus pobuzihii (7.2%), Enterococcus faecium (7.2%), Bacillus indicus (6.3%) and Staphylococcus carnosus (3.8%). Distinct bacterial dynamics with the emergence of T. halophilus at third month (10(6)CFU/g), L. pobuzihii at sixth month (10(6)CFU/g), S. carnosus at three to six months (10(4)CFU/g) and B. indicus at six to nine months (10(5)CFU/g) in both the production centres was observed during ngari fermentation. However, the other two dominant bacteria S. cohnii and E. faecium were isolated throughout the fermentation with the population of 10(6)CFU/g and 10(4)CFU/g respectively. Culture-independent PCR-DGGE analysis further showed the presence of additional species, in which Kocuria halotolerans and Macrococcus caseolyticus disappeared during fermentation while Clostridium irregulare and

  15. Population dynamics of estuarine amphipods in Cochin backwaters

    Digital Repository Service at National Institute of Oceanography (India)

    Nair, K.K.C.; Gopalakrishnan, T.C.; Venugopal, P.; Peter, G.; Jayalakshmy, K.V.; Rao, T.S.S.

    Population dynamics of 11 gammarid amphipod species (belonging to 9 genera), collected from Cochin backwaters, have been studied for the first time, based on an year round collection. The species are : Corophium triaenonyx Stebbing, Photis digitata...

  16. Drivers of waterfowl population dynamics : from teal to swans

    OpenAIRE

    Koons, D. N.; Gunnarsson, Gunnar; Schmutz, J. A.; Rotella, J. J.

    2014-01-01

    Waterfowl are among the best studied and most extensively monitored species in the world. Given their global importance for sport and subsistence hunting, viewing and ecosystem functioning, great effort has been devoted since the middle part of the 20th century to understanding both the environmental and demographic mechanisms that influence waterfowl population and community dynamics. Here we use comparative approaches to summarise and contrast our understanding of waterfowl population dynam...

  17. Passivity analysis of higher order evolutionary dynamics and population games

    KAUST Repository

    Mabrok, Mohamed

    2017-01-05

    Evolutionary dynamics describe how the population composition changes in response to the fitness levels, resulting in a closed-loop feedback system. Recent work established a connection between passivity theory and certain classes of population games, namely so-called “stable games”. In particular, it was shown that a combination of stable games and (an analogue of) passive evolutionary dynamics results in stable convergence to Nash equilibrium. This paper considers the converse question of necessary conditions for evolutionary dynamics to exhibit stable behaviors for all generalized stable games. Using methods from robust control analysis, we show that if an evolutionary dynamic does not satisfy a passivity property, then it is possible to construct a generalized stable game that results in instability. The results are illustrated on selected evolutionary dynamics with particular attention to replicator dynamics, which are also shown to be lossless, a special class of passive systems.

  18. A linear model of population dynamics

    Science.gov (United States)

    Lushnikov, A. A.; Kagan, A. I.

    2016-08-01

    The Malthus process of population growth is reformulated in terms of the probability w(n,t) to find exactly n individuals at time t assuming that both the birth and the death rates are linear functions of the population size. The master equation for w(n,t) is solved exactly. It is shown that w(n,t) strongly deviates from the Poisson distribution and is expressed in terms either of Laguerre’s polynomials or a modified Bessel function. The latter expression allows for considerable simplifications of the asymptotic analysis of w(n,t).

  19. Population dynamics in rural South Australia.

    Science.gov (United States)

    Hugo, G J; Smailes, P J

    1992-01-01

    The authors examine recent trends in Australia in turnaround migration, or the movement of the population from urban to rural areas. "The paper assesses the major changes which have occurred in population trends within the non-metropolitan sector of the nation, South Australia and, in particular, a study area in the lower north region of South Australia. The analysis of the case study region draws upon a survey undertaken in 1968-1970 and partially replicated in 1980 and 1990. It appears that for Australia in general and for the study area the turnaround is continuing but at a slower pace and in a more spatially concentrated pattern." excerpt

  20. Population dynamical responses to climate change

    DEFF Research Database (Denmark)

    Forchhammer, Mads; Schmidt, Niels Martin; Høye, Toke Thomas

    2008-01-01

    , the effects of climate change may potentially extend through any of these interactions. In this chapter, we focus on the extent to which evolutionarily distinct species at different trophic levels respond to similar changes in climate. By using a broad spectrum of statistically and ecologically founded...... and three out of five wader species, displayed significant direct density dependence. Only two species (sanderling and long-tailed skua) displayed dynamics characterised by delayed density dependence. The direct effects of previous winter's snow were related to over-wintering strategies of resident...... of arctic fox were not significantly related to changes in lemming abundance, both the stoat and the breeding of long-tailed skua were mainly related to lemming dynamics. The predator-prey system at Zackenberg differentiates from previously described systems in high-arctic Greenland, which, we suggest...

  1. Dynamics of a structured neuron population

    International Nuclear Information System (INIS)

    Pakdaman, Khashayar; Salort, Delphine; Perthame, Benoît

    2010-01-01

    We study the dynamics of assemblies of interacting neurons. For large fully connected networks, the dynamics of the system can be described by a partial differential equation reminiscent of age-structure models used in mathematical ecology, where the 'age' of a neuron represents the time elapsed since its last discharge. The nonlinearity arises from the connectivity J of the network. We prove some mathematical properties of the model that are directly related to qualitative properties. On the one hand, we prove that it is well-posed and that it admits stationary states which, depending upon the connectivity, can be unique or not. On the other hand, we study the long time behaviour of solutions; both for small and large J, we prove the relaxation to the steady state describing asynchronous firing of the neurons. In the middle range, numerical experiments show that periodic solutions appear expressing re-synchronization of the network and asynchronous firing

  2. POPULATION DYNAMICS OF THE WANDERING ALBATROSS ...

    African Journals Online (AJOL)

    Changes in several demographic parameters that appear to be influenced by both environmental and anthropogenic effects are described. From 1994–2001, the proportion of first-time breeders in the population was positively correlated with the maximum ENSO (Niño 3) index, whereas from 1984–2000 the annual survival ...

  3. Short Communication: Occurrence and Population Dynamics of ...

    African Journals Online (AJOL)

    The dangerous tomato leaf miner pest (Tuta absoluta), which was reported to have crossed into Ethiopia via the Sudan in 2012, has scared tomato producing farmers across the country. Therefore, a study was conducted using pheromone traps to elucidate the occurrence of the insect pest and to monitor its population ...

  4. Phenotypic Resistance and the Dynamics of Bacterial Escape from Phage Control

    Science.gov (United States)

    Bull, James J.; Vegge, Christina Skovgaard; Schmerer, Matthew; Chaudhry, Waqas Nasir; Levin, Bruce R.

    2014-01-01

    The canonical view of phage - bacterial interactions in dense, liquid cultures is that the phage will eliminate most of the sensitive cells; genetic resistance will then ascend to restore high bacterial densities. Yet there are various mechanisms by which bacteria may remain sensitive to phages but still attain high densities in their presence – because bacteria enter a transient state of reduced adsorption. Importantly, these mechanisms may be cryptic and inapparent prior to the addition of phage yet result in a rapid rebound of bacterial density after phage are introduced. We describe mathematical models of these processes and suggest how different types of this ‘phenotypic’ resistance may be elucidated. We offer preliminary in vitro studies of a previously characterized E. coli model system and Campylobacter jejuni illustrating apparent phenotypic resistance. As phenotypic resistance may be specific to the receptors used by phages, awareness of its mechanisms may identify ways of improving the choice of phages for therapy. Phenotypic resistance can also explain several enigmas in the ecology of phage-bacterial dynamics. Phenotypic resistance does not preclude the evolution of genetic resistance and may often be an intermediate step to genetic resistance. PMID:24743264

  5. Nonlinear population dynamics in a bounded habitat.

    Science.gov (United States)

    Colombo, E H; Anteneodo, C

    2018-02-27

    A key issue in ecology is whether a population will survive long term or go extinct. This is the question we address in this paper for a population in a bounded habitat. We will restrict our study to the case of a single species in a one-dimensional habitat of length L. The evolution of the population density distribution ρ(x, t), where x is the position and t the time, is governed by elementary processes such as growth and dispersal, which, in standard models, are typically described by a constant per capita growth rate and normal diffusion, respectively. However, feedbacks in the regulatory mechanisms and external factors can produce density-dependent rates. Therefore, we consider a generalization of the standard evolution equation, which, after dimensional scaling and assuming large carrying capacity, becomes ∂ t ρ=∂ x (ρ ν-1 ∂ x ρ)+ρ μ , where μ,ν∈R. This equation is complemented by absorbing boundaries, mimicking adverse conditions outside the habitat. For this nonlinear problem, we obtain, analytically, exact expressions of the critical habitat size L c for population survival, as a function of the exponents and initial conditions. We find that depending on the values of the exponents (ν, μ), population survival can occur for either L > L c , L < L c or for any L. This generalizes the usual statement that L c represents the minimum habitat size. In addition, nonlinearities introduce dependence on the initial conditions, affecting L c . Copyright © 2018. Published by Elsevier Ltd.

  6. The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy.

    Science.gov (United States)

    Trauner, Andrej; Liu, Qingyun; Via, Laura E; Liu, Xin; Ruan, Xianglin; Liang, Lili; Shi, Huimin; Chen, Ying; Wang, Ziling; Liang, Ruixia; Zhang, Wei; Wei, Wang; Gao, Jingcai; Sun, Gang; Brites, Daniela; England, Kathleen; Zhang, Guolong; Gagneux, Sebastien; Barry, Clifton E; Gao, Qian

    2017-04-19

    Combination therapy is one of the most effective tools for limiting the emergence of drug resistance in pathogens. Despite the widespread adoption of combination therapy across diseases, drug resistance rates continue to rise, leading to failing treatment regimens. The mechanisms underlying treatment failure are well studied, but the processes governing successful combination therapy are poorly understood. We address this question by studying the population dynamics of Mycobacterium tuberculosis within tuberculosis patients undergoing treatment with different combinations of antibiotics. By combining very deep whole genome sequencing (~1000-fold genome-wide coverage) with sequential sputum sampling, we were able to detect transient genetic diversity driven by the apparently continuous turnover of minor alleles, which could serve as the source of drug-resistant bacteria. However, we report that treatment efficacy has a clear impact on the population dynamics: sufficient drug pressure bears a clear signature of purifying selection leading to apparent genetic stability. In contrast, M. tuberculosis populations subject to less drug pressure show markedly different dynamics, including cases of acquisition of additional drug resistance. Our findings show that for a pathogen like M. tuberculosis, which is well adapted to the human host, purifying selection constrains the evolutionary trajectory to resistance in effectively treated individuals. Nonetheless, we also report a continuous turnover of minor variants, which could give rise to the emergence of drug resistance in cases of drug pressure weakening. Monitoring bacterial population dynamics could therefore provide an informative metric for assessing the efficacy of novel drug combinations.

  7. Bacterial meningitis in Finland, 1995-2014: a population-based observational study.

    Science.gov (United States)

    Polkowska, Aleksandra; Toropainen, Maija; Ollgren, Jukka; Lyytikäinen, Outi; Nuorti, J Pekka

    2017-06-06

    Bacterial meningitis remains an important cause of morbidity and mortality worldwide. Its epidemiological characteristics, however, are changing due to new vaccines and secular trends. Conjugate vaccines against Haemophilus influenzae type b and Streptococcus pneumoniae (10-valent) were introduced in 1986 and 2010 in Finland. We assessed the disease burden and long-term trends of five common causes of bacterial meningitis in a population-based observational study. A case was defined as isolation of S. pneumoniae , Neisseria meningitidis , Streptococcus agalactiae , Listeria monocytogenes or H. influenzae from cerebrospinal fluid and reported to national, population-based laboratory surveillance system during 1995-2014. We evaluated changes in incidence rates (Poisson or negative binomial regression), case fatality proportions (χ 2 ) and age distribution of cases (Wilcoxon rank-sum). During 1995-2014, S. pneumoniae and N. meningitidis accounted for 78% of the total 1361 reported bacterial meningitis cases. H. influenzae accounted for 4% of cases (92% of isolates were non-type b). During the study period, the overall rate of bacterial meningitis per 1 00 000 person-years decreased from 1.88 cases in 1995 to 0.70 cases in 2014 (4% annual decline (95% CI 3% to 5%). This was primarily due to a 9% annual reduction in rates of N. meningitidis (95% CI 7% to 10%) and 2% decrease in S. pneumoniae (95% CI 1% to 4%). The median age of cases increased from 31 years in 1995-2004 to 43 years in 2005-2014 (p=0.0004). Overall case fatality proportion (10%) did not change from 2004 to 2009 to 2010-2014. Substantial decreases in bacterial meningitis were associated with infant conjugate vaccination against pneumococcal meningitis and secular trend in meningococcal meningitis in the absence of vaccination programme. Ongoing epidemiological surveillance is needed to identify trends, evaluate serotype distribution, assess vaccine impact and develop future vaccination strategies

  8. Human population dynamics in Europe over the Last Glacial Maximum

    Science.gov (United States)

    Tallavaara, Miikka; Luoto, Miska; Korhonen, Natalia; Järvinen, Heikki; Seppä, Heikki

    2015-01-01

    The severe cooling and the expansion of the ice sheets during the Last Glacial Maximum (LGM), 27,000–19,000 y ago (27–19 ky ago) had a major impact on plant and animal populations, including humans. Changes in human population size and range have affected our genetic evolution, and recent modeling efforts have reaffirmed the importance of population dynamics in cultural and linguistic evolution, as well. However, in the absence of historical records, estimating past population levels has remained difficult. Here we show that it is possible to model spatially explicit human population dynamics from the pre-LGM at 30 ky ago through the LGM to the Late Glacial in Europe by using climate envelope modeling tools and modern ethnographic datasets to construct a population calibration model. The simulated range and size of the human population correspond significantly with spatiotemporal patterns in the archaeological data, suggesting that climate was a major driver of population dynamics 30–13 ky ago. The simulated population size declined from about 330,000 people at 30 ky ago to a minimum of 130,000 people at 23 ky ago. The Late Glacial population growth was fastest during Greenland interstadial 1, and by 13 ky ago, there were almost 410,000 people in Europe. Even during the coldest part of the LGM, the climatically suitable area for human habitation remained unfragmented and covered 36% of Europe. PMID:26100880

  9. Effective population size and evolutionary dynamics in outbred ...

    Indian Academy of Sciences (India)

    RESEARCH ARTICLE. Effective population size and evolutionary dynamics in outbred laboratory populations of Drosophila. LAURENCE D. MUELLER1∗, AMITABH JOSHI1,2, MARTA SANTOS1 and MICHAEL R. ROSE1. 1Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA.

  10. Ruffed grouse population dynamics in the central and southern Appalachians

    Science.gov (United States)

    John M. Giuliano Tirpak; C. Allan Miller; Thomas J. Allen; Steve Bittner; David A. Buehler; John W. Edwards; Craig A. Harper; William K. Igo; Gary W. Norman; M. Seamster; Dean F. Stauffer

    2006-01-01

    Ruffed grouse (Bonasa urnbellus; hereafter grouse) populations in the central and southern Appalachians are in decline. However, limited information on the dynamics of these populations prevents the development of effective management strategies to reverse these trends. We used radiotelemetry data collected on grouse to parameterize 6 models of...

  11. The frankincense tree of Ethiopia : ecology, productivity and population dynamics

    NARCIS (Netherlands)

    Eshete Wassie, A.

    2011-01-01

    Keywords: Boswellian papyrifera, Frankincense tree, matrix model, population dynamics,
    population bottleneck, tapping.

    Combretum – Terminalia woodlands and Acacia – Commiphora woodlands are the two
    dominant vegetation types that cover large parts of the dry land areas in

  12. Population dynamics of the seabob shrimp Xiphopenaeus kroyeri ...

    African Journals Online (AJOL)

    The population dynamics, including the sex ratio, reproductive period, individual growth and longevity, and population structure of the shrimp Xiphopenaeus kroyeri, are described. The shrimps were collected monthly from July 2005 to June 2007 at four sites in Ubatuba Bay, Brazil. The salinity, temperature, depth, organic ...

  13. Population dynamics and distribution of the coffee berry borer ...

    African Journals Online (AJOL)

    Population dynamics and distribution of coffee berry borer, Hypothenemus hampei (Ferrari) (Coleoptera: Scolytidae) were studied on Coffea arabica L. in southwestern region of Ethiopia. Thirty coffee trees were sampled at weekly intervals from 2000 to 2001. Findings of this study showed that coffee berry borer population ...

  14. The dynamic instability in the hook/flagellum system that triggers bacterial flicks

    Science.gov (United States)

    Jabbarzadeh, Mehdi; Fu, Henry

    2017-11-01

    Dynamical bending, buckling, and polymorphic transformations of the flagellum are known to affect bacterial motility, but run-reverse-flick motility of monotrichous bacteria also involves the even more flexible hook, which connects the flagellum to the cell body. Here, we identify the dynamic buckling mechanism that produces flicks in Vibrio alginolyticus. Estimates of forces and torques on the hook from experimental observations suggest that flicks are triggered at stresses below the hook's static Euler buckling criterion. Using an accurate linearization of the Kirchoff rod model for the hook in a model of a swimming bacterium with rigid flagellum, we show that as hook stiffness decreases there is a transition from on-axis flagellar rotation with small hook deflections to flagellar precession with large deflections. When flagellum flexibility is incorporated, the precession is disrupted by significant flagellar bending - i.e., incipient flicks. The predicted onset of dynamic instabilities corresponds well with experimentally observed flick events.

  15. Combination of 16S rRNA variable regions provides a detailed analysis of bacterial community dynamics in the lungs of cystic fibrosis patients

    Directory of Open Access Journals (Sweden)

    Doud Melissa S

    2010-02-01

    Full Text Available Abstract Chronic bronchopulmonary bacterial infections remain the most common cause of morbidity and mortality among patients with cystic fibrosis (CF. Recent community sequencing work has now shown that the bacterial community in the CF lung is polymicrobial. Identifying bacteria in the CF lung through sequencing can be costly and is not practical for many laboratories. Molecular techniques such as terminal restriction fragment length polymorphism or amplicon length heterogeneity-polymerase chain reaction (LH-PCR can provide many laboratories with the ability to study CF bacterial communities without costly sequencing. The aim of this study was to determine if the use of LH-PCR with multiple hypervariable regions of the 16S rRNA gene could be used to identify organisms found in sputum DNA. This work also determined if LH-PCR could be used to observe the dynamics of lung infections over a period of time. Nineteen samples were analysed with the V1 and the V1_V2 region of the 16S rRNA gene. Based on the amplicon size present in the V1_V2 region, Pseudomonas aeruginosa was confirmed to be in all 19 samples obtained from the patients. The V1 region provided a higher power of discrimination between bacterial profiles of patients. Both regions were able to identify trends in the bacterial population over a period of time. LH profiles showed that the CF lung community is dynamic and that changes in the community may in part be driven by the patient's antibiotic treatment. LH-PCR is a tool that is well suited for studying bacterial communities and their dynamics.

  16. Modelling the Dynamics of an Aedes albopictus Population

    Directory of Open Access Journals (Sweden)

    Thomas Anung Basuki

    2010-08-01

    Full Text Available We present a methodology for modelling population dynamics with formal means of computer science. This allows unambiguous description of systems and application of analysis tools such as simulators and model checkers. In particular, the dynamics of a population of Aedes albopictus (a species of mosquito and its modelling with the Stochastic Calculus of Looping Sequences (Stochastic CLS are considered. The use of Stochastic CLS to model population dynamics requires an extension which allows environmental events (such as changes in the temperature and rainfalls to be taken into account. A simulator for the constructed model is developed via translation into the specification language Maude, and used to compare the dynamics obtained from the model with real data.

  17. Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation

    Directory of Open Access Journals (Sweden)

    Justin Wright

    2017-11-01

    ranges, indicating niche-specific responses of these autochthonous populations. Altogether, our findings suggest that monitored natural attenuation is an appropriate remediation strategy for DCM contamination, and that high-throughput sequencing technologies are a robust method for assessing the potential role of biodegrading bacterial assemblages in the apparent reduction of DCM concentrations in environmental scenarios.

  18. Null controllability of a nonlinear population dynamics problem

    OpenAIRE

    Traore, Oumar

    2006-01-01

    We establish a null controllability result for a nonlinear population dynamics model. In our model, the birth term is nonlocal and describes the recruitment process in newborn individuals population. Using a derivation of Leray-Schauder fixed point theorem and Carleman inequality for the adjoint system, we show that for all given initial density, there exists an internal control acting on a small open set of the domain and leading the population to extinction.

  19. Population dynamics of metastable growth-rate phenotypes.

    Directory of Open Access Journals (Sweden)

    Lindsay S Moore

    Full Text Available Neo-Darwinian evolution has presented a paradigm for population dynamics built on random mutations and selection with a clear separation of time-scales between single-cell mutation rates and the rate of reproduction. Laboratory experiments on evolving populations until now have concentrated on the fixation of beneficial mutations. Following the Darwinian paradigm, these experiments probed populations at low temporal resolution dictated by the rate of rare mutations, ignoring the intermediate evolving phenotypes. Selection however, works on phenotypes rather than genotypes. Research in recent years has uncovered the complexity of genotype-to-phenotype transformation and a wealth of intracellular processes including epigenetic inheritance, which operate on a wide range of time-scales. Here, by studying the adaptation dynamics of genetically rewired yeast cells, we show a novel type of population dynamics in which the intracellular processes intervene in shaping the population structure. Under constant environmental conditions, we measure a wide distribution of growth rates that coexist in the population for very long durations (>100 generations. Remarkably, the fastest growing cells do not take over the population on the time-scale dictated by the width of the growth-rate distributions and simple selection. Additionally, we measure significant fluctuations in the population distribution of various phenotypes: the fraction of exponentially-growing cells, the distributions of single-cell growth-rates and protein content. The observed fluctuations relax on time-scales of many generations and thus do not reflect noisy processes. Rather, our data show that the phenotypic state of the cells, including the growth-rate, for large populations in a constant environment is metastable and varies on time-scales that reflect the importance of long-term intracellular processes in shaping the population structure. This lack of time-scale separation between the

  20. Geography, European colonization, and past population dynamics in Africa

    OpenAIRE

    Vaz Silva, Luis

    2005-01-01

    Past population dynamics in Africa have remained largely elusive due to the lack of demographic data. Researchers are understandably deterred from trying to explain what is not known and African historical population estimates suffer from this lack of interest. In this paper I explain present day African population densities using mostly ecological factors as explanatory variables. I find evidence supporting the view that ecological factors deeply affected precolonial patterns of human settle...

  1. Coupling population dynamics with earth system models: the POPEM model.

    Science.gov (United States)

    Navarro, Andrés; Moreno, Raúl; Jiménez-Alcázar, Alfonso; Tapiador, Francisco J

    2017-09-16

    Precise modeling of CO 2 emissions is important for environmental research. This paper presents a new model of human population dynamics that can be embedded into ESMs (Earth System Models) to improve climate modeling. Through a system dynamics approach, we develop a cohort-component model that successfully simulates historical population dynamics with fine spatial resolution (about 1°×1°). The population projections are used to improve the estimates of CO 2 emissions, thus transcending the bulk approach of existing models and allowing more realistic non-linear effects to feature in the simulations. The module, dubbed POPEM (from Population Parameterization for Earth Models), is compared with current emission inventories and validated against UN aggregated data. Finally, it is shown that the module can be used to advance toward fully coupling the social and natural components of the Earth system, an emerging research path for environmental science and pollution research.

  2. EFFECT OF REFINED PETROLEUM PRODUCTS CONTAMINATION ON BACTERIAL POPULATION AND PHYSICOCHEMICAL CHARACTERISTICS OF CULTIVATED AGRICULTURAL SOIL

    Directory of Open Access Journals (Sweden)

    Adewale Sogo Olalemi

    2012-10-01

    Full Text Available An investigation into the effect of refined petroleum products contamination on bacterial population and physicochemical characteristics of cultivated agricultural soil was carried out. The soil samples obtained from the Teaching and Research Farm, Obakekere, Federal University of Technology, Akure, Ondo State were contaminated with varying volumes of petrol, diesel and kerosene. The results revealed higher bacterial populations in uncontaminated soils than contaminated soils. The counts of bacteria ranged from 3.0 × 105 to 5.0 × 105 cfu/g in uncontaminated soils and 1.0 × 105 to 3.0 × 105 cfu/g in contaminated soils. The isolated bacteria were identified as Bacillus subtilis, Flavobacterium lutescens, Micrococcus luteus, Corynebacterium variabilis, Pseudomonas fluorescens. The contamination had no significant effect on pH, potassium, sodium, organic carbon and nitrogen content of the soils, while the moisture, calcium, phosphorus and magnesium content of the contaminated soils were significantly different (P < 0.05 compared with the uncontaminated soils. The ability of Bacillus subtilis, Flavobacterium lutescens, Micrococcus luteus, and Pseudomonas fluorescens to utilize the refined petroleum products suggest that these bacteria had potential to bioremediate petroleum contaminated soils.

  3. Bacterial communities associated with invasive populations of Bactrocera dorsalis (Diptera: Tephritidae) in China.

    Science.gov (United States)

    Liu, L J; Martinez-Sañudo, I; Mazzon, L; Prabhakar, C S; Girolami, V; Deng, Y L; Dai, Y; Li, Z H

    2016-12-01

    The oriental fruit fly Bactrocera dorsalis (Hendel) is a destructive insect pest of a wide range of fruits and vegetables. This pest is an invasive species and is currently distributed in some provinces of China. To recover the symbiotic bacteria of B. dorsalis from different invasion regions in China, we researched the bacterial diversity of this fruit fly among one laboratory colony (Guangdong, China) and 15 wild populations (14 sites in China and one site in Thailand) using DNA-based approaches. The construction of 16S rRNA gene libraries allowed the identification of 24 operational taxonomic units of associated bacteria at the 3% distance level, and these were affiliated with 3 phyla, 5 families, and 13 genera. The higher bacterial diversity was recovered in wild populations compared with the laboratory colony and in samples from early term invasion regions compared with samples from late term invasion regions. Moreover, Klebsiella pneumoniae and Providencia sp. were two of the most frequently recovered bacteria, present in flies collected from three different regions in China where B. dorsalis is invasive. This study for the first time provides a systemic investigation of the symbiotic bacteria of B. dorsalis from different invasion regions in China.

  4. Impact of bioremediation treatments on the biodegradation of buried oil and predominant bacterial populations

    International Nuclear Information System (INIS)

    Swannell, R.P.J.; Mitchell, D.J.; Waterhouse, J.C.; Miskin, I.P.; Head, I.M.; Petch, S.; Jones, D.M.; Willis, A.; Lee, K.; Lepo, J.E.

    2000-01-01

    The feasibility of using mineral fertilizers as a bioremediation treatment for oil buried in fine sediments was tested in field trials at a site in the south-west of England. The plots were divided into three blocks of four treatments including untreated, fertilized, oiled unfertilized and oiled fertilized plots. The changes in residual hydrocarbons were monitored to study the biodegradation of Arabian Light Crude Oil which is known to have a high portion of biodegradable components. Samples were extracted at random points at intervals of 0, 42 and 101 days. The analysis process identified a range of aliphatic and aromatic hydrocarbons, as well as a range of geochemical biomarkers. The final results suggested that the oil in the fertilized plots was more degraded than in the oiled, unfertilized control plots. Three way, factorial analysis of variance was used to analyse the data from the oiled fertilized and oiled unfertilized plots. No significant effect of treatment on the degradation of aromatic hydrocarbons was observed. The results also showed that oil treatment and treatment with oil and fertilizer increased the abundance of hydrocarbon-degrading bacterial population. One significant observation was that different bacterial populations were stimulated in response to oil alone and a bioremediation treatment. It was concluded that the addition of inorganic fertilizers to the oiled oxic fine sediment substantially enhanced the level of biodegradation compared to untreated oiled sediment. Bioremediation is a feasible treatment for oil spills where the oil is buried in fine sediment. 14 refs., 1 tab., 4 figs

  5. What is Growth? Concurrent determination of a bacterial population's many shades of growth

    Science.gov (United States)

    Lambert, Guillaume; Kussell, Edo

    2013-03-01

    One of the most exciting developments in the study of the physics of microbial life is the ability to precisely monitor stochastic variations of gene expression in individual cells. A fundamental question is whether these variations improve the long-term ability of a population to adapt to new environments. While variations in gene expression in bacteria are easily measured through the use of reporter systems such as green fluorescent proteins and its variants, precise determination of a cell's growth rate, and how it is influenced by its immediate environment, remains challenging. Here, we show that many conflicting and ambiguous definitions of bacterial growth can actually be used interchangeably in E. coli. Indeed, by monitoring small populations of E. coli bacteria inside a microfluidic device, we show that seemingly independent measurements of growth (elongation rate and the average division time, for instance) agree very precisely with one another. We combine these definitions with the population's length and age distribution to very precisely quantify the influence of temperature variations on a population's growth rate. We conclude by using coalescence theory to describe the evolution of a population's genetic structure over time.

  6. Molecular approaches for viable bacterial population and transcriptional analyses in a rodent model of dental caries

    Science.gov (United States)

    Klein, Marlise I.; Scott-Anne, Kathleen M.; Gregoire, Stacy; Rosalen, Pedro L.; Koo, Hyun

    2012-01-01

    SUMMARY Culturing methods are the primary approach for microbiological analysis of plaque-biofilms in rodent models of dental caries. In this study, we developed strategies for isolation of DNA and RNA from in vivo formed plaque-biofilms to analyze the viable bacterial population and gene expression. Plaque-biofilm samples from rats were treated with propidium monoazide to isolate DNA from viable cells, and the purified DNA was used to quantify total bacteria and S. mutans population via qPCR and specific primers; the same samples were also analyzed by colony forming unit (CFU) counting. In parallel, RNA was isolated from plaque-biofilm samples (from same animals) and used for transcriptional analyses via RT-qPCR. The viable population of both S. mutans and total bacteria assessed by qPCR were positively correlated with the CFU data (P0.8). However, the qPCR data showed higher bacterial cell counts, particularly for total bacteria (vs. CFU). Moreover, S. mutans proportion in the plaque-biofilm determined by qPCR analysis showed strong correlation with incidence of smooth-surface caries (P=0.0022, r=0.71). The purified RNAs presented high RNA integrity numbers (>7), which allowed measurement of the expression of genes that are critical for S. mutans virulence (e.g. gtfB and gtfC). Our data show that the viable microbial population and the gene expression can be analyzed simultaneously, providing a global assessment of the infectious aspect of the disease dental caries. Our approach could enhance the value of the current rodent model in further understanding the pathophysiology of this disease and facilitating the exploration of novel anti-caries therapies. PMID:22958384

  7. Dynamic Properties of the Alkaline Vesicle Population at Hippocampal Synapses

    Science.gov (United States)

    Röther, Mareike; Brauner, Jan M.; Ebert, Katrin; Welzel, Oliver; Jung, Jasmin; Bauereiss, Anna; Kornhuber, Johannes; Groemer, Teja W.

    2014-01-01

    In compensatory endocytosis, scission of vesicles from the plasma membrane to the cytoplasm is a prerequisite for intravesicular reacidification and accumulation of neurotransmitter molecules. Here, we provide time-resolved measurements of the dynamics of the alkaline vesicle population which appears upon endocytic retrieval. Using fast perfusion pH-cycling in live-cell microscopy, synapto-pHluorin expressing rat hippocampal neurons were electrically stimulated. We found that the relative size of the alkaline vesicle population depended significantly on the electrical stimulus size: With increasing number of action potentials the relative size of the alkaline vesicle population expanded. In contrast to that, increasing the stimulus frequency reduced the relative size of the population of alkaline vesicles. Measurement of the time constant for reacification and calculation of the time constant for endocytosis revealed that both time constants were variable with regard to the stimulus condition. Furthermore, we show that the dynamics of the alkaline vesicle population can be predicted by a simple mathematical model. In conclusion, here a novel methodical approach to analyze dynamic properties of alkaline vesicles is presented and validated as a convenient method for the detection of intracellular events. Using this method we show that the population of alkaline vesicles is highly dynamic and depends both on stimulus strength and frequency. Our results implicate that determination of the alkaline vesicle population size may provide new insights into the kinetics of endocytic retrieval. PMID:25079223

  8. Enhanced Microgrid Dynamic Performance Using a Modulated Power Filter Based on Enhanced Bacterial Foraging Optimization

    Directory of Open Access Journals (Sweden)

    Ahmed M. Othman

    2017-06-01

    Full Text Available This paper presents a design of microgrid (MG with enhanced dynamic performance. Distributed energy resources (DER are widely used in MGs to match the various load types and profiles. DERs include solar PV cells, wind energy sources, fuel cells, batteries, micro gas-engines and storage elements. MG will include AC/DC circuits, developed power electronics devices, inverters and power electronic controllers. A novel modulated power filters (MPF device will be applied in MG design. Enhanced bacterial foraging optimization (EBFO will be proposed to optimize and set the MPF parameters to enhance and tune the MG dynamic response. Recent dynamic control is applied to minimize the harmonic reference content. EBFO will adapt the gains of MPF dynamic control. The present research achieves an enhancement of MG dynamic performance, in addition to ensuring improvements in the power factor, bus voltage profile and power quality. MG operation will be evaluated by the dynamic response to be fine-tuned by MPF based on EBFO. Digital simulations have validated the results to show the effectiveness and efficient improvement by the proposed strategy.

  9. Dynamical quorum sensing and clustering dynamics in a population of spatially distributed active rotators

    Science.gov (United States)

    Sakaguchi, Hidetsugu; Maeyama, Satomi

    2013-02-01

    A model of clustering dynamics is proposed for a population of spatially distributed active rotators. A transition from excitable to oscillatory dynamics is induced by the increase of the local density of active rotators. It is interpreted as dynamical quorum sensing. In the oscillation regime, phase waves propagate without decay, which generates an effectively long-range interaction in the clustering dynamics. The clustering process becomes facilitated and only one dominant cluster appears rapidly as a result of the dynamical quorum sensing. An exact localized solution is found to a simplified model equation, and the competitive dynamics between two localized states is studied numerically.

  10. Dynamics of bacterial communities before and after distribution in a full-scale drinking water network

    KAUST Repository

    El Chakhtoura, Joline

    2015-05-01

    Understanding the biological stability of drinking water distribution systems is imperative in the framework of process control and risk management. The objective of this research was to examine the dynamics of the bacterial community during drinking water distribution at high temporal resolution. Water samples (156 in total) were collected over short time-scales (minutes/hours/days) from the outlet of a treatment plant and a location in its corresponding distribution network. The drinking water is treated by biofiltration and disinfectant residuals are absent during distribution. The community was analyzed by 16S rRNA gene pyrosequencing and flow cytometry as well as conventional, culture-based methods. Despite a random dramatic event (detected with pyrosequencing and flow cytometry but not with plate counts), the bacterial community profile at the two locations did not vary significantly over time. A diverse core microbiome was shared between the two locations (58-65% of the taxa and 86-91% of the sequences) and found to be dependent on the treatment strategy. The bacterial community structure changed during distribution, with greater richness detected in the network and phyla such as Acidobacteria and Gemmatimonadetes becoming abundant. The rare taxa displayed the highest dynamicity, causing the major change during water distribution. This change did not have hygienic implications and is contingent on the sensitivity of the applied methods. The concept of biological stability therefore needs to be revised. Biostability is generally desired in drinking water guidelines but may be difficult to achieve in large-scale complex distribution systems that are inherently dynamic.

  11. Dynamics of bacterial communities before and after distribution in a full-scale drinking water network.

    Science.gov (United States)

    El-Chakhtoura, Joline; Prest, Emmanuelle; Saikaly, Pascal; van Loosdrecht, Mark; Hammes, Frederik; Vrouwenvelder, Hans

    2015-05-01

    Understanding the biological stability of drinking water distribution systems is imperative in the framework of process control and risk management. The objective of this research was to examine the dynamics of the bacterial community during drinking water distribution at high temporal resolution. Water samples (156 in total) were collected over short time-scales (minutes/hours/days) from the outlet of a treatment plant and a location in its corresponding distribution network. The drinking water is treated by biofiltration and disinfectant residuals are absent during distribution. The community was analyzed by 16S rRNA gene pyrosequencing and flow cytometry as well as conventional, culture-based methods. Despite a random dramatic event (detected with pyrosequencing and flow cytometry but not with plate counts), the bacterial community profile at the two locations did not vary significantly over time. A diverse core microbiome was shared between the two locations (58-65% of the taxa and 86-91% of the sequences) and found to be dependent on the treatment strategy. The bacterial community structure changed during distribution, with greater richness detected in the network and phyla such as Acidobacteria and Gemmatimonadetes becoming abundant. The rare taxa displayed the highest dynamicity, causing the major change during water distribution. This change did not have hygienic implications and is contingent on the sensitivity of the applied methods. The concept of biological stability therefore needs to be revised. Biostability is generally desired in drinking water guidelines but may be difficult to achieve in large-scale complex distribution systems that are inherently dynamic. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Strongly Deterministic Population Dynamics in Closed Microbial Communities

    Directory of Open Access Journals (Sweden)

    Zak Frentz

    2015-10-01

    Full Text Available Biological systems are influenced by random processes at all scales, including molecular, demographic, and behavioral fluctuations, as well as by their interactions with a fluctuating environment. We previously established microbial closed ecosystems (CES as model systems for studying the role of random events and the emergent statistical laws governing population dynamics. Here, we present long-term measurements of population dynamics using replicate digital holographic microscopes that maintain CES under precisely controlled external conditions while automatically measuring abundances of three microbial species via single-cell imaging. With this system, we measure spatiotemporal population dynamics in more than 60 replicate CES over periods of months. In contrast to previous studies, we observe strongly deterministic population dynamics in replicate systems. Furthermore, we show that previously discovered statistical structure in abundance fluctuations across replicate CES is driven by variation in external conditions, such as illumination. In particular, we confirm the existence of stable ecomodes governing the correlations in population abundances of three species. The observation of strongly deterministic dynamics, together with stable structure of correlations in response to external perturbations, points towards a possibility of simple macroscopic laws governing microbial systems despite numerous stochastic events present on microscopic levels.

  13. Generational Spreading Speed and the Dynamics of Population Range Expansion.

    Science.gov (United States)

    Bateman, Andrew W; Neubert, Michael G; Krkošek, Martin; Lewis, Mark A

    2015-09-01

    Some of the most fundamental quantities in population ecology describe the growth and spread of populations. Population dynamics are often characterized by the annual rate of increase, λ, or the generational rate of increase, R0. Analyses involving R0 have deepened our understanding of disease dynamics and life-history complexities beyond that afforded by analysis of annual growth alone. While range expansion is quantified by the annual spreading speed, a spatial analog of λ, an R0-like expression for the rate of spread is missing. Using integrodifference models, we derive the appropriate generational spreading speed for populations with complex (stage-structured) life histories. The resulting measure, relevant to locations near the expanding edge of a (re)colonizing population, incorporates both local population growth and explicit spatial dispersal rather than solely growth across a population, as is the case for R0. The calculations for generational spreading speed are often simpler than those for annual spreading speed, and analytic or partial analytic solutions can yield insight into the processes that facilitate or slow a population's spatial spread. We analyze the spatial dynamics of green crabs, sea otters, and teasel as examples to demonstrate the flexibility of our methods and the intuitive insights that they afford.

  14. Lethal Consequences of Overcoming Metabolic Restrictions Imposed on a Cooperative Bacterial Population.

    Science.gov (United States)

    Goo, Eunhye; Kang, Yongsung; Lim, Jae Yun; Ham, Hyeonheui; Hwang, Ingyu

    2017-02-28

    Quorum sensing (QS) controls cooperative activities in many Proteobacteria In some species, QS-dependent specific metabolism contributes to the stability of the cooperation. However, the mechanism by which QS and metabolic networks have coevolved to support stable public good cooperation and maintenance of the cooperative group remains unknown. Here we explored the underlying mechanisms of QS-controlled central metabolism in the evolutionary aspects of cooperation. In Burkholderia glumae , the QS-dependent glyoxylate cycle plays an important role in cooperativity. A bifunctional QS-dependent transcriptional regulator, QsmR, rewired central metabolism to utilize the glyoxylate cycle rather than the tricarboxylic acid cycle. Defects in the glyoxylate cycle caused metabolic imbalance and triggered high expression of the stress-responsive chaperonin GroEL. High-level expression of GroEL in glyoxylate cycle mutants interfered with the biosynthesis of a public resource, oxalate, by physically interrupting the oxalate biosynthetic enzyme ObcA. Under such destabilized cooperativity conditions, spontaneous mutations in the qsmR gene in glyoxylate cycle mutants occurred to relieve metabolic stresses, but these mutants lost QsmR-mediated pleiotropy. Overcoming the metabolic restrictions imposed on the population of cooperators among glyoxylate cycle mutants resulted in the occurrence and selection of spontaneous qsmR mutants despite the loss of other important functions. These results provide insight into how QS bacteria have evolved to maintain stable cooperation via QS-mediated metabolic coordination. IMPORTANCE We address how quorum sensing (QS) has coevolved with metabolic networks to maintain bacterial sociality. We found that QS-mediated metabolic rewiring is critical for sustainable bacterial cooperation in Burkholderia glumae The loss of the glyoxylate cycle triggered the expression of the stress-responsive molecular chaperonin GroEL. Excessive biosynthesis of Gro

  15. A quantitative test of population genetics using spatiogenetic patterns in bacterial colonies.

    Science.gov (United States)

    Korolev, Kirill S; Xavier, João B; Nelson, David R; Foster, Kevin R

    2011-10-01

    It is widely accepted that population-genetics theory is the cornerstone of evolutionary analyses. Empirical tests of the theory, however, are challenging because of the complex relationships between space, dispersal, and evolution. Critically, we lack quantitative validation of the spatial models of population genetics. Here we combine analytics, on- and off-lattice simulations, and experiments with bacteria to perform quantitative tests of the theory. We study two bacterial species, the gut microbe Escherichia coli and the opportunistic pathogen Pseudomonas aeruginosa, and show that spatiogenetic patterns in colony biofilms of both species are accurately described by an extension of the one-dimensional stepping-stone model. We use one empirical measure, genetic diversity at the colony periphery, to parameterize our models and show that we can then accurately predict another key variable: the degree of short-range cell migration along an edge. Moreover, the model allows us to estimate other key parameters, including effective population size (density) at the expansion frontier. While our experimental system is a simplification of natural microbial community, we argue that it constitutes proof of principle that the spatial models of population genetics can quantitatively capture organismal evolution.

  16. Interplay of Noisy Gene Expression and Dynamics Explains Patterns of Bacterial Operon Organization

    Science.gov (United States)

    Igoshin, Oleg

    2011-03-01

    Bacterial chromosomes are organized into operons -- sets of genes co-transcribed into polycistronic messenger RNA. Hypotheses explaining the emergence and maintenance of operons include proportional co-regulation, horizontal transfer of intact ``selfish'' operons, emergence via gene duplication, and co-production of physically interacting proteins to speed their association. We hypothesized an alternative: operons can reduce or increase intrinsic gene expression noise in a manner dependent on the post-translational interactions, thereby resulting in selection for or against operons in depending on the network architecture. We devised five classes of two-gene network modules and show that the effects of operons on intrinsic noise depend on class membership. Two classes exhibit decreased noise with co-transcription, two others reveal increased noise, and the remaining one does not show a significant difference. To test our modeling predictions we employed bioinformatic analysis to determine the relationship gene expression noise and operon organization. The results confirm the overrepresentation of noise-minimizing operon architectures and provide evidence against other hypotheses. Our results thereby suggest a central role for gene expression noise in selecting for or maintaining operons in bacterial chromosomes. This demonstrates how post-translational network dynamics may provide selective pressure for organizing bacterial chromosomes, and has practical consequences for designing synthetic gene networks. This work is supported by National Institutes of Health grant 1R01GM096189-01.

  17. Predicting the dynamics of bacterial growth inhibition by ribosome-targeting antibiotics

    Science.gov (United States)

    Greulich, Philip; Doležal, Jakub; Scott, Matthew; Evans, Martin R.; Allen, Rosalind J.

    2017-12-01

    Understanding how antibiotics inhibit bacteria can help to reduce antibiotic use and hence avoid antimicrobial resistance—yet few theoretical models exist for bacterial growth inhibition by a clinically relevant antibiotic treatment regimen. In particular, in the clinic, antibiotic treatment is time-dependent. Here, we use a theoretical model, previously applied to steady-state bacterial growth, to predict the dynamical response of a bacterial cell to a time-dependent dose of ribosome-targeting antibiotic. Our results depend strongly on whether the antibiotic shows reversible transport and/or low-affinity ribosome binding (‘low-affinity antibiotic’) or, in contrast, irreversible transport and/or high affinity ribosome binding (‘high-affinity antibiotic’). For low-affinity antibiotics, our model predicts that growth inhibition depends on the duration of the antibiotic pulse, and can show a transient period of very fast growth following removal of the antibiotic. For high-affinity antibiotics, growth inhibition depends on peak dosage rather than dose duration, and the model predicts a pronounced post-antibiotic effect, due to hysteresis, in which growth can be suppressed for long times after the antibiotic dose has ended. These predictions are experimentally testable and may be of clinical significance.

  18. Bacterial dynamics in model cheese systems, aiming at safety and quality of Portuguese-style traditional ewe's cheeses.

    Science.gov (United States)

    Pereira, Cláudia I; Graça, João A; Ogando, Natacha S; Gomes, Ana M P; Malcata, F Xavier

    2009-11-01

    An experiment using model ewe's milk cheeses was designed to characterize microbial interactions that arise in actual raw milk cheese environments. These model cheeses were manufactured according to Portuguese artisanal practices, except that the microbial load and biodiversity were fully controlled: single potential pathogens and spoilage bacteria, or a combination thereof, were combined at various initial inoculum levels in sterilized raw ewe's milk with several lactic acid bacteria (LAB) normally found in traditional cheeses. Viable microbial counts were monitored throughout a 60-day ripening period. Two alternative mathematical approaches were used to fit the experimental data generated in terms of population dynamics: percent of inhibition and D-values. These were able to explain the complex competitive interactions between the contaminant microorganisms and the LAB adventitious populations. In general, the tested LAB were less able to inhibit contaminants present in combination and in higher concentrations. Lactococcus lactis, with its strong acidifying potential, was the most effective factor in controlling the unwanted bacterial population, especially single Staphylococcus aureus. The two lactobacilli studied, especially Lactobacillus brevis, were shown to be less effective; Escherichia coli and Listeria innocua were the contaminants least inhibited by the LAB.

  19. Population and evolutionary dynamics in spatially structured seasonally varying environments.

    Science.gov (United States)

    Reid, Jane M; Travis, Justin M J; Daunt, Francis; Burthe, Sarah J; Wanless, Sarah; Dytham, Calvin

    2018-03-25

    Increasingly imperative objectives in ecology are to understand and forecast population dynamic and evolutionary responses to seasonal environmental variation and change. Such population and evolutionary dynamics result from immediate and lagged responses of all key life-history traits, and resulting demographic rates that affect population growth rate, to seasonal environmental conditions and population density. However, existing population dynamic and eco-evolutionary theory and models have not yet fully encompassed within-individual and among-individual variation, covariation, structure and heterogeneity, and ongoing evolution, in a critical life-history trait that allows individuals to respond to seasonal environmental conditions: seasonal migration. Meanwhile, empirical studies aided by new animal-tracking technologies are increasingly demonstrating substantial within-population variation in the occurrence and form of migration versus year-round residence, generating diverse forms of 'partial migration' spanning diverse species, habitats and spatial scales. Such partially migratory systems form a continuum between the extreme scenarios of full migration and full year-round residence, and are commonplace in nature. Here, we first review basic scenarios of partial migration and associated models designed to identify conditions that facilitate the maintenance of migratory polymorphism. We highlight that such models have been fundamental to the development of partial migration theory, but are spatially and demographically simplistic compared to the rich bodies of population dynamic theory and models that consider spatially structured populations with dispersal but no migration, or consider populations experiencing strong seasonality and full obligate migration. Second, to provide an overarching conceptual framework for spatio-temporal population dynamics, we define a 'partially migratory meta-population' system as a spatially structured set of locations that can

  20. The weak shall inherit: bacteriocin-mediated interactions in bacterial populations.

    Directory of Open Access Journals (Sweden)

    Hadeel Majeed

    Full Text Available Evolutionary arms race plays a major role in shaping biological diversity. In microbial systems, competition often involves chemical warfare and the production of bacteriocins, narrow-spectrum toxins aimed at killing closely related strains by forming pores in their target's membrane or by degrading the target's RNA or DNA. Although many empirical and theoretical studies describe competitive exclusion of bacteriocin-sensitive strains by producers of bacteriocins, the dynamics among producers are largely unknown.We used a reporter-gene assay to show that the bacterial response to bacteriocins' treatment mirrors the inflicted damage Potent bacteriocins are lethal to competing strains, but at sublethal doses can serve as strong inducing agents, enhancing their antagonists' bacteriocin production. In contrast, weaker bacteriocins are less toxic to their competitors and trigger mild bacteriocin expression. We used empirical and numerical models to explore the role of cross-induction in the arms race between bacteriocin-producing strains. We found that in well-mixed, unstructured environments where interactions are global, producers of weak bacteriocins are selectively advantageous and outcompete producers of potent bacteriocins. However, in spatially structured environments, where interactions are local, each producer occupies its own territory, and competition takes place only in "no man's lands" between territories, resulting in much slower dynamics.The models we present imply that producers of potent bacteriocins that trigger a strong response in neighboring bacteriocinogenic strains are doomed, while producers of weak bacteriocins that trigger a mild response in bacteriocinogenic strains flourish. This counter-intuitive outcome might explain the preponderance of weak bacteriocin producers in nature. However, the described scenario is prolonged in spatially structured environments thus promoting coexistence, allowing migration and evolution, and

  1. feedback between population and evolutionary dynamics determines the fate of social microbial populations.

    Directory of Open Access Journals (Sweden)

    Alvaro Sanchez

    Full Text Available The evolutionary spread of cheater strategies can destabilize populations engaging in social cooperative behaviors, thus demonstrating that evolutionary changes can have profound implications for population dynamics. At the same time, the relative fitness of cooperative traits often depends upon population density, thus leading to the potential for bi-directional coupling between population density and the evolution of a cooperative trait. Despite the potential importance of these eco-evolutionary feedback loops in social species, they have not yet been demonstrated experimentally and their ecological implications are poorly understood. Here, we demonstrate the presence of a strong feedback loop between population dynamics and the evolutionary dynamics of a social microbial gene, SUC2, in laboratory yeast populations whose cooperative growth is mediated by the SUC2 gene. We directly visualize eco-evolutionary trajectories of hundreds of populations over 50-100 generations, allowing us to characterize the phase space describing the interplay of evolution and ecology in this system. Small populations collapse despite continual evolution towards increased cooperative allele frequencies; large populations with a sufficient number of cooperators "spiral" to a stable state of coexistence between cooperator and cheater strategies. The presence of cheaters does not significantly affect the equilibrium population density, but it does reduce the resilience of the population as well as its ability to adapt to a rapidly deteriorating environment. Our results demonstrate the potential ecological importance of coupling between evolutionary dynamics and the population dynamics of cooperatively growing organisms, particularly in microbes. Our study suggests that this interaction may need to be considered in order to explain intraspecific variability in cooperative behaviors, and also that this feedback between evolution and ecology can critically affect the

  2. Co-infection alters population dynamics of infectious disease

    Science.gov (United States)

    Susi, Hanna; Barrès, Benoit; Vale, Pedro F.; Laine, Anna-Liisa

    2015-01-01

    Co-infections by multiple pathogen strains are common in the wild. Theory predicts co-infections to have major consequences for both within- and between-host disease dynamics, but data are currently scarce. Here, using common garden populations of Plantago lanceolata infected by two strains of the pathogen Podosphaera plantaginis, either singly or under co-infection, we find the highest disease prevalence in co-infected treatments both at the host genotype and population levels. A spore-trapping experiment demonstrates that co-infected hosts shed more transmission propagules than singly infected hosts, thereby explaining the observed change in epidemiological dynamics. Our experimental findings are confirmed in natural pathogen populations—more devastating epidemics were measured in populations with higher levels of co-infection. Jointly, our results confirm the predictions made by theoretical and experimental studies for the potential of co-infection to alter disease dynamics across a large host–pathogen metapopulation. PMID:25569306

  3. Interacting trophic forcing and the population dynamics of herring

    DEFF Research Database (Denmark)

    Lindegren, Martin; Ostman, Orjan; Gardmark, Anna

    2011-01-01

    . Using a statistical, age-structured modeling approach, we demonstrate the relative importance and influence of bottom-up (e.g., climate, zooplankton availability) and top-down (i.e., fishing and predation) factors on the population dynamics of Bothnian Sea herring (Clupea harengus) throughout its life......Small pelagic fish occupy a central position in marine ecosystems worldwide, largely by determining the energy transfer from lower trophic levels to predators at the top of the food web, including humans. Population dynamics of small pelagic fish may therefore be regulated neither strictly bottom......-up nor top-down, but rather through multiple external and internal drivers. While in many studies single drivers have been identified, potential synergies of multiple factors, as well as their relative importance in regulating population dynamics of small pelagic fish, is a largely unresolved issue...

  4. Adaptive Dynamics, Control, and Extinction in Networked Populations

    Science.gov (United States)

    2015-07-09

    extinction . VI. CONCLUSIONS We have presented a method for predicting extinction in stochastic network systems by analyzing a pair-based proxy model...including games on networks (e.g., [40], [41]). Further, we expect that our method of continuously varying a parameter while tracking the path to extinction ...Adaptive Dynamics, Control, and Extinction in Networked Populations Ira B. Schwartz US Naval Research Laboratory Code 6792 Nonlinear System Dynamics

  5. Effects of Cover Crop Species and Season on Population Dynamics of Escherichia coli and Listeria innocua in Soil

    Science.gov (United States)

    Reed-Jones, Neiunna L.; Marine, Sasha Cahn; Everts, Kathryne L.

    2016-01-01

    Cover crops provide several ecosystem services, but their impact on enteric bacterial survival remains unexplored. The influence of cover cropping on foodborne pathogen indicator bacteria was assessed in five cover crop/green manure systems: cereal rye, hairy vetch, crimson clover, hairy vetch-rye and crimson clover-rye mixtures, and bare ground. Cover crop plots were inoculated with Escherichia coli and Listeria innocua in the fall of 2013 and 2014 and tilled into the soil in the spring to form green manure. Soil samples were collected and the bacteria enumerated. Time was a factor for all bacterial populations studied in all fields (P innocua diminished somewhat but persisted, independently of season. In an organic field, the cover crop was a factor for E. coli in year 1 (P = 0.004) and for L. innocua in year 2 (P = 0.011). In year 1, E. coli levels were highest in the rye and hairy vetch-rye plots. In year 2, L. innocua levels were higher in hairy vetch-rye (P = 0.01) and hairy vetch (P = 0.03) plots than in the rye plot. Bacterial populations grew (P innocua numbers were observed after tilling (P innocua abundance in a transitional field (P < 0.05). Overall, the impacts of cover crops/green manures on bacterial population dynamics in soil varied, being influenced by bacterial species, time from inoculation, soil temperature, rainfall, and tillage; this reveals the need for long-term studies. PMID:26729724

  6. A general method for modeling population dynamics and its applications.

    Science.gov (United States)

    Shestopaloff, Yuri K

    2013-12-01

    Studying populations, be it a microbe colony or mankind, is important for understanding how complex systems evolve and exist. Such knowledge also often provides insights into evolution, history and different aspects of human life. By and large, populations' prosperity and decline is about transformation of certain resources into quantity and other characteristics of populations through growth, replication, expansion and acquisition of resources. We introduce a general model of population change, applicable to different types of populations, which interconnects numerous factors influencing population dynamics, such as nutrient influx and nutrient consumption, reproduction period, reproduction rate, etc. It is also possible to take into account specific growth features of individual organisms. We considered two recently discovered distinct growth scenarios: first, when organisms do not change their grown mass regardless of nutrients availability, and the second when organisms can reduce their grown mass by several times in a nutritionally poor environment. We found that nutrient supply and reproduction period are two major factors influencing the shape of population growth curves. There is also a difference in population dynamics between these two groups. Organisms belonging to the second group are significantly more adaptive to reduction of nutrients and far more resistant to extinction. Also, such organisms have substantially more frequent and lesser in amplitude fluctuations of population quantity for the same periodic nutrient supply (compared to the first group). Proposed model allows adequately describing virtually any possible growth scenario, including complex ones with periodic and irregular nutrient supply and other changing parameters, which present approaches cannot do.

  7. Long-Term Bacterial Dynamics in a Full-Scale Drinking Water Distribution System

    Science.gov (United States)

    Prest, E. I.; Weissbrodt, D. G.; Hammes, F.; van Loosdrecht, M. C. M.; Vrouwenvelder, J. S.

    2016-01-01

    Large seasonal variations in microbial drinking water quality can occur in distribution networks, but are often not taken into account when evaluating results from short-term water sampling campaigns. Temporal dynamics in bacterial community characteristics were investigated during a two-year drinking water monitoring campaign in a full-scale distribution system operating without detectable disinfectant residual. A total of 368 water samples were collected on a biweekly basis at the water treatment plant (WTP) effluent and at one fixed location in the drinking water distribution network (NET). The samples were analysed for heterotrophic plate counts (HPC), Aeromonas plate counts, adenosine-tri-phosphate (ATP) concentrations, and flow cytometric (FCM) total and intact cell counts (TCC, ICC), water temperature, pH, conductivity, total organic carbon (TOC) and assimilable organic carbon (AOC). Multivariate analysis of the large dataset was performed to explore correlative trends between microbial and environmental parameters. The WTP effluent displayed considerable seasonal variations in TCC (from 90 × 103 cells mL-1 in winter time up to 455 × 103 cells mL-1 in summer time) and in bacterial ATP concentrations (water temperature variations. These fluctuations were not detected with HPC and Aeromonas counts. The water in the network was predominantly influenced by the characteristics of the WTP effluent. The increase in ICC between the WTP effluent and the network sampling location was small (34 × 103 cells mL-1 on average) compared to seasonal fluctuations in ICC in the WTP effluent. Interestingly, the extent of bacterial growth in the NET was inversely correlated to AOC concentrations in the WTP effluent (Pearson’s correlation factor r = -0.35), and positively correlated with water temperature (r = 0.49). Collecting a large dataset at high frequency over a two year period enabled the characterization of previously undocumented seasonal dynamics in the

  8. Long-Term Bacterial Dynamics in a Full-Scale Drinking Water Distribution System

    KAUST Repository

    Prest, E. I.

    2016-10-28

    Large seasonal variations in microbial drinking water quality can occur in distribution networks, but are often not taken into account when evaluating results from short-term water sampling campaigns. Temporal dynamics in bacterial community characteristics were investigated during a two-year drinking water monitoring campaign in a full-scale distribution system operating without detectable disinfectant residual. A total of 368 water samples were collected on a biweekly basis at the water treatment plant (WTP) effluent and at one fixed location in the drinking water distribution network (NET). The samples were analysed for heterotrophic plate counts (HPC), Aeromonas plate counts, adenosine-tri-phosphate (ATP) concentrations, and flow cytometric (FCM) total and intact cell counts (TCC, ICC), water temperature, pH, conductivity, total organic carbon (TOC) and assimilable organic carbon (AOC). Multivariate analysis of the large dataset was performed to explore correlative trends between microbial and environmental parameters. The WTP effluent displayed considerable seasonal variations in TCC (from 90 × 103 cells mL-1 in winter time up to 455 × 103 cells mL-1 in summer time) and in bacterial ATP concentrations (<1–3.6 ng L-1), which were congruent with water temperature variations. These fluctuations were not detected with HPC and Aeromonas counts. The water in the network was predominantly influenced by the characteristics of the WTP effluent. The increase in ICC between the WTP effluent and the network sampling location was small (34 × 103 cells mL-1 on average) compared to seasonal fluctuations in ICC in the WTP effluent. Interestingly, the extent of bacterial growth in the NET was inversely correlated to AOC concentrations in the WTP effluent (Pearson’s correlation factor r = -0.35), and positively correlated with water temperature (r = 0.49). Collecting a large dataset at high frequency over a two year period enabled the characterization of previously

  9. Long-Term Bacterial Dynamics in a Full-Scale Drinking Water Distribution System.

    Science.gov (United States)

    Prest, E I; Weissbrodt, D G; Hammes, F; van Loosdrecht, M C M; Vrouwenvelder, J S

    2016-01-01

    Large seasonal variations in microbial drinking water quality can occur in distribution networks, but are often not taken into account when evaluating results from short-term water sampling campaigns. Temporal dynamics in bacterial community characteristics were investigated during a two-year drinking water monitoring campaign in a full-scale distribution system operating without detectable disinfectant residual. A total of 368 water samples were collected on a biweekly basis at the water treatment plant (WTP) effluent and at one fixed location in the drinking water distribution network (NET). The samples were analysed for heterotrophic plate counts (HPC), Aeromonas plate counts, adenosine-tri-phosphate (ATP) concentrations, and flow cytometric (FCM) total and intact cell counts (TCC, ICC), water temperature, pH, conductivity, total organic carbon (TOC) and assimilable organic carbon (AOC). Multivariate analysis of the large dataset was performed to explore correlative trends between microbial and environmental parameters. The WTP effluent displayed considerable seasonal variations in TCC (from 90 × 103 cells mL-1 in winter time up to 455 × 103 cells mL-1 in summer time) and in bacterial ATP concentrations (water temperature variations. These fluctuations were not detected with HPC and Aeromonas counts. The water in the network was predominantly influenced by the characteristics of the WTP effluent. The increase in ICC between the WTP effluent and the network sampling location was small (34 × 103 cells mL-1 on average) compared to seasonal fluctuations in ICC in the WTP effluent. Interestingly, the extent of bacterial growth in the NET was inversely correlated to AOC concentrations in the WTP effluent (Pearson's correlation factor r = -0.35), and positively correlated with water temperature (r = 0.49). Collecting a large dataset at high frequency over a two year period enabled the characterization of previously undocumented seasonal dynamics in the distribution

  10. Long-Term Bacterial Dynamics in a Full-Scale Drinking Water Distribution System.

    Directory of Open Access Journals (Sweden)

    E I Prest

    Full Text Available Large seasonal variations in microbial drinking water quality can occur in distribution networks, but are often not taken into account when evaluating results from short-term water sampling campaigns. Temporal dynamics in bacterial community characteristics were investigated during a two-year drinking water monitoring campaign in a full-scale distribution system operating without detectable disinfectant residual. A total of 368 water samples were collected on a biweekly basis at the water treatment plant (WTP effluent and at one fixed location in the drinking water distribution network (NET. The samples were analysed for heterotrophic plate counts (HPC, Aeromonas plate counts, adenosine-tri-phosphate (ATP concentrations, and flow cytometric (FCM total and intact cell counts (TCC, ICC, water temperature, pH, conductivity, total organic carbon (TOC and assimilable organic carbon (AOC. Multivariate analysis of the large dataset was performed to explore correlative trends between microbial and environmental parameters. The WTP effluent displayed considerable seasonal variations in TCC (from 90 × 103 cells mL-1 in winter time up to 455 × 103 cells mL-1 in summer time and in bacterial ATP concentrations (<1-3.6 ng L-1, which were congruent with water temperature variations. These fluctuations were not detected with HPC and Aeromonas counts. The water in the network was predominantly influenced by the characteristics of the WTP effluent. The increase in ICC between the WTP effluent and the network sampling location was small (34 × 103 cells mL-1 on average compared to seasonal fluctuations in ICC in the WTP effluent. Interestingly, the extent of bacterial growth in the NET was inversely correlated to AOC concentrations in the WTP effluent (Pearson's correlation factor r = -0.35, and positively correlated with water temperature (r = 0.49. Collecting a large dataset at high frequency over a two year period enabled the characterization of previously

  11. Selective labelling and eradication of antibiotic-tolerant bacterial populations in Pseudomonas aeruginosa biofilms

    Science.gov (United States)

    Chua, Song Lin; Yam, Joey Kuok Hoong; Hao, Piliang; Adav, Sunil S.; Salido, May Margarette; Liu, Yang; Givskov, Michael; Sze, Siu Kwan; Tolker-Nielsen, Tim; Yang, Liang

    2016-01-01

    Drug resistance and tolerance greatly diminish the therapeutic potential of antibiotics against pathogens. Antibiotic tolerance by bacterial biofilms often leads to persistent infections, but its mechanisms are unclear. Here we use a proteomics approach, pulsed stable isotope labelling with amino acids (pulsed-SILAC), to quantify newly expressed proteins in colistin-tolerant subpopulations of Pseudomonas aeruginosa biofilms (colistin is a ‘last-resort' antibiotic against multidrug-resistant Gram-negative pathogens). Migration is essential for the formation of colistin-tolerant biofilm subpopulations, with colistin-tolerant cells using type IV pili to migrate onto the top of the colistin-killed biofilm. The colistin-tolerant cells employ quorum sensing (QS) to initiate the formation of new colistin-tolerant subpopulations, highlighting multicellular behaviour in antibiotic tolerance development. The macrolide erythromycin, which has been previously shown to inhibit the motility and QS of P. aeruginosa, boosts biofilm eradication by colistin. Our work provides insights on the mechanisms underlying the formation of antibiotic-tolerant populations in bacterial biofilms and indicates research avenues for designing more efficient treatments against biofilm-associated infections. PMID:26892159

  12. DNA thermodynamic stability and supercoil dynamics determine the gene expression program during the bacterial growth cycle.

    Science.gov (United States)

    Sobetzko, Patrick; Glinkowska, Monika; Travers, Andrew; Muskhelishvili, Georgi

    2013-07-01

    The chromosomal DNA polymer constituting the cellular genetic material is primarily a device for coding information. Whilst the gene sequences comprise the digital (discontinuous) linear code, physiological alterations of the DNA superhelical density generate in addition analog (continuous) three-dimensional information essential for regulation of both chromosome compaction and gene expression. Insight into the relationship between the DNA analog information and the digital linear code is of fundamental importance for understanding genetic regulation. Our previous study in the model organism Escherichia coli suggested that the chromosomal gene order and a spatiotemporal gradient of DNA superhelicity associated with DNA replication determine the growth phase-dependent gene transcription. In this study we reveal a general gradient of DNA thermodynamic stability correlated with the polarity of chromosomal replication and manifest in the spatiotemporal pattern of gene transcription during the bacterial growth cycle. Furthermore, by integrating the physical and dynamic features of the transcribed sequences with their functional content we identify spatiotemporal domains of gene expression encompassing different functions. We thus provide both an insight into the organisational principle of the bacterial growth program and a novel holistic methodology for exploring chromosomal dynamics.

  13. Network evolution induced by the dynamical rules of two populations

    International Nuclear Information System (INIS)

    Platini, Thierry; Zia, R K P

    2010-01-01

    We study the dynamical properties of a finite dynamical network composed of two interacting populations, namely extrovert (a) and introvert (b). In our model, each group is characterized by its size (N a and N b ) and preferred degree (κ a and κ b a ). The network dynamics is governed by the competing microscopic rules of each population that consist of the creation and destruction of links. Starting from an unconnected network, we give a detailed analysis of the mean field approach which is compared to Monte Carlo simulation data. The time evolution of the restricted degrees (k bb ) and (k ab ) presents three time regimes and a non-monotonic behavior well captured by our theory. Surprisingly, when the population sizes are equal N a = N b , the ratio of the restricted degree θ 0 = (k ab )/(k bb ) appears to be an integer in the asymptotic limits of the three time regimes. For early times (defined by t 1 = κ b ) the total number of links presents a linear evolution, where the two populations are indistinguishable and where θ 0 = 1. Interestingly, in the intermediate time regime (defined for t 1 2 ∝κ a and for which θ 0 = 5), the system reaches a transient stationary state, where the number of contacts among introverts remains constant while the number of connections increases linearly in the extrovert population. Finally, due to the competing dynamics, the network presents a frustrated stationary state characterized by a ratio θ 0 = 3

  14. The population and evolutionary dynamics of Vibrio cholerae and its bacteriophage: conditions for maintaining phage-limited communities.

    Science.gov (United States)

    Wei, Yan; Kirby, Amy; Levin, Bruce R

    2011-12-01

    Although bacteriophage have been reported to be the most abundant organisms on earth, little is known about their contribution to the ecology of natural communities of their host bacteria. Most importantly, what role do these viral parasitoids play in regulating the densities of bacterial populations? To address this question, we use experimental communities of Vibrio cholerae and its phage in continuous culture, and we use mathematical models to explore the population dynamic and evolutionary conditions under which phage, rather than resources, will limit the densities of these bacteria. The results of our experiments indicate that single species of bacterial viruses cannot maintain the density of V. cholerae populations at levels much lower than that anticipated on the basis of resources alone. On the other hand, as few as two species of phage can maintain these bacteria at densities more than two orders of magnitude lower than the densities of the corresponding phage-free controls for extensive periods. Using mathematical models and short-term experiments, we explore the population dynamic processes responsible for these results. We discuss the implications of this experimental and theoretical study for the population and evolutionary dynamics of natural populations of bacteria and phage.

  15. Stochastic population dynamics of a montane ground-dwelling squirrel.

    Directory of Open Access Journals (Sweden)

    Jeffrey A Hostetler

    Full Text Available Understanding the causes and consequences of population fluctuations is a central goal of ecology. We used demographic data from a long-term (1990-2008 study and matrix population models to investigate factors and processes influencing the dynamics and persistence of a golden-mantled ground squirrel (Callospermophilus lateralis population, inhabiting a dynamic subalpine habitat in Colorado, USA. The overall deterministic population growth rate λ was 0.94±SE 0.05 but it varied widely over time, ranging from 0.45±0.09 in 2006 to 1.50±0.12 in 2003, and was below replacement (λ<1 for 9 out of 18 years. The stochastic population growth rate λ(s was 0.92, suggesting a declining population; however, the 95% CI on λ(s included 1.0 (0.52-1.60. Stochastic elasticity analysis showed that survival of adult females, followed by survival of juvenile females and litter size, were potentially the most influential vital rates; analysis of life table response experiments revealed that the same three life history variables made the largest contributions to year-to year changes in λ. Population viability analysis revealed that, when the influences of density dependence and immigration were not considered, the population had a high (close to 1.0 in 50 years probability of extinction. However, probability of extinction declined to as low as zero when density dependence and immigration were considered. Destabilizing effects of stochastic forces were counteracted by regulating effects of density dependence and rescue effects of immigration, which allowed our study population to bounce back from low densities and prevented extinction. These results suggest that dynamics and persistence of our study population are determined synergistically by density-dependence, stochastic forces, and immigration.

  16. A general modeling framework for describing spatially structured population dynamics

    Science.gov (United States)

    Sample, Christine; Fryxell, John; Bieri, Joanna; Federico, Paula; Earl, Julia; Wiederholt, Ruscena; Mattsson, Brady; Flockhart, Tyler; Nicol, Sam; Diffendorfer, James E.; Thogmartin, Wayne E.; Erickson, Richard A.; Norris, D. Ryan

    2017-01-01

    Variation in movement across time and space fundamentally shapes the abundance and distribution of populations. Although a variety of approaches model structured population dynamics, they are limited to specific types of spatially structured populations and lack a unifying framework. Here, we propose a unified network-based framework sufficiently novel in its flexibility to capture a wide variety of spatiotemporal processes including metapopulations and a range of migratory patterns. It can accommodate different kinds of age structures, forms of population growth, dispersal, nomadism and migration, and alternative life-history strategies. Our objective was to link three general elements common to all spatially structured populations (space, time and movement) under a single mathematical framework. To do this, we adopt a network modeling approach. The spatial structure of a population is represented by a weighted and directed network. Each node and each edge has a set of attributes which vary through time. The dynamics of our network-based population is modeled with discrete time steps. Using both theoretical and real-world examples, we show how common elements recur across species with disparate movement strategies and how they can be combined under a unified mathematical framework. We illustrate how metapopulations, various migratory patterns, and nomadism can be represented with this modeling approach. We also apply our network-based framework to four organisms spanning a wide range of life histories, movement patterns, and carrying capacities. General computer code to implement our framework is provided, which can be applied to almost any spatially structured population. This framework contributes to our theoretical understanding of population dynamics and has practical management applications, including understanding the impact of perturbations on population size, distribution, and movement patterns. By working within a common framework, there is less chance

  17. A general modeling framework for describing spatially structured population dynamics.

    Science.gov (United States)

    Sample, Christine; Fryxell, John M; Bieri, Joanna A; Federico, Paula; Earl, Julia E; Wiederholt, Ruscena; Mattsson, Brady J; Flockhart, D T Tyler; Nicol, Sam; Diffendorfer, Jay E; Thogmartin, Wayne E; Erickson, Richard A; Norris, D Ryan

    2018-01-01

    Variation in movement across time and space fundamentally shapes the abundance and distribution of populations. Although a variety of approaches model structured population dynamics, they are limited to specific types of spatially structured populations and lack a unifying framework. Here, we propose a unified network-based framework sufficiently novel in its flexibility to capture a wide variety of spatiotemporal processes including metapopulations and a range of migratory patterns. It can accommodate different kinds of age structures, forms of population growth, dispersal, nomadism and migration, and alternative life-history strategies. Our objective was to link three general elements common to all spatially structured populations (space, time and movement) under a single mathematical framework. To do this, we adopt a network modeling approach. The spatial structure of a population is represented by a weighted and directed network. Each node and each edge has a set of attributes which vary through time. The dynamics of our network-based population is modeled with discrete time steps. Using both theoretical and real-world examples, we show how common elements recur across species with disparate movement strategies and how they can be combined under a unified mathematical framework. We illustrate how metapopulations, various migratory patterns, and nomadism can be represented with this modeling approach. We also apply our network-based framework to four organisms spanning a wide range of life histories, movement patterns, and carrying capacities. General computer code to implement our framework is provided, which can be applied to almost any spatially structured population. This framework contributes to our theoretical understanding of population dynamics and has practical management applications, including understanding the impact of perturbations on population size, distribution, and movement patterns. By working within a common framework, there is less chance

  18. Population dynamics in the capitalist world-economy

    OpenAIRE

    Danna, D.

    2014-01-01

    World-systems analysis has given scant attention to population dynamics. Overlooked are large-scale macrohistorical population trends and their microhistorical foundation on procreative decisions-decisions which are taken by a historically changing subject of procreation: local elders or other authorities, head(s) of the household, couples, and women. The discipline of demography is also not as helpful as it could be, given its basis in modernization theory, which fails to recognize intention...

  19. Technological change, population dynamics, and natural resource depletion

    OpenAIRE

    Schaefer, Andreas

    2014-01-01

    In this paper, we integrate fertility and educational choices into a scale-invariant model of directed technological change with non-renewable natural resources, in order to reveal the interaction between population dynamics, technological change, and natural resource depletion. In line with empirical regularities, skill-biased technological change induces a decline in population growth and a transitory increase in the depletion rate of natural resources. In the long-run, the depletion rate a...

  20. Effect of buctril super (Bromoxynil herbicide on soil microbial biomass and bacterial population

    Directory of Open Access Journals (Sweden)

    Zafar Abbas

    2014-02-01

    Full Text Available The present study aimed to evaluate the effect of bromoxynil herbicide on soil microorganisms, with the hypothesis that this herbicide caused suppression in microbial activity and biomass by exerting toxic effect on them. Nine sites of Punjab province (Pakistan those had been exposed to bromoxynil herbicide for about last ten years designated as soil 'A' were surveyed in 2011 and samples were collected and analyzed for Microbial Biomass Carbon (MBC, Biomass Nitrogen (MBN, Biomass Phosphorus (MBP and bacterial population. Simultaneously, soil samples from the same areas those were not exposed to herbicide designated as soil 'B' were taken. At all the sites MBC, MBN and MBP ranged from 131 to 457, 1.22 to 13.1 and 0.59 to 3.70 µg g-1 in the contaminated soils (Soil A, which was 187 to 573, 1.70 to 14.4 and 0.72 to 4.12 µg g-1 in the soils without contamination (soil B. Bacterial population ranged from 0.67 to 1.84x10(8 and 0.87 to 2.37x10(8 cfu g-1 soil in the soils A and B, respectively. Bromoxynil residues ranged from 0.09 to 0.24 mg kg-1 at all the sites in soil A. But no residues were detected in the soil B. Due to lethal effect of bromoxynil residues on the above parameters, considerable decline in these parameters was observed in the contaminated soils. Results depicted that the herbicide had left toxic effects on soil microbial parameters, thus confirmed that continuous use of this herbicide affected the quality of soil and sustainable crop production.

  1. An individual-based model of Zebrafish population dynamics accounting for energy dynamics

    DEFF Research Database (Denmark)

    Beaudouin, Remy; Goussen, Benoit; Piccini, Benjamin

    2015-01-01

    Developing population dynamics models for zebrafish is crucial in order to extrapolate from toxicity data measured at the organism level to biological levels relevant to support and enhance ecological risk assessment. To achieve this, a dynamic energy budget for individual zebrafish (DEB model) w...

  2. DMPD: Structural and functional analyses of bacterial lipopolysaccharides. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 12106784 Structural and functional analyses of bacterial lipopolysaccharides. Carof...html) (.csml) Show Structural and functional analyses of bacterial lipopolysaccharides. PubmedID 12106784 Ti...tle Structural and functional analyses of bacterial lipopolysaccharides. Authors

  3. French invasive Asian tiger mosquito populations harbor reduced bacterial microbiota and genetic diversity compared to Vietnamese autochthonous relatives

    Directory of Open Access Journals (Sweden)

    Guillaume eMinard

    2015-09-01

    Full Text Available The Asian tiger mosquito Aedes albopictus is one of the most significant pathogen vectors of the 21st century. Originating from Asia, it has invaded a wide range of eco-climatic regions worldwide. The insect-associated microbiota is now recognized to play a significant role in host biology. While genetic diversity bottlenecks are known to result from biological invasions, the resulting shifts in host-associated microbiota diversity has not been thoroughly investigated. To address this subject, we compared four autochthonous Ae. albopictus populations in Vietnam, the native area of Ae. albopictus, and three populations recently introduced to Metropolitan France, with the aim of documenting whether these populations display differences in host genotype and bacterial microbiota. Population-level genetic diversity (microsatellite markers and COI haplotype and bacterial diversity (16S rDNA metabarcoding were compared between field-caught mosquitoes. Bacterial microbiota from the whole insect bodies were largely dominated by Wolbachia pipientis. Targeted analysis of the gut microbiota revealed a greater bacterial diversity in which a fraction was common between French and Vietnamese populations. The genus Dysgonomonas was the most prevalent and abundant across all studied populations. Overall genetic diversities of both hosts and bacterial microbiota were significantly reduced in recently established populations of France compared to the autochthonous populations of Vietnam. These results open up many important avenues of investigation in order to link the process of geographical invasion to shifts in commensal and symbiotic microbiome communities, as such shifts may have dramatic impacts on the biology and/or vector competence of invading hematophagous insects.

  4. A population-level model from the microscopic dynamics in Escherichia coli chemotaxis via Langevin approximation

    International Nuclear Information System (INIS)

    He Zhuo-Ran; Wu Tai-Lin; Ouyang Qi; Tu Yu-Hai

    2012-01-01

    Recent extensive studies of Escherichia coli (E. coli) chemotaxis have achieved a deep understanding of its microscopic control dynamics. As a result, various quantitatively predictive models have been developed to describe the chemotactic behavior of E. coli motion. However, a population-level partial differential equation (PDE) that rationally incorporates such microscopic dynamics is still insufficient. Apart from the traditional Keller–Segel (K–S) equation, many existing population-level models developed from the microscopic dynamics are integro-PDEs. The difficulty comes mainly from cell tumbles which yield a velocity jumping process. Here, we propose a Langevin approximation method that avoids such a difficulty without appreciable loss of precision. The resulting model not only quantitatively reproduces the results of pathway-based single-cell simulators, but also provides new inside information on the mechanism of E. coli chemotaxis. Our study demonstrates a possible alternative in establishing a simple population-level model that allows for the complex microscopic mechanisms in bacterial chemotaxis

  5. Estimating Traveler Populations at Airport and Cruise Terminals for Population Distribution and Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Jochem, Warren C [ORNL; Sims, Kelly M [ORNL; Bright, Eddie A [ORNL; Urban, Marie L [ORNL; Rose, Amy N [ORNL; Coleman, Phil R [ORNL; Bhaduri, Budhendra L [ORNL

    2013-01-01

    In recent years, uses of high-resolution population distribution databases are increasing steadily for environmental, socioeconomic, public health, and disaster-related research and operations. With the development of daytime population distribution, temporal resolution of such databases has been improved. However, the lack of incorporation of transitional population, namely business and leisure travelers, leaves a significant population unaccounted for within the critical infrastructure networks, such as at transportation hubs. This paper presents two general methodologies for estimating passenger populations in airport and cruise port terminals at a high temporal resolution which can be incorporated into existing population distribution models. The methodologies are geographically scalable and are based on, and demonstrate how, two different transportation hubs with disparate temporal population dynamics can be modeled utilizing publicly available databases including novel data sources of flight activity from the Internet which are updated in near-real time. The airport population estimation model shows great potential for rapid implementation for a large collection of airports on a national scale, and the results suggest reasonable accuracy in the estimated passenger traffic. By incorporating population dynamics at high temporal resolutions into population distribution models, we hope to improve the estimates of populations exposed to or at risk to disasters, thereby improving emergency planning and response, and leading to more informed policy decisions.

  6. Radiation resistance of bacterial populations, isolated from the environment of the radiation sterilization plant type JS-6900, Debrecen

    International Nuclear Information System (INIS)

    Gazso, L.; Igali, S.; Daroczy, E.

    1978-01-01

    The radiation resistance of bacterial populations isolated from the air of an industrial sterilization plant loaded with an activity of 250000 Ci was investigated before loading and a year after loading with 60 Co. The mean D 10 value of the 23 strains isolated before loading was 73 krad with a maximum of 173 krad. The mean D 10 value of the 26 strains isolated a year after loading was 32 krad with a maximum of 156 krad. It was not possible to detect any increase in radiation resistance of bacterial populations isolated from the irradiation room after one year of running radiation sterilization of disposable medical supplies. (author)

  7. Identification and dynamic modeling of biomarkers for bacterial uptake and effect of sulfonamide antimicrobials

    International Nuclear Information System (INIS)

    Richter, Merle K.; Focks, Andreas; Siegfried, Barbara; Rentsch, Daniel; Krauss, Martin; Schwarzenbach, René P.; Hollender, Juliane

    2013-01-01

    The effects of sulfathiazole (STA) on Escherichia coli with glucose as a growth substrate was investigated to elucidate the effect-based reaction of sulfonamides in bacteria and to identify biomarkers for bacterial uptake and effect. The predominant metabolite was identified as pterine-sulfathiazole by LC-high resolution mass spectrometry. The formation of pterine-sulfathiazole per cell was constant and independent of the extracellular STA concentrations, as they exceeded the modeled half-saturation concentration K M S of 0.011 μmol L −1 . The concentration of the dihydrofolic acid precursor para-aminobenzoic acid (pABA) increased with growth and with concentrations of the competitor STA. This increase was counteracted for higher STA concentrations by growth inhibition as verified by model simulation of pABA dynamics. The EC value for the inhibition of pABA increase was 6.9 ± 0.7 μmol L −1 STA, which is similar to that calculated from optical density dynamics indicating that pABA is a direct biomarker for the SA effect. - Highlights: ► Elucidation of the effect-based reaction of sulfonamides in bacteria. ► Identification of a biomarker for uptake and effect-based reaction of sulfonamides. ► Investigation of a biomarker for the bacterial growth inhibition by sulfonamides. ► Quantitative mechanistic modeling of biomarker dynamics using enzyme kinetics. ► Mechanistic quantitative linking of sulfonamide concentrations and effects. - Identification of specific biomarkers for the uptake and effect-based reaction of sulfonamides in bacteria and resulting growth inhibition.

  8. Population Dynamics of the East African Sleeping Sickness ...

    African Journals Online (AJOL)

    Mathematical models of the East African sleeping sickness epidemiology are presented. This paper is aimed at modelling the dynamics of the disease as it affects the human and domestic animal populations. The mathematical model is extended to include the contact rate of the tsetse flies with the wild park animals that ...

  9. The Onchorcerciasis Disease: Population Dynamics of Its Host And ...

    African Journals Online (AJOL)

    Onchocerciasis disease is a debilitating disease that hampers the well-being and productive capacity of an affected person. In this work, we looked at the population dynamics of the Host (Man), the Vector (Simulium Damnosium – the Blackfly ) and the possible Microfilaria output of the worm in the Host via Mathematical ...

  10. Population Dynamics of the Giant African River Prawn ...

    African Journals Online (AJOL)

    USER

    Growth, mortality, recruitment, yield-per-recruit and present rate of exploitation of the African river prawn Macrobrachium vollenhovenii were ... The present study is the first report on the population dynamics of the species in the Cross River Estuary,. Nigeria, and provides ..... Sea Demersal Fish Comm. 1979/G/24, 26 pp.

  11. Population dynamics of the invasive fish, Gambusia affinis , in ...

    African Journals Online (AJOL)

    The alien invasive Gambusia affinis is one of the most widely introduced fish species on the planet, and has established in freshwater ecosystems across South Africa. The invasion ecology and, in particular, the population dynamics of the species in this country are, however, poorly understood. In this study the relative ...

  12. Binary Populations and Stellar Dynamics in Young Clusters

    Science.gov (United States)

    Vanbeveren, D.; Belkus, H.; Van Bever, J.; Mennekens, N.

    2008-06-01

    We first summarize work that has been done on the effects of binaries on theoretical population synthesis of stars and stellar phenomena. Next, we highlight the influence of stellar dynamics in young clusters by discussing a few candidate UFOs (unconventionally formed objects) like intermediate mass black holes, η Car, ζ Pup, γ2 Velorum and WR 140.

  13. Population Dynamics of Southern Pine Beetle in Forest Landscapes

    Science.gov (United States)

    Andrew Birt

    2011-01-01

    Southern pine beetle (SPB) is an important pest of Southeastern United States pine forests. Periodic regional outbreaks are characterized by localized areas of tree mortality (infestations) surrounded by areas with little or no damage. Ultimately, this spatiotemporal pattern of tree mortality is driven by the dynamics of SPB populations—more specifically, by rates of...

  14. Termite Population Dynamics in Arenic Kandiudults as Influenced by ...

    African Journals Online (AJOL)

    Termites have been identified as one of the major pests of cassava in Nigeria especially on infested soils. Termite Population Dynamics in Arenic Kandiudults as Influenced by Tillage and Organic Manure Sources in a Cassava Farm in Owerri, Southeastern Nigeria, was investigated in this study. Three years of field trials ...

  15. Breeding seasonality and population dynamics of the catfish Schilbe ...

    African Journals Online (AJOL)

    Twelve consecutive months length frequency data (N = 6999) and FiSAT software were used in the study of the dynamics of exploited population the catfish Schilbe mystus in the Cross River Nigeria. Variation in monthly mean gonadosmtic index showed two peaks, March and September and this indicates that the species ...

  16. The population dynamics of the estuarine isopod Exosphaeroma ...

    African Journals Online (AJOL)

    The population dynamics of the estuarine isopod, Exosphaeroma hylocoetes, was investigated monthly from February 2006 to August 2007 in three temporarily open/closed Eastern Cape estuaries, the East and West Kleinemonde and Kasouga Estuaries. Mean isopod abundances and biomasses ranged between 0 and ...

  17. Network evolution induced by the dynamical rules of two populations

    Science.gov (United States)

    Platini, Thierry; Zia, R. K. P.

    2010-10-01

    We study the dynamical properties of a finite dynamical network composed of two interacting populations, namely extrovert (a) and introvert (b). In our model, each group is characterized by its size (Na and Nb) and preferred degree (κa and \\kappa_b\\ll \\kappa_a ). The network dynamics is governed by the competing microscopic rules of each population that consist of the creation and destruction of links. Starting from an unconnected network, we give a detailed analysis of the mean field approach which is compared to Monte Carlo simulation data. The time evolution of the restricted degrees langkbbrang and langkabrang presents three time regimes and a non-monotonic behavior well captured by our theory. Surprisingly, when the population sizes are equal Na = Nb, the ratio of the restricted degree θ0 = langkabrang/langkbbrang appears to be an integer in the asymptotic limits of the three time regimes. For early times (defined by t introverts remains constant while the number of connections increases linearly in the extrovert population. Finally, due to the competing dynamics, the network presents a frustrated stationary state characterized by a ratio θ0 = 3.

  18. COMPARISON OF SAMPLING TECHNIQUES USED IN STUDYING LEPIDOPTERA POPULATION DYNAMICS

    Science.gov (United States)

    Four methods (light traps, foliage samples, canvas bands, and gypsy moth egg mass surveys) that are used to study the population dynamics of foliage-feeding Lepidoptera were compared for 10 species, including gypsy moth, Lymantria dispar L. Samples were collected weekly at 12 sit...

  19. Population dynamics of soil microbes and diversity of Bacillus ...

    African Journals Online (AJOL)

    Population dynamics of soil microbes and diversity of Bacillus thuringiensis in agricultural and botanic garden soils of India. ... The PDF file you selected should load here if your Web browser has a PDF reader plug-in installed (for example, a recent version of Adobe Acrobat Reader). If you would like more information about ...

  20. Population dynamics and spatial behaviour of Microtus tatricus (Arvicolinae, Rodentia)

    Czech Academy of Sciences Publication Activity Database

    Rudá, M.; Kocian, Ľ.; Martínková, Natália; Žiak, D.

    2010-01-01

    Roč. 55, č. 1 (2010), s. 85-88 ISSN 0001-7051 Institutional research plan: CEZ:AV0Z60930519 Keywords : Tatra vole * population dynamics * spatial activity Subject RIV: EH - Ecology, Behaviour Impact factor: 0.985, year: 2010

  1. Individual based model of slug population and spatial dynamics

    NARCIS (Netherlands)

    Choi, Y.H.; Bohan, D.A.; Potting, R.P.J.; Semenov, M.A.; Glen, D.M.

    2006-01-01

    The slug, Deroceras reticulatum, is one of the most important pests of agricultural and horticultural crops in UK and Europe. In this paper, a spatially explicit individual based model (IbM) is developed to study the dynamics of a population of D. reticulatum. The IbM establishes a virtual field

  2. Predicting population and community dynamics: the type of aggregation matters

    NARCIS (Netherlands)

    Meyer, K.; Schiffers, T.; Münkemüller, T.; Schädler, M.; Calabrese, J.; Basset, A.; Breulmann, M.; Duquesne, S.; Hidding, B.; Huth, A.; Schöb, C.; Voorde, van de T.F.J.

    2010-01-01

    When investigating complex ecological dynamics at the population or community level, we necessarily need to abstract and aggregate ecological information. The way in which information is aggregated may be crucial for the outcome of the study. In this paper, we suggest that in addition to the

  3. Inmate Population Dynamics at the United States Disciplinary Barracks.

    Science.gov (United States)

    1983-08-04

    Prisoner population growth. 2. Prisoner popula- . tion forecasting. 3. Military prisoner overcrowding at USDB. 4. Elements of prisoner population . 5...of decisions in the Army. This thesis was initiated as a result not of overwhelming problems of overcrowding or of any particular problems or crises...AUG 83 UNCLASSIFIED F/il 5/9 N 12.2 Ln 1,6 1 2 .0 I~ii~ L 111U2 ICROCOP RSLUINTSCHR NAIOALBUEA F TAD336 1%- 2> Inmate Population Dynamics at the United

  4. Radial propagation in population dynamics with density-dependent diffusion

    Science.gov (United States)

    Ngamsaad, Waipot

    2014-01-01

    Population dynamics that evolve in a radial symmetric geometry are investigated. The nonlinear reaction-diffusion model, which depends on population density, is employed as the governing equation for this system. The approximate analytical solution to this equation is found. It shows that the population density evolves from the initial state and propagates in a traveling-wave-like manner for a long-time scale. If the distance is insufficiently long, the curvature has an ineluctable influence on the density profile and front speed. In comparison, the analytical solution is in agreement with the numerical solution.

  5. Rethinking the logistic approach for population dynamics of mutualistic interactions.

    Science.gov (United States)

    García-Algarra, Javier; Galeano, Javier; Pastor, Juan Manuel; Iriondo, José María; Ramasco, José J

    2014-12-21

    Mutualistic communities have an internal structure that makes them resilient to external perturbations. Late research has focused on their stability and the topology of the relations between the different organisms to explain the reasons of the system robustness. Much less attention has been invested in analyzing the systems dynamics. The main population models in use are modifications of the r-K formulation of logistic equation with additional terms to account for the benefits produced by the interspecific interactions. These models have shortcomings as the so-called r-K formulation diverges under some conditions. In this work, we introduce a model for population dynamics under mutualism that preserves the original logistic formulation. It is mathematically simpler than the widely used type II models, although it shows similar complexity in terms of fixed points and stability of the dynamics. We perform an analytical stability analysis and numerical simulations to study the model behavior in general interaction scenarios including tests of the resilience of its dynamics under external perturbations. Despite its simplicity, our results indicate that the model dynamics shows an important richness that can be used to gain further insights in the dynamics of mutualistic communities. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. Population dynamics of king eiders breeding in northern Alaska

    Science.gov (United States)

    Bentzen, Rebecca L.; Powell, Abby N.

    2012-01-01

    The North American population of king eiders (Somateria spectabilis) has declined by more than 50% since the late 1970s for unknown reasons. King eiders spend most of their lives in remote areas, forcing managers to make regulatory and conservation decisions based on very little information. We incorporated available published estimates of vital rates with new estimates to build a female, stage-based matrix population model for king eiders and examine the processes underlying population dynamics of king eiders breeding at 2 sites, Teshekpuk and Kuparuk, on the coastal plain of northern Alaska and wintering around the Bering Sea (2001–2010). We predicted a decreasing population (λ = 0.981, 95% CI: 0.978–0.985), and that population growth was most sensitive to changes in adult female survival (sensitivity = 0.92). Low duckling survival may be a bottleneck to productivity (variation in ducking survival accounted for 66% of retrospective variation in λ). Adult survival was high (0.94) and invariant (σ = 0.0002, 95% CI: 0.0000–0.0007); however, catastrophic events could have a major impact and we need to consider how to mitigate and manage threats to adult survival. A hypothetical oil spill affecting breeding females in a primary spring staging area resulted in a severe population decline; although, transient population dynamics were relatively stable. However, if no catastrophic events occur, the more variable reproductive parameters (duckling and nest survival) may be more responsive to management actions.

  7. [Population dynamics and armed violence in Colombia, 1985-2010].

    Science.gov (United States)

    Salaya, Hernán Eduardo; Rodríguez, Jesús

    2014-09-01

    Describe changes in the population structure of Colombia's municipalities in relation to internal displacement in response to armed violence. A descriptive ecological study was carried out. Secondary sources were consulted, taken from the Consolidated Registry of Displaced Population and from the National Administrative Department of Statistics, to calculate expulsion and reception rates for population displaced by violence from 2002 to 2010. Based on these rates, four groups were created of municipalities in the extreme quartile for each rate during the entire period, which were classified as high expulsion, low expulsion, high reception, and low reception. Subsequently, population pyramids and structure indicators were constructed for each group of municipalities for two comparative reference years (1985 and 2010). Municipalities with high expulsion or reception rates experienced a slower epidemiological transition, with lower mean ages and aging indices. The high expulsion group had the least regression, based on the Sundbärg index. In the high reception group, the masculinity ratio decreased the most, especially among the economically active population, and it had the highest population growth. Population dynamics in Colombia have been affected by armed violence and changes in these dynamics are not uniform across the country, leading to important social, economic, and cultural consequences. This study is useful for decision-making and public policy making.

  8. Central-marginal population dynamics in species invasions

    Directory of Open Access Journals (Sweden)

    Qinfeng eGuo

    2014-06-01

    Full Text Available The species’ range limits and associated central-marginal (C-M; i.e., from species range center to margin population dynamics continue to draw increasing attention because of their importance for current emerging issues such as biotic invasions and epidemic diseases under global change. Previous studies have mainly focused on species borders and C-M process in natural settings for native species. More recently, growing efforts are devoted to examine the C-M patterns and process for invasive species partly due to their relatively short history, highly dynamic populations, and management implications. Here I examine recent findings and information gaps related to (1 the C-M population dynamics linked to species invasions, and (2 the possible effects of climate change and land use on the C-M patterns and processes. Unlike most native species that are relatively stable (some even having contracting populations or ranges, many invasive species are still spreading fast and form new distribution or abundance centers. Because of the strong nonlinearity of population demographic or vital rates (i.e. birth, death, immigration and emigration across the C-M gradients and the increased complexity of species ranges due to habitat fragmentation, multiple introductions, range-wide C-M comparisons and simulation involving multiple vital rates are needed in the future.

  9. Dandruff is associated with disequilibrium in the proportion of the major bacterial and fungal populations colonizing the scalp.

    Directory of Open Access Journals (Sweden)

    Cécile Clavaud

    Full Text Available The bacterial and fungal communities associated with dandruff were investigated using culture-independent methodologies in the French subjects. The major bacterial and fungal species inhabiting the scalp subject's were identified by cloning and sequencing of the conserved ribosomal unit regions (16S for bacterial and 28S-ITS for fungal and were further quantified by quantitative PCR. The two main bacterial species found on the scalp surface were Propionibacterium acnes and Staphylococcus epidermidis, while Malassezia restricta was the main fungal inhabitant. Dandruff was correlated with a higher incidence of M. restricta and S. epidermidis and a lower incidence of P. acnes compared to the control population (p<0.05. These results suggested for the first time using molecular methods, that dandruff is linked to the balance between bacteria and fungi of the host scalp surface.

  10. Stochastic population dynamics in populations of western terrestrial garter snakes with divergent life histories.

    Science.gov (United States)

    Miller, David A; Clark, William R; Arnold, Stevan J; Bronikowski, Anne M

    2011-08-01

    Comparative evaluations of population dynamics in species with temporal and spatial variation in life-history traits are rare because they require long-term demographic time series from multiple populations. We present such an analysis using demographic data collected during the interval 1978-1996 for six populations of western terrestrial garter snakes (Thamnophis elegans) from two evolutionarily divergent ecotypes. Three replicate populations from a slow-living ecotype, found in mountain meadows of northeastern California, were characterized by individuals that develop slowly, mature late, reproduce infrequently with small reproductive effort, and live longer than individuals of three populations of a fast-living ecotype found at lakeshore locales. We constructed matrix population models for each of the populations based on 8-13 years of data per population and analyzed both deterministic dynamics based on mean annual vital rates and stochastic dynamics incorporating annual variation in vital rates. (1) Contributions of highly variable vital rates to fitness (lambda(s)) were buffered against the negative effects of stochastic variation, and this relationship was consistent with differences between the meadow (M-slow) and lakeshore (L-fast) ecotypes. (2) Annual variation in the proportion of gravid females had the greatest negative effect among all vital rates on lambda(s). The magnitude of variation in the proportion of gravid females and its effect on lambda(s) was greater in M-slow than L-fast populations. (3) Variation in the proportion of gravid females, in turn, depended on annual variation in prey availability, and its effect on lambda(s) was 4 23 times greater in M-slow than L-fast populations. In addition to differences in stochastic dynamics between ecotypes, we also found higher mean mortality rates across all age classes in the L-fast populations. Our results suggest that both deterministic and stochastic selective forces have affected the evolution of

  11. Aspiration dynamics of multi-player games in finite populations

    Science.gov (United States)

    Du, Jinming; Wu, Bin; Altrock, Philipp M.; Wang, Long

    2014-01-01

    On studying strategy update rules in the framework of evolutionary game theory, one can differentiate between imitation processes and aspiration-driven dynamics. In the former case, individuals imitate the strategy of a more successful peer. In the latter case, individuals adjust their strategies based on a comparison of their pay-offs from the evolutionary game to a value they aspire, called the level of aspiration. Unlike imitation processes of pairwise comparison, aspiration-driven updates do not require additional information about the strategic environment and can thus be interpreted as being more spontaneous. Recent work has mainly focused on understanding how aspiration dynamics alter the evolutionary outcome in structured populations. However, the baseline case for understanding strategy selection is the well-mixed population case, which is still lacking sufficient understanding. We explore how aspiration-driven strategy-update dynamics under imperfect rationality influence the average abundance of a strategy in multi-player evolutionary games with two strategies. We analytically derive a condition under which a strategy is more abundant than the other in the weak selection limiting case. This approach has a long-standing history in evolutionary games and is mostly applied for its mathematical approachability. Hence, we also explore strong selection numerically, which shows that our weak selection condition is a robust predictor of the average abundance of a strategy. The condition turns out to differ from that of a wide class of imitation dynamics, as long as the game is not dyadic. Therefore, a strategy favoured under imitation dynamics can be disfavoured under aspiration dynamics. This does not require any population structure, and thus highlights the intrinsic difference between imitation and aspiration dynamics. PMID:24598208

  12. Past and present population dynamics of narwhals Monodon monoceros

    DEFF Research Database (Denmark)

    Garde, Eva

    , meat and mattak. Concerns have been raised about the sustainability of the hunt, which have led to implementation of hunting quotas in both countries. Hunting quotas are usually calculated from population dynamics models where survival and reproductive rates, based on reliable age distributions...... of both marine and terrestrial mammals, although the technique still requires both optimization and further validation. In addition, the thesis includes a study of past population dynamics in narwhals. We have investigated the genetic response to climate change and the emographic history of the narwhal......, are vital. Estimation of life history parameters for the narwhal has previously been hindered by lack of a reliable age estimation technique. The Aspartic Acid Racemization (AAR) technique is a relatively novel method that I have applied to narwhals. This PhD thesis focuses, in part, on current population...

  13. Hierarchical population model with a carrying capacity distribution for bacterial biofilms

    Science.gov (United States)

    Indekeu, J. O.; Sznajd-Weron, K.

    2003-12-01

    In order to describe biological colonies with a conspicuous hierarchical structure, a time- and space-discrete model for the growth of a rapidly saturating local biological population N(x,t) is derived from a hierarchical random deposition process previously studied in statistical physics. Two biologically relevant parameters, the probabilities of birth, B, and of death, D, determine the carrying capacity K. Due to the randomness the population depends strongly on position x and there is a distribution of carrying capacities, Π(K). This distribution has self-similar character owing to the exponential slowing down of the growth, assumed in this hierarchical model. The most probable carrying capacity and its probability are studied as a function of B and D. The effective growth rate decreases with time, roughly as in a Verhulst process. The model is possibly applicable, for example, to bacteria forming a “towering pillar” biofilm, a structure poorly described by standard Eden or diffusion-limited-aggregation models. The bacteria divide on randomly distributed nutrient-rich regions and are exposed to a random local bactericidal agent (antibiotic spray). A gradual overall temperature or chemical change away from optimal growth conditions reduces bacterial reproduction, while biofilm development degrades antimicrobial susceptibility, causing stagnation into a stationary state.

  14. Shaping bacterial population behavior through computer-interfaced control of individual cells.

    Science.gov (United States)

    Chait, Remy; Ruess, Jakob; Bergmiller, Tobias; Tkačik, Gašper; Guet, Călin C

    2017-11-16

    Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment. This integrated platform broadly enables experiments that bridge individual and population behaviors. We demonstrate: (i) population structuring by independent closed-loop control of gene expression in many individual cells, (ii) cell-cell variation control during antibiotic perturbation, (iii) hybrid bio-digital circuits in single cells, and freely specifiable digital communication between individual bacteria. These examples showcase the potential for real-time integration of theoretical models with measurement and control of many individual cells to investigate and engineer microbial population behavior.

  15. Phylogenetic and metagenomic analyses of substrate-dependent bacterial temporal dynamics in microbial fuel cells.

    Directory of Open Access Journals (Sweden)

    Husen Zhang

    Full Text Available Understanding the microbial community structure and genetic potential of anode biofilms is key to improve extracellular electron transfers in microbial fuel cells. We investigated effect of substrate and temporal dynamics of anodic biofilm communities using phylogenetic and metagenomic approaches in parallel with electrochemical characterizations. The startup non-steady state anodic bacterial structures were compared for a simple substrate, acetate, and for a complex substrate, landfill leachate, using a single-chamber air-cathode microbial fuel cell. Principal coordinate analysis showed that distinct community structures were formed with each substrate type. The bacterial diversity measured as Shannon index decreased with time in acetate cycles, and was restored with the introduction of leachate. The change of diversity was accompanied by an opposite trend in the relative abundance of Geobacter-affiliated phylotypes, which were acclimated to over 40% of total Bacteria at the end of acetate-fed conditions then declined in the leachate cycles. The transition from acetate to leachate caused a decrease in output power density from 243±13 mW/m2 to 140±11 mW/m2, accompanied by a decrease in Coulombic electron recovery from 18±3% to 9±3%. The leachate cycles selected protein-degrading phylotypes within phylum Synergistetes. Metagenomic shotgun sequencing showed that leachate-fed communities had higher cell motility genes including bacterial chemotaxis and flagellar assembly, and increased gene abundance related to metal resistance, antibiotic resistance, and quorum sensing. These differentially represented genes suggested an altered anodic biofilm community in response to additional substrates and stress from the complex landfill leachate.

  16. 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

    2011-03-01

    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

  17. Fed-Batch Production of Bacterial Ghosts Using Dielectric Spectroscopy for Dynamic Process Control.

    Science.gov (United States)

    Meitz, Andrea; Sagmeister, Patrick; Lubitz, Werner; Herwig, Christoph; Langemann, Timo

    2016-03-24

    The Bacterial Ghost (BG) platform technology evolved from a microbiological expression system incorporating the ϕX174 lysis gene E. E-lysis generates empty but structurally intact cell envelopes (BGs) from Gram-negative bacteria which have been suggested as candidate vaccines, immunotherapeutic agents or drug delivery vehicles. E-lysis is a highly dynamic and complex biological process that puts exceptional demands towards process understanding and control. The development of a both economic and robust fed-batch production process for BGs required a toolset capable of dealing with rapidly changing concentrations of viable biomass during the E-lysis phase. This challenge was addressed using a transfer function combining dielectric spectroscopy and soft-sensor based biomass estimation for monitoring the rapid decline of viable biomass during the E-lysis phase. The transfer function was implemented to a feed-controller, which followed the permittivity signal closely and was capable of maintaining a constant specific substrate uptake rate during lysis phase. With the described toolset, we were able to increase the yield of BG production processes by a factor of 8-10 when compared to currently used batch procedures reaching lysis efficiencies >98%. This provides elevated potentials for commercial application of the Bacterial Ghost platform technology.

  18. Fed-Batch Production of Bacterial Ghosts Using Dielectric Spectroscopy for Dynamic Process Control

    Directory of Open Access Journals (Sweden)

    Andrea Meitz

    2016-03-01

    Full Text Available The Bacterial Ghost (BG platform technology evolved from a microbiological expression system incorporating the ϕX174 lysis gene E. E-lysis generates empty but structurally intact cell envelopes (BGs from Gram-negative bacteria which have been suggested as candidate vaccines, immunotherapeutic agents or drug delivery vehicles. E-lysis is a highly dynamic and complex biological process that puts exceptional demands towards process understanding and control. The development of a both economic and robust fed-batch production process for BGs required a toolset capable of dealing with rapidly changing concentrations of viable biomass during the E-lysis phase. This challenge was addressed using a transfer function combining dielectric spectroscopy and soft-sensor based biomass estimation for monitoring the rapid decline of viable biomass during the E-lysis phase. The transfer function was implemented to a feed-controller, which followed the permittivity signal closely and was capable of maintaining a constant specific substrate uptake rate during lysis phase. With the described toolset, we were able to increase the yield of BG production processes by a factor of 8–10 when compared to currently used batch procedures reaching lysis efficiencies >98%. This provides elevated potentials for commercial application of the Bacterial Ghost platform technology.

  19. Modeling structured population dynamics using data from unmarked individuals

    Science.gov (United States)

    Grant, Evan H. Campbell; Zipkin, Elise; Thorson, James T.; See, Kevin; Lynch, Heather J.; Kanno, Yoichiro; Chandler, Richard; Letcher, Benjamin H.; Royle, J. Andrew

    2014-01-01

    The study of population dynamics requires unbiased, precise estimates of abundance and vital rates that account for the demographic structure inherent in all wildlife and plant populations. Traditionally, these estimates have only been available through approaches that rely on intensive mark–recapture data. We extended recently developed N-mixture models to demonstrate how demographic parameters and abundance can be estimated for structured populations using only stage-structured count data. Our modeling framework can be used to make reliable inferences on abundance as well as recruitment, immigration, stage-specific survival, and detection rates during sampling. We present a range of simulations to illustrate the data requirements, including the number of years and locations necessary for accurate and precise parameter estimates. We apply our modeling framework to a population of northern dusky salamanders (Desmognathus fuscus) in the mid-Atlantic region (USA) and find that the population is unexpectedly declining. Our approach represents a valuable advance in the estimation of population dynamics using multistate data from unmarked individuals and should additionally be useful in the development of integrated models that combine data from intensive (e.g., mark–recapture) and extensive (e.g., counts) data sources.

  20. Population dynamics and climate change: what are the links?

    Science.gov (United States)

    Stephenson, Judith; Newman, Karen; Mayhew, Susannah

    2010-06-01

    Climate change has been described as the biggest global health threat of the 21(st) century. World population is projected to reach 9.1 billion by 2050, with most of this growth in developing countries. While the principal cause of climate change is high consumption in the developed countries, its impact will be greatest on people in the developing world. Climate change and population can be linked through adaptation (reducing vulnerability to the adverse effects of climate change) and, more controversially, through mitigation (reducing the greenhouse gases that cause climate change). The contribution of low-income, high-fertility countries to global carbon emissions has been negligible to date, but is increasing with the economic development that they need to reduce poverty. Rapid population growth endangers human development, provision of basic services and poverty eradication and weakens the capacity of poor communities to adapt to climate change. Significant mass migration is likely to occur in response to climate change and should be regarded as a legitimate response to the effects of climate change. Linking population dynamics with climate change is a sensitive issue, but family planning programmes that respect and protect human rights can bring a remarkable range of benefits. Population dynamics have not been integrated systematically into climate change science. The contribution of population growth, migration, urbanization, ageing and household composition to mitigation and adaptation programmes needs urgent investigation.

  1. A comprehensive mechanistic model for simulating algal-bacterial growth dynamics in photobioreactors.

    Science.gov (United States)

    Shriwastav, Amritanshu; Ashok, Vaishali; Thomas, Jeenu; Bose, Purnendu

    2018-01-01

    A comprehensive mechanistic model with state of the art understanding and assumptions is presented to simulate major processes in a photobioreactor for describing the algal-bacterial growth dynamics. The model includes a total of 37 state variables that broadly cover all the essential physiological and physico-chemical processes in such a system. Model parameters are first calibrated with batch experimental data, and thereafter, extensive validation of the model is carried with long term independent experimental data in diverse conditions. The developed model is able to capture the complex system behavior with reasonable accuracy. Also, the comprehensive mathematical formulation with realistic assumptions make this model a valuable tool for gaining better insights into the complex system behavior. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Bacterial promoter prediction: Selection of dynamic and static physical properties of DNA for reliable sequence classification.

    Science.gov (United States)

    Ryasik, Artem; Orlov, Mikhail; Zykova, Evgenia; Ermak, Timofei; Sorokin, Anatoly

    2018-01-30

    Predicting promoter activity of DNA fragment is an important task for computational biology. Approaches using physical properties of DNA to predict bacterial promoters have recently gained a lot of attention. To select an adequate set of physical properties for training a classifier, various characteristics of DNA molecule should be taken into consideration. Here, we present a systematic approach that allows us to select less correlated properties for classification by means of both correlation and cophenetic coefficients as well as concordance matrices. To prove this concept, we have developed the first classifier that uses not only sequence and static physical properties of DNA fragment, but also dynamic properties of DNA open states. Therefore, the best performing models with accuracy values up to 90% for all types of sequences were obtained. Furthermore, we have demonstrated that the classifier can serve as a reliable tool enabling promoter DNA fragments to be distinguished from promoter islands despite the similarity of their nucleotide sequences.

  3. Following an imaginary Campylobacter population from farm to fork and beyond: a bacterial perspective.

    Science.gov (United States)

    Wassenaar, T M

    2011-09-01

    It has been known for decades that poultry meat is the most common single source for campylobacteriosis, yet the problem has not been solved. This review identifies some of the reasons why our attempts to reduce the incidence of this pathogen have largely failed. Based on the literature, the events a virtual population of Campylobacter may encounter, from growing in the gut of a broiler to eventually infecting humans and causing disease, are reviewed. Most steps in the farm-to-fork process are well studied, though there are gaps in our knowledge about survival and spread of Campylobacter populations before they enter the farm. Key events in the farm-to-fork chain that are suitable targets for prevention and control, to reduce food-borne campylobacteriosis, are indicated. Novel insights into the pathogenic mechanism responsible for disease in humans are summarized, which hypothesize that an overactive immune response is the reason for the typical inflammatory diarrhoea. A role of genetic microheterogeneity within a clonal population in this chain of events is being proposed here. The human host is not necessary for the survival of the bacterial species, nor have these bacteria specifically evolved to cause disease in that host. More likely, the species evolved for a commensal life in birds, and human disease can be considered as collateral damage owing to an unfortunate host-microbe interaction. The indirect environmental burden that results from poultry production should not be ignored as it may pose a diffuse, but possibly significant risk factor for disease. © 2011 The Author. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

  4. Molecular characterization of microbial population dynamics during sildenafil citrate degradation.

    Science.gov (United States)

    De Felice, Bruna; Argenziano, Carolina; Guida, Marco; Trifuoggi, Marco; Russo, Francesca; Condorelli, Valerio; Inglese, Mafalda

    2009-02-01

    Little is known about pharmaceutical and personal care products pollutants (PPCPs), but there is a growing interest in how they might impact the environment and microbial communities. The widespread use of Viagra (sildenafil citrate) has attracted great attention because of the high usage rate, the unpredictable disposal and the unknown potential effects on wildlife and the environment. Until now information regarding the impact of Viagra on microbial community in water environment has not been reported. In this research, for the first time, the genetic profile of the microbial community, developing in a Viagra polluted water environment, was evaluated by means of the 16S and 18S rRNA genes, for bacteria and fungi, respectively, amplified by polymerase chain reaction (PCR) and separated using the denaturing gradient gel electrophoresis (DGGE) technique. The DGGE results revealed a complex microbial community structure with most of the population persisting throughout the experimental period. DNA sequences from bands observed in the different denaturing gradient gel electrophoresis profiles exhibited the highest degree of identity to uncultured bacteria and fungi found previously mainly in polluted environmental and treating bioreactors. Biotransformation ability of sildenafil citrate by the microbial pool was studied and the capability of these microorganisms to detoxify a polluted water ecosystem was assessed. The bacterial and fungal population was able to degrade sildenafil citrate entirely. Additionally, assays conducted on Daphnia magna, algal growth inhibition assay and cell viability determination on HepG2 human cells showed that biotransformation products obtained from the bacterial growth was not toxic. The higher removal efficiency for sildenafil citrate and the lack of toxicity by the biotransformation products obtained showed that the microbial community identified here represented a composite population that might have biotechnological relevance to

  5. Changes in Population Dynamics in Mutualistic versus Pathogenic Viruses

    Directory of Open Access Journals (Sweden)

    Marilyn J. Roossinck

    2011-01-01

    Full Text Available Although generally regarded as pathogens, viruses can also be mutualists. A number of examples of extreme mutualism (i.e., symbiogenesis have been well studied. Other examples of mutualism are less common, but this is likely because viruses have rarely been thought of as having any beneficial effects on their hosts. The effect of mutualism on the population dynamics of viruses is a topic that has not been addressed experimentally. However, the potential for understanding mutualism and how a virus might become a mutualist may be elucidated by understanding these dynamics.

  6. Changes in population dynamics in mutualistic versus pathogenic viruses.

    Science.gov (United States)

    Roossinck, Marilyn J

    2011-01-01

    Although generally regarded as pathogens, viruses can also be mutualists. A number of examples of extreme mutualism (i.e., symbiogenesis) have been well studied. Other examples of mutualism are less common, but this is likely because viruses have rarely been thought of as having any beneficial effects on their hosts. The effect of mutualism on the population dynamics of viruses is a topic that has not been addressed experimentally. However, the potential for understanding mutualism and how a virus might become a mutualist may be elucidated by understanding these dynamics.

  7. Lineage grammars: describing, simulating and analyzing population dynamics.

    Science.gov (United States)

    Spiro, Adam; Cardelli, Luca; Shapiro, Ehud

    2014-07-21

    Precise description of the dynamics of biological processes would enable the mathematical analysis and computational simulation of complex biological phenomena. Languages such as Chemical Reaction Networks and Process Algebras cater for the detailed description of interactions among individuals and for the simulation and analysis of ensuing behaviors of populations. However, often knowledge of such interactions is lacking or not available. Yet complete oblivion to the environment would make the description of any biological process vacuous. Here we present a language for describing population dynamics that abstracts away detailed interaction among individuals, yet captures in broad terms the effect of the changing environment, based on environment-dependent Stochastic Tree Grammars (eSTG). It is comprised of a set of stochastic tree grammar transition rules, which are context-free and as such abstract away specific interactions among individuals. Transition rule probabilities and rates, however, can depend on global parameters such as population size, generation count, and elapsed time. We show that eSTGs conveniently describe population dynamics at multiple levels including cellular dynamics, tissue development and niches of organisms. Notably, we show the utilization of eSTG for cases in which the dynamics is regulated by environmental factors, which affect the fate and rate of decisions of the different species. eSTGs are lineage grammars, in the sense that execution of an eSTG program generates the corresponding lineage trees, which can be used to analyze the evolutionary and developmental history of the biological system under investigation. These lineage trees contain a representation of the entire events history of the system, including the dynamics that led to the existing as well as to the extinct individuals. We conclude that our suggested formalism can be used to easily specify, simulate and analyze complex biological systems, and supports modular

  8. A novel bacterial symbiont association in the hispid beetle, Octodonta nipae (Coleoptera: Chrysomelidae), their dynamics and phylogeny.

    Science.gov (United States)

    Ali, Habib; Muhammad, Abrar; Islam, Saif Ul; Islam, Waqar; Hou, Youming

    2018-03-27

    The hispid leaf beetle, Octodonta nipae (Maulik), (Coleoptera: Chrysomelidae), is a devastating pest of palm cultivation worldwide. Endosymbiotic bacteria in the genus Wolbachia are arguably one of the most abundant bacterial group associated with arthropods. Owing to its critical effects on host reproduction, Wolbachia has garnered much attention as a prospective future tool for insect pest management. However, their association, infection dynamics, and functionality remain unknown in this insect pest. Here, we diagnosis for the first time, the infection prevalence, and occurrence of Wolbachia in O. nipae. Experimental evidence by the exploration of wsp gene vindicate that O. nipae is naturally infected with bacterial symbiont of genus Wolbachia, showing a complete maternal inheritance with shared a common Wolbachia strain (wNip). Moreover, MLST (gatB, fbpA, coxA, ftsZ, and hcpA) analysis enabled the detections of new sequence type (ST-484), suggesting a particular genotypic association of O. nipae and Wolbachia. Subsequently, quantitative real-time PCR (qPCR) assay demonstrated variable infection density across different life stages (eggs, larvae, pupae and adult male and female), body parts (head, thorax, abdomen), and tissues (ovaries, testes, and guts). Infection density was higher in egg and female adult stage, as well as abdomen and reproductive tissues as compared to other samples. Interestingly, Wolbachia harbored dominantly in a female than the male adult, while, no significant differences were observed between male and female body parts and tissues. Phylogeny of Wolbachia infection associated with O. nipae rectified from all tested life stages were unique and fall within the same monophyletic supergroup-A of Wolbachia clades. The infection density of symbiont is among the valuable tool to understand their biological influence on hosts, and this latest discovery would facilitate the future investigations to understand the host-symbiont complications and

  9. Daily dynamics of bacterial numbers, CO2 emissions from soil and relationships between their wavelike fluctuations and succession of the microbial community

    Science.gov (United States)

    Semenov, A. M.; Bubnov, I. A.; Semenov, V. M.; Semenova, E. V.; Zelenev, V. V.; Semenova, N. A.

    2013-08-01

    The daily dynamics of the number of copiotrophic and oligotrophic bacteria (in colony-forming units) and CO2 emissions from cultivated soils after short- and long-term disturbances were studied for 25-27 days in a microfield experiment. The relationship of the wavelike fluctuations of the bacterial number and CO2 emission with the succession of the soil microbial community was determined by the polymerase chain reaction method—denaturing gradient gel electrophoresis (PCR-DGGE). Short-term disturbances involved the application of organic or mineral fertilizers, pesticides, and plant residues to the soils of different plots. The long-term effect was a result of using biological and intensive farming systems for three years. The short-term disturbances resulted in increased peaks of the bacterial number, the significance of which was confirmed by harmonics analysis. The daily dynamics of the structure of the soil microbial community, which was studied for 27 days by the DGGE method, also had an oscillatory pattern. Statistical processing of the data (principal components analysis, harmonics and cross-correlation analyses) has revealed significant fluctuations in the structure of microbial communities coinciding with those of the bacterial populations. The structure of the microbial community changed within each peak of the dynamics of the bacterial number (but not from peak to peak), pointing to the cyclical character of the short-term succession. The long-term effects resulted in a less intense response of the microbiota—a lower rate of CO2 emission from the soil cultivated according to the organic farming system.

  10. Acid-suppression medications and bacterial gastroenteritis: a population-based cohort study.

    Science.gov (United States)

    Wei, Li; Ratnayake, Lasantha; Phillips, Gabby; McGuigan, Chris C; Morant, Steve V; Flynn, Robert W; Mackenzie, Isla S; MacDonald, Thomas M

    2017-06-01

    To investigate whether acid-suppression medicines (ASMs) increase the risk of bacterial gastroenteritis. A population-based, propensity-score matched cohort study using a record-linkage database in Tayside, UK. The study consisted of 188 323 exposed to ASMs (proton-pump inhibitors and histamine-2 receptor antagonists) and 376 646 controls (a propensity-score matched cohort from the rest of population who were not exposed to ASMs) between 1999 and 2013. The main outcome measure was a positive stool test for Clostridium difficile, Campylobacter, Salmonella, Shigella or Escherichia coli O157. The association between ASMs and risk of bacterial gastroenteritis was assessed by a Cox regression model. There were 22 705 positive test results (15 273 C. difficile [toxin positive], 6590 Campylobacter, 852 Salmonella, 129 Shigella and 193 E. coli O157, not mutually exclusive) with a total of 5 729 743 person-years follow up time in Tayside, 1999-2013. The adjusted hazard ratios for culture positive diarrhoea for the proton-pump inhibitors and histamine-2 receptor antagonists exposed vs. unexposed cohort were 2.72 (95% confidence interval [CI] 2.33, 3.17) during follow-up time for samples submitted from the community and 1.28 (95% CI 1.08, 1.52) for samples submitted from hospitals. Compared with the unexposed cohort, patients in the exposed group had increased risks of C. difficile and Campylobacter [adjusted hazard ratios of 1.70 (95% CI 1.28, 2.25), 3.71 (95% CI 3.04, 4.53) for community samples, and 1.42 (95% CI 1.17, 1.71), 4.53 (95% CI 1.75, 11.8) for hospital samples, respectively]. The results suggest that community prescribed ASMs were associated with increased rates of C. difficile and Campylobacter positive gastroenteritis in both the community and hospital settings. © 2017 The Authors. British Journal of Clinical Pharmacology published by John Wiley & Sons Ltd on behalf of British Pharmacological Society.

  11. How predation and landscape fragmentation affect vole population dynamics.

    Directory of Open Access Journals (Sweden)

    Trine Dalkvist

    Full Text Available BACKGROUND: Microtine species in Fennoscandia display a distinct north-south gradient from regular cycles to stable populations. The gradient has often been attributed to changes in the interactions between microtines and their predators. Although the spatial structure of the environment is known to influence predator-prey dynamics of a wide range of species, it has scarcely been considered in relation to the Fennoscandian gradient. Furthermore, the length of microtine breeding season also displays a north-south gradient. However, little consideration has been given to its role in shaping or generating population cycles. Because these factors covary along the gradient it is difficult to distinguish their effects experimentally in the field. The distinction is here attempted using realistic agent-based modelling. METHODOLOGY/PRINCIPAL FINDINGS: By using a spatially explicit computer simulation model based on behavioural and ecological data from the field vole (Microtus agrestis, we generated a number of repeated time series of vole densities whose mean population size and amplitude were measured. Subsequently, these time series were subjected to statistical autoregressive modelling, to investigate the effects on vole population dynamics of making predators more specialised, of altering the breeding season, and increasing the level of habitat fragmentation. We found that fragmentation as well as the presence of specialist predators are necessary for the occurrence of population cycles. Habitat fragmentation and predator assembly jointly determined cycle length and amplitude. Length of vole breeding season had little impact on the oscillations. SIGNIFICANCE: There is good agreement between our results and the experimental work from Fennoscandia, but our results allow distinction of causation that is hard to unravel in field experiments. We hope our results will help understand the reasons for cycle gradients observed in other areas. Our results

  12. Detrimental effects of commercial zinc oxide and silver nanomaterials on bacterial populations and performance of wastewater systems

    Science.gov (United States)

    Mboyi, Anza-vhudziki; Kamika, Ilunga; Momba, MaggyN. B.

    2017-08-01

    The widespread use of commercial nanomaterials (NMs) in consumer products has raised environmental concerns as they can enter and affect the efficiency of the wastewater treatment plants. In this study the effect of various concentrations of zinc oxide NMs (nZnO) and silver NMs (nAg) on the selected wastewater bacterial species (Bacillus licheniformis, Brevibacillus laterosporus and Pseudomonas putida) was ascertained at different pH levels (pH 2, 7 and 10). Lethal concentrations (LC) of NMs and parameters such as chemical oxygen demand (COD) and dissolved oxygen (DO) were taken into consideration to assess the performance of a wastewater batch reactor. Bacterial isolates were susceptible to varying concentrations of both nZnO and nAg at pH 2, 7 and 10. It was found that a change in pH did not significantly affect the toxicity of test NMs towards target bacterial isolates. All bacterial species were significantly inhibited (p 0.05) in COD removal in the presence of increasing concentrations of NMs, which resulted in increasing releases of COD. Noticeably, there was no significant difference (p > 0.05) in the decrease in DO uptake in the presence of increasing NM concentrations for all bacterial isolates. The toxic effects of the target NMs on bacterial populations in wastewater may negatively impact the performance of biological treatment processes and may thus affect the efficiency of wastewater treatment plants in producing effluent of high quality.

  13. Association between Toll-like receptor 9 gene polymorphisms and risk of bacterial meningitis in a Chinese population.

    Science.gov (United States)

    Wang, X H; Shi, H P; Li, F J

    2016-07-25

    We determined whether two common single nucleotide polymorphisms (SNPs) in the Toll-like receptor 9 gene (TLR9) (TLR9+2848 rs352140 and TLR9-1237 rs5743836) influenced susceptibility to bacterial meningitis in a Chinese population. The study comprised 126 patients with bacterial meningitis and 252 control subjects, all of whom were recruited from the Tuberculosis Hospital of Shanxi Province. Genotyping of TLR9+2848 rs352140 and TLR9-1237 rs5743836 was performed by polymerase chain reaction coupled with restriction fragment length polymorphism. Using logistic regression analysis, we found that individuals with the AA genotype were associated with an increased risk of bacterial meningitis compared with those with the GG genotype (OR = 0.43, 95%CI = 0.19-0.95; P = 0.03). In a recessive model, the AA genotype was correlated with an elevated risk of bacterial meningitis compared with the GG+GA genotype (OR = 0.49, 95%CI = 0.22-0.99; P = 0.04). However, no significant differences were observed in the association between the TLR9-1237 rs5743836 polymorphism and the risk of bacterial meningitis in the codominant, dominant, or recessive models. In conclusion, the results of our study suggest an association between the TLR9+2848 polymorphism and a reduced risk of bacterial meningitis in the codominant and recessive models.

  14. Structured population dynamics: continuous size and discontinuous stage structures.

    Science.gov (United States)

    Buffoni, Giuseppe; Pasquali, Sara

    2007-04-01

    A nonlinear stochastic model for the dynamics of a population with either a continuous size structure or a discontinuous stage structure is formulated in the Eulerian formalism. It takes into account dispersion effects due to stochastic variability of the development process of the individuals. The discrete equations of the numerical approximation are derived, and an analysis of the existence and stability of the equilibrium states is performed. An application to a copepod population is illustrated; numerical results of Eulerian and Lagrangian models are compared.

  15. Dynamics of N-person snowdrift games in structured populations.

    Science.gov (United States)

    Santos, Marta D; Pinheiro, Flávio L; Santos, Francisco C; Pacheco, Jorge M

    2012-12-21

    In many real-life situations, the completion of a task by a group toward achieving a common goal requires the cooperation of at least some of its members, who share the required workload. Such cases are conveniently modeled by the N-person snowdrift game, an example of a Public Goods Game. Here we study how an underlying network of contacts affects the evolutionary dynamics of collective action modeled in terms of such a Public Goods Game. We analyze the impact of different types of networks in the global, population-wide dynamics of cooperators and defectors. We show that homogeneous social structures enhance the chances of coordinating toward stable levels of cooperation, while heterogeneous network structures create multiple internal equilibria, departing significantly from the reference scenario of a well-mixed, structureless population. Copyright © 2012 Elsevier Ltd. All rights reserved.

  16. [Population dynamics of oligosporous actinomycetes in Chernozem soil].

    Science.gov (United States)

    Zenova, G M; Mikhaĭlova, N V; Zviagintsev, D G

    2000-01-01

    Investigation of the dynamics of an oligosporous actinomycete population in chernozem soil in the course of succession induced by soil wetting allowed us to reveal the time intervals and conditions optimal for the isolation of particular oligosporous actinomycetes. Saccharopolysporas and microbisporas proved to be best isolated in the early and late stages of succession, whereas actinomycetes of the subgroup Actinomadura and saccharomonosporas could be best isolated in the early and intermediate stages of succession.

  17. Development of paradigms for the dynamics of structured populations

    Energy Technology Data Exchange (ETDEWEB)

    1994-10-01

    This is a technical progress report on the dynamics of predator-prey systems in a patchy environment. A new phenomenon that might contribute to outbreaks in systems of discrete patches has been determined using a discrete time model with both spatial and age structure. A model for a single species in a patchy environment with migration, local population growth and disasters with in patches has been formulated and a brief description is included.

  18. Scaling up population dynamic processes in a ladybird–aphid

    Czech Academy of Sciences Publication Activity Database

    Houdková, Kateřina; Kindlmann, Pavel

    2006-01-01

    Roč. 48, - (2006), s. 323-332 ISSN 1438-3896 R&D Projects: GA ČR(CZ) GEDIV/06/E013; GA MŠk(CZ) LC06073; GA AV ČR(CZ) IAA6087301; GA ČR(CZ) GD206/03/H034 Keywords : Aphids * Egg window * Ladybirds * Metapopulation * Model * Population dynamics Subject RIV: EH - Ecology, Behaviour Impact factor: 1.534, year: 2006

  19. Integrating population dynamics into mapping human exposure to seismic hazard

    Directory of Open Access Journals (Sweden)

    S. Freire

    2012-11-01

    Full Text Available Disaster risk is not fully characterized without taking into account vulnerability and population exposure. Assessment of earthquake risk in urban areas would benefit from considering the variation of population distribution at more detailed spatial and temporal scales, and from a more explicit integration of this improved demographic data with existing seismic hazard maps. In the present work, "intelligent" dasymetric mapping is used to model population dynamics at high spatial resolution in order to benefit the analysis of spatio-temporal exposure to earthquake hazard in a metropolitan area. These night- and daytime-specific population densities are then classified and combined with seismic intensity levels to derive new spatially-explicit four-class-composite maps of human exposure. The presented approach enables a more thorough assessment of population exposure to earthquake hazard. Results show that there are significantly more people potentially at risk in the daytime period, demonstrating the shifting nature of population exposure in the daily cycle and the need to move beyond conventional residence-based demographic data sources to improve risk analyses. The proposed fine-scale maps of human exposure to seismic intensity are mainly aimed at benefiting visualization and communication of earthquake risk, but can be valuable in all phases of the disaster management process where knowledge of population densities is relevant for decision-making.

  20. High-pressure processing applied to cooked sausages: bacterial populations during chilled storage.

    Science.gov (United States)

    Yuste, J; Pla, R; Capellas, M; Ponce, E; Mor-Mur, M

    2000-08-01

    Vacuum-packaged cooked sausages were pressurized at 500 MPa for 5 or 15 min at mild temperature (65 degrees C) and later stored at 2 and 8 degrees C for 18 weeks. Counts of aerobic mesophiles and psychrotrophs, lactic acid bacteria, enterobacteria, Baird-Parker microbiota, and Listeria spp. were determined 1 day and 3, 6, 9, 12, 15, and 18 weeks after treatment and compared with those of cooked sausages treated at 80 to 85 degrees C for 40 min. Pressurization generated reductions of about 4 log CFU/g in psychrotrophs and lactic acid bacteria. Enterobacteria and Listeria proved the most pressure sensitive; insignificant or no growth was detected throughout the study. Heat treatment inactivated psychrotrophs and enterobacteria similarly to pressure treatment. Listeria monocytogenes and enterotoxigenic Staphylococcus aureus were not found in treated samples. In general, there was no significant difference in counts of any bacterial populations either among treatments or between storage temperatures. High-pressure processing at mild temperature is an effective preservation method that can replace heat pasteurization applied to some cooked meat and poultry products after packaging.

  1. Border Collision Bifurcations in a Generalized Model of Population Dynamics

    Directory of Open Access Journals (Sweden)

    Lilia M. Ladino

    2016-01-01

    Full Text Available We analyze the dynamics of a generalized discrete time population model of a two-stage species with recruitment and capture. This generalization, which is inspired by other approaches and real data that one can find in literature, consists in considering no restriction for the value of the two key parameters appearing in the model, that is, the natural death rate and the mortality rate due to fishing activity. In the more general case the feasibility of the system has been preserved by posing opportune formulas for the piecewise map defining the model. The resulting two-dimensional nonlinear map is not smooth, though continuous, as its definition changes as any border is crossed in the phase plane. Hence, techniques from the mathematical theory of piecewise smooth dynamical systems must be applied to show that, due to the existence of borders, abrupt changes in the dynamic behavior of population sizes and multistability emerge. The main novelty of the present contribution with respect to the previous ones is that, while using real data, richer dynamics are produced, such as fluctuations and multistability. Such new evidences are of great interest in biology since new strategies to preserve the survival of the species can be suggested.

  2. Building the bridge between animal movement and population dynamics.

    Science.gov (United States)

    Morales, Juan M; Moorcroft, Paul R; Matthiopoulos, Jason; Frair, Jacqueline L; Kie, John G; Powell, Roger A; Merrill, Evelyn H; Haydon, Daniel T

    2010-07-27

    While the mechanistic links between animal movement and population dynamics are ecologically obvious, it is much less clear when knowledge of animal movement is a prerequisite for understanding and predicting population dynamics. GPS and other technologies enable detailed tracking of animal location concurrently with acquisition of landscape data and information on individual physiology. These tools can be used to refine our understanding of the mechanistic links between behaviour and individual condition through 'spatially informed' movement models where time allocation to different behaviours affects individual survival and reproduction. For some species, socially informed models that address the movements and average fitness of differently sized groups and how they are affected by fission-fusion processes at relevant temporal scales are required. Furthermore, as most animals revisit some places and avoid others based on their previous experiences, we foresee the incorporation of long-term memory and intention in movement models. The way animals move has important consequences for the degree of mixing that we expect to find both within a population and between individuals of different species. The mixing rate dictates the level of detail required by models to capture the influence of heterogeneity and the dynamics of intra- and interspecific interaction.

  3. [Analysis on age structure and dynamics of Kindonia uniflora populations].

    Science.gov (United States)

    Zhang, Wenhui; Li, Jingxia; Li, Hong; Liu, Xiangjun

    2004-04-01

    Kindonia uniflora is a perennial clone herbaceous plant, and also, a native endangered plant in China. This paper studied its age structure, life table and survivorship curve in different habitats in Taibai mountain area. The results indicated that the age structure and dynamics of K. uniflora populations in the Betula utilis forest at altitude 2500-2700 m, in the Abies fargesii forest at altitude 2700-2900 m, and in the Larix chinensis forest at altitude 2900-3100 m had the similar pattern and developing tendency. The number of younger ramets at 1-2 years old or older than 5 years was less, and the number of ramets at 3-5 years old was the highest in the age structures. The negative values of dx (dead number), qx (mortality rate) and Kx (Killing rate) in the life table showed the increasing rate of the population sizes during the age stage. The survivorship curve of K. uniflora populations in different habitats belonged to Deevey C after 3-5 years old. The mortality rate of populations during 5-10 years stage was higher, and was stable after 10 years old. As for the characters of asexual propagation and clone growth, the rhizomes of the populations were in humus of soil, and developed and expanded as guerilla line style. During growth season, only one leaf grew above ground at every inter-node, and the population growth and development were rarely influenced by external factors. The forest communities, such as Betula utilis, Abies fargesii and Larix chinensis forest, in which K. uniflora populations lived, were at middle or higher mountain, where there were rarely disturbance from human being. Therefore, the habitats for K. uniflora populations to live were relatively stable. As the altitude increased, the disturbances from human being became less, the density of K. uniflora populations increased, the life cycle expanded, the peak of population death delayed, and the population living strategy changed to adapt to the habitats. K. uniflora populations preferred to

  4. Paths and patterns: the biology and physics of swimming bacterial populations

    Science.gov (United States)

    Kessler, J. O.; Strittmatter, R. P.; Swartz, D. L.; Wiseley, D. A.; Wojciechowski, M. F.

    1995-01-01

    The velocity distribution of swimming micro-organisms depends on directional cues supplied by the environment. Directional swimming within a bounded space results in the accumulation of organisms near one or more surfaces. Gravity, gradients of chemical concentration and illumination affect the motile behaviour of individual swimmers. Concentrated populations of organisms scatter and absorb light or consume molecules, such as oxygen. When supply is one-sided, consumption creates gradients; the presence of the population alters the intensity and the symmetry of the environmental cues. Patterns of cues interact dynamically with patterns of the consumer population. In suspensions, spatial variations in the concentration of organisms are equivalent to variations of mean mass density of the fluid. When organisms accumulate in one region whilst moving away from another region, the force of gravity causes convection that translocates both organisms and dissolved substances. The geometry of the resulting concentration-convection patterns has features that are remarkably reproducible. Of interest for biology are (1) the long-range organisation achieved by organisms that do not communicate, and (2) that the entire system, consisting of fluid, cells, directional supply of consumables, boundaries and gravity, generates a dynamic that improves the organisms' habitat by enhancing transport and mixing. Velocity distributions of the bacterium Bacillus subtilis have been measured within the milieu of the spatially and temporally varying oxygen concentration which they themselves create. These distributions of swimming speed and direction are the fundamental ingredients required for a quantitative mathematical treatment of the patterns. The quantitative measurement of swimming behaviour also contributes to our understanding of aerotaxis of individual cells.

  5. An EPA pilot study characterizing fungal and bacterial populations at homes after flooding events at the Martin Peña Channel community-Puerto Rico

    Science.gov (United States)

    The overall objective of this program is to characterize fungal and bacterial populations in the MPC residences in San Juan, Puerto Rico, following flooding events. These profiles will be generated by comparing the fungal and bacterial populations in two groups of residences: hom...

  6. Microbial population analysis of the salivary glands of ticks; a possible strategy for the surveillance of bacterial pathogens.

    Directory of Open Access Journals (Sweden)

    Yongjin Qiu

    Full Text Available Ticks are one of the most important blood-sucking vectors for infectious microorganisms in humans and animals. When feeding they inject saliva, containing microbes, into the host to facilitate the uptake of blood. An understanding of the microbial populations within their salivary glands would provide a valuable insight when evaluating the vectorial capacity of ticks. Three tick species (Ixodes ovatus, I. persulcatus and Haemaphysalis flava were collected in Shizuoka Prefecture of Japan between 2008 and 2011. Each tick was dissected and the salivary glands removed. Bacterial communities in each salivary gland were characterized by 16S amplicon pyrosequencing using a 454 GS-Junior Next Generation Sequencer. The Ribosomal Database Project (RDP Classifier was used to classify sequence reads at the genus level. The composition of the microbial populations of each tick species were assessed by principal component analysis (PCA using the Metagenomics RAST (MG-RAST metagenomic analysis tool. Rickettsia-specific PCR was used for the characterization of rickettsial species. Almost full length of 16S rDNA was amplified in order to characterize unclassified bacterial sequences obtained in I. persulcatus female samples. The numbers of bacterial genera identified for the tick species were 71 (I. ovatus, 127 (I. persulcatus and 59 (H. flava. Eighteen bacterial genera were commonly detected in all tick species. The predominant bacterial genus observed in all tick species was Coxiella. Spiroplasma was detected in Ixodes, and not in H. flava. PCA revealed that microbial populations in tick salivary glands were different between tick species, indicating that host specificities may play an important role in determining the microbial complement. Four female I. persulcatus samples contained a high abundance of several sequences belonging to Alphaproteobacteria symbionts. This study revealed the microbial populations within the salivary glands of three species of

  7. Characterization of the rate and temperature sensitivities of bacterial remineralization of dissolved organic phosphorus by natural populations

    Directory of Open Access Journals (Sweden)

    Angelicque E. White

    2012-08-01

    Full Text Available Production, transformation, and degradation are the principal components of the cycling of dissolved organic matter (DOM in marine systems. Heterotrophic Bacteria (and Archaea play a large part in this cycling via enzymatic decomposition and intracellular transformations of organic material to inorganic carbon (C, nitrogen (N , and phosphorus (P. The rate and magnitude of inorganic nutrient regeneration from DOM is related to the elemental composition and lability of DOM substrates as well as the nutritional needs of the mediating organisms. While many previous efforts have focused on C and N cycling of DOM, less is known in regards to the controls of organic P utilization and remineralization by natural populations of bacteria. In order to constrain the relative time scales and degradation of select dissolved organic P (DOP compounds we have conducted a series of experiments focused on (1 assessment of the short-term lability of a range of DOP compounds, (2 characterization of labile DOP remineralization rates and (3 examination of temperature sensitivities of labile DOP remineralization for varying bacterial populations. Results reinforce previous findings of monoester and polyphosphate lability and the relative recalcitrance of a model phosphonate: 2-aminoethylphosphonate. High resolution time-series of P monoester remineralization indicates decay constants on the order of 0.67-7.04 d-1 for bacterial populations isolated from coastal and open ocean surface waters. The variability of these rates is predictably related to incubation temperature and initial concentrations of heterotrophic bacteria. Additional controls on DOP hydrolysis included seasonal shifts in bacterial populations and the physiological state of bacteria at the initiation of DOP addition experiments. Composite results indicate that bacterial hydrolysis of P-monoesters exceeds bacterial P demand and thus DOP remineralization efficiency may control P availability to autotrophs.

  8. On the population dynamics of the malaria vector

    International Nuclear Information System (INIS)

    Ngwa, G.A.

    2005-10-01

    A deterministic differential equation model for the population dynamics of the human malaria vector is derived and studied. Conditions for the existence and stability of a non-zero steady state vector population density are derived. These reveal that a threshold parameter, the vectorial basic reproduction number, exist and the vector can establish itself in the community if and only if this parameter exceeds unity. When a non-zero steady state population density exists, it can be stable but it can also be driven to instability via a Hopf Bifurcation to periodic solutions, as a parameter is varied in parameter space. By considering a special case, an asymptotic perturbation analysis is used to derive the amplitude of the oscillating solutions for the full non-linear system. The present modelling exercise and results show that it is possible to study the population dynamics of disease vectors, and hence oscillatory behaviour as it is often observed in most indirectly transmitted infectious diseases of humans, without recourse to external seasonal forcing. (author)

  9. Drivers of waterfowl population dynamics: from teal to swans

    Science.gov (United States)

    Koons, David N.; Gunnarsson, Gunnar; Schmutz, Joel A.; Rotella, Jay J.

    2014-01-01

    Waterfowl are among the best studied and most extensively monitored species in the world. Given their global importance for sport and subsistence hunting, viewing and ecosystem functioning, great effort has been devoted since the middle part of the 20th century to understanding both the environmental and demographic mechanisms that influence waterfowl population and community dynamics. Here we use comparative approaches to summarise and contrast our understanding ofwaterfowl population dynamics across species as short-lived as the teal Anas discors and A.crecca to those such as the swans Cygnus sp. which have long life-spans. Specifically, we focus on population responses to vital rate perturbations across life history strategies, discuss bottom-up and top-down responses of waterfowlpopulations to global change, and summarise our current understanding of density dependence across waterfowl species. We close by identifying research needs and highlight ways to overcome the challenges of sustainably managing waterfowl populations in the 21st century.

  10. Evolutionary dynamics of dengue virus populations within the mosquito vector.

    Science.gov (United States)

    Lambrechts, Louis; Lequime, Sebastian

    2016-12-01

    To date, dengue virus evolution has mainly been addressed by studies conducted at the between-host level. Like other pathogens with high mutation rate and rapid replication, dengue viruses also evolve during the course of an infection. Over the last few years, the advent of deep-sequencing technologies has facilitated studies of dengue virus populations at the within-host level. Here, we review recent advances on the evolutionary dynamics of dengue virus populations within their mosquito vector. We discuss how identifying the evolutionary forces acting on dengue virus populations within the mosquito can shed light on the processes underlying vector-virus interactions and the evolution of epidemiologically relevant traits. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Linking animal population dynamics to alterations in foraging behaviour

    DEFF Research Database (Denmark)

    Nabe-Nielsen, Jacob; Sibly, Richard; Tougaard, Jakob

    the animals’ ability to forage efficiently and to sustain their energy intake, is influenced by noise emitted from wind turbines and ships. The energy levels in turn affect their survival. The fine-scale movements of the simulated animals was governed by a spatial memory, which allowed the model to produce......Background/Question/Methods The survival of animal populations is strongly influenced by the individuals’ ability to forage efficiently, yet there are few studies of how populations respond when disturbances cause animals to deviate from their natural foraging behavior. Animals that respond...... that are increasingly exposed to noise from ships, wind turbines, etc. In the present study we investigate how the dynamics of the harbor porpoise population (Phocoena phocoena) in the inner Danish waters is influenced by disturbances using an agent- based simulation model. In the model animal movement, and hence...

  12. Bacterial meningitis in solid organ transplant recipients: a population-based prospective study

    NARCIS (Netherlands)

    van Veen, K. E. B.; Brouwer, M. C.; van der Ende, A.; van de Beek, D.

    2016-01-01

    Solid organ transplant (SOT) recipients are at risk of infections of the central nervous system. However, the incidence and clinical course of bacterial meningitis in SOT recipients are unclear. We studied occurrence, disease course, and prognosis of bacterial meningitis in SOT recipients in the

  13. Numerical modeling of the dynamic response of a bioluminescent bacterial biosensor.

    Science.gov (United States)

    Affi, Mahmoud; Solliec, Camille; Legentilhomme, Patrick; Comiti, Jacques; Legrand, Jack; Jouanneau, Sulivan; Thouand, Gérald

    2016-12-01

    Water quality and water management are worldwide issues. The analysis of pollutants and in particular, heavy metals, is generally conducted by sensitive but expensive physicochemical methods. Other alternative methods of analysis, such as microbial biosensors, have been developed for their potential simplicity and expected moderate cost. Using a biosensor for a long time generates many changes in the growth of the immobilized bacteria and consequently alters the robustness of the detection. This work simulated the operation of a biosensor for the long-term detection of cadmium and improved our understanding of the bioluminescence reaction dynamics of bioreporter bacteria inside an agarose matrix. The choice of the numerical tools is justified by the difficulty to measure experimentally in every condition the biosensor functioning during a long time (several days). The numerical simulation of a biomass profile is made by coupling the diffusion equation and the consumption/reaction of the nutrients by the bacteria. The numerical results show very good agreement with the experimental profiles. The growth model verified that the bacterial growth is conditioned by both the diffusion and the consumption of the nutrients. Thus, there is a high bacterial density in the first millimeter of the immobilization matrix. The growth model has been very useful for the development of the bioluminescence model inside the gel and shows that a concentration of oxygen greater than or equal to 22 % of saturation is required to maintain a significant level of bioluminescence. A continuous feeding of nutrients during the process of detection of cadmium leads to a biofilm which reduces the diffusion of nutrients and restricts the presence of oxygen from the first layer of the agarose (1 mm) and affects the intensity of the bioluminescent reaction. The main advantage of this work is to link experimental works with numerical models of growth and bioluminescence in order to provide a

  14. Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature.

    Science.gov (United States)

    Bargiela, Rafael; Mapelli, Francesca; Rojo, David; Chouaia, Bessem; Tornés, Jesús; Borin, Sara; Richter, Michael; Del Pozo, Mercedes V; Cappello, Simone; Gertler, Christoph; Genovese, María; Denaro, Renata; Martínez-Martínez, Mónica; Fodelianakis, Stilianos; Amer, Ranya A; Bigazzi, David; Han, Xifang; Chen, Jianwei; Chernikova, Tatyana N; Golyshina, Olga V; Mahjoubi, Mouna; Jaouanil, Atef; Benzha, Fatima; Magagnini, Mirko; Hussein, Emad; Al-Horani, Fuad; Cherif, Ameur; Blaghen, Mohamed; Abdel-Fattah, Yasser R; Kalogerakis, Nicolas; Barbas, Coral; Malkawi, Hanan I; Golyshin, Peter N; Yakimov, Michail M; Daffonchio, Daniele; Ferrer, Manuel

    2015-06-29

    Two of the largest crude oil-polluted areas in the world are the semi-enclosed Mediterranean and Red Seas, but the effect of chronic pollution remains incompletely understood on a large scale. We compared the influence of environmental and geographical constraints and anthropogenic forces (hydrocarbon input) on bacterial communities in eight geographically separated oil-polluted sites along the coastlines of the Mediterranean and Red Seas. The differences in community compositions and their biodegradation potential were primarily associated (P polluted sites than in pristine ones where accidental oil spills occurred. We propose that low temperature increases bacterial richness while decreasing catabolic diversity and that chronic pollution promotes catabolic diversification. Our results further suggest that the bacterial populations in chronically polluted sites may respond more promptly in degrading petroleum after accidental oil spills.

  15. Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature

    KAUST Repository

    Bargiela, Rafael

    2015-06-29

    Two of the largest crude oil-polluted areas in the world are the semi-enclosed Mediterranean and Red Seas, but the effect of chronic pollution remains incompletely understood on a large scale. We compared the influence of environmental and geographical constraints and anthropogenic forces (hydrocarbon input) on bacterial communities in eight geographically separated oil-polluted sites along the coastlines of the Mediterranean and Red Seas. The differences in community compositions and their biodegradation potential were primarily associated (P < 0.05) with both temperature and chemical diversity. Furthermore, we observed a link between temperature and chemical and biological diversity that was stronger in chronically polluted sites than in pristine ones where accidental oil spills occurred. We propose that low temperature increases bacterial richness while decreasing catabolic diversity and that chronic pollution promotes catabolic diversification. Our results further suggest that the bacterial populations in chronically polluted sites may respond more promptly in degrading petroleum after accidental oil spills.

  16. Trends and population dynamics of a Velvet Scoter (Melanitta fusca) population: influence of density dependence and winter climate

    NARCIS (Netherlands)

    Hartman, G.; Kölzsch, A.; Larsson, K.; Nordberg, M.; Höglund, J.

    2013-01-01

    As many seaduck populations around the world have been reported to be in decline, there is an increasing demand for knowledge about intrinsic and extrinsic factors determining population dynamics of these species. In this study, we analyzed long-term dynamics of the summer population of Velvet

  17. DMPD: Role of Nods in bacterial infection. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 17379560 Role of Nods in bacterial infection. Bourhis LL, Werts C. Microbes Infect.... 2007 Apr;9(5):629-36. Epub 2007 Jan 27. (.png) (.svg) (.html) (.csml) Show Role of Nods in bacterial infection.... PubmedID 17379560 Title Role of Nods in bacterial infection. Authors Bourhis LL, Werts C. Publication M

  18. DMPD: Targeting bacterial endotoxin: two sides of a coin. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 17405910 Targeting bacterial endotoxin: two sides of a coin. Bosshart H, Heinzelman...n M. Ann N Y Acad Sci. 2007 Jan;1096:1-17. (.png) (.svg) (.html) (.csml) Show Targeting bacterial endotoxin: two sides of a coin.... PubmedID 17405910 Title Targeting bacterial endotoxin: two sides of a coin. Authors Bo

  19. DMPD: The actions of bacterial DNA on murine macrophages. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 10534106 The actions of bacterial DNA on murine macrophages. Sester DP, Stacey KJ, ...Sweet MJ, Beasley SJ, Cronau SL, Hume DA. J Leukoc Biol. 1999 Oct;66(4):542-8. (.png) (.svg) (.html) (.csml) Show The... actions of bacterial DNA on murine macrophages. PubmedID 10534106 Title The actions of bacterial D

  20. Population Dynamics of Early Human Migration in Britain

    Science.gov (United States)

    Vahia, Mayank N.; Ladiwala, Uma; Mahathe, Pavan; Mathur, Deepak

    2016-01-01

    Background Early human migration is largely determined by geography and human needs. These are both deterministic parameters when small populations move into unoccupied areas where conflicts and large group dynamics are not important. The early period of human migration into the British Isles provides such a laboratory which, because of its relative geographical isolation, may allow some insights into the complex dynamics of early human migration and interaction. Method and Results We developed a simulation code based on human affinity to habitable land, as defined by availability of water sources, altitude, and flatness of land, in choosing the path of migration. Movement of people on the British island over the prehistoric period from their initial entry points was simulated on the basis of data from the megalithic period. Topographical and hydro-shed data from satellite databases was used to define habitability, based on distance from water bodies, flatness of the terrain, and altitude above sea level. We simulated population movement based on assumptions of affinity for more habitable places, with the rate of movement tempered by existing populations. We compared results of our computer simulations with genetic data and show that our simulation can predict fairly accurately the points of contacts between different migratory paths. Such comparison also provides more detailed information about the path of peoples’ movement over ~2000 years before the present era. Conclusions We demonstrate an accurate method to simulate prehistoric movements of people based upon current topographical satellite data. Our findings are validated by recently-available genetic data. Our method may prove useful in determining early human population dynamics even when no genetic information is available. PMID:27148959

  1. Diversity and dynamics of dominant and rare bacterial taxa in replicate sequencing batch reactors operated under different solids retention time

    KAUST Repository

    Bagchi, Samik

    2014-10-19

    In this study, 16S rRNA gene pyrosequencing was applied in order to provide a better insight on the diversity and dynamics of total, dominant, and rare bacterial taxa in replicate lab-scale sequencing batch reactors (SBRs) operated at different solids retention time (SRT). Rank-abundance curves showed few dominant operational taxonomic units (OTUs) and a long tail of rare OTUs in all reactors. Results revealed that there was no detectable effect of SRT (2 vs. 10 days) on Shannon diversity index and OTU richness of both dominant and rare taxa. Nonmetric multidimensional scaling analysis showed that the total, dominant, and rare bacterial taxa were highly dynamic during the entire period of stable reactor performance. Also, the rare taxa were more dynamic than the dominant taxa despite expected low invasion rates because of the use of sterile synthetic media.

  2. Mechanistic description of population dynamics using dynamic energy budget theory incorporated into integral projection models

    NARCIS (Netherlands)

    Smallegange, I.M.; Caswell, H.; Toorians, M.E.M.; de Roos, A.M.

    1. Integral projection models (IPMs) provide a powerful approach to investigate ecological and rapid evolutionary change in quantitative life-history characteristics and population dynamics. IPMs are constructed from functions that describe the demographic rates – survival, growth and reproduction –

  3. Population dynamics of minimally cognitive individuals. Part I: Introducing knowledge into the dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Schmieder, R.W.

    1995-07-01

    The author presents a new approach for modeling the dynamics of collections of objects with internal structure. Based on the fact that the behavior of an individual in a population is modified by its knowledge of other individuals, a procedure for accounting for knowledge in a population of interacting objects is presented. It is assumed that each object has partial (or complete) knowledge of some (or all) other objects in the population. The dynamical equations for the objects are then modified to include the effects of this pairwise knowledge. This procedure has the effect of projecting out what the population will do from the much larger space of what it could do, i.e., filtering or smoothing the dynamics by replacing the complex detailed physical model with an effective model that produces the behavior of interest. The procedure therefore provides a minimalist approach for obtaining emergent collective behavior. The use of knowledge as a dynamical quantity, and its relationship to statistical mechanics, thermodynamics, information theory, and cognition microstructure are discussed.

  4. Cooperation guided by the coexistence of imitation dynamics and aspiration dynamics in structured populations

    Science.gov (United States)

    Xu, Kuangyi; Li, Kun; Cong, Rui; Wang, Long

    2017-02-01

    In the framework of the evolutionary game theory, two fundamentally different mechanisms, the imitation process and the aspiration-driven dynamics, can be adopted by players to update their strategies. In the former case, individuals imitate the strategy of a more successful peer, while in the latter case individuals change their strategies based on a comparison of payoffs they collect in the game to their own aspiration levels. Here we explore how cooperation evolves for the coexistence of these two dynamics. Intriguingly, cooperation reaches its lowest level when a certain moderate fraction of individuals pick aspiration-level-driven rule while the others choose pairwise comparison rule. Furthermore, when individuals can adjust their update rules besides their strategies, either imitation dynamics or aspiration-driven dynamics will finally take over the entire population, and the stationary cooperation level is determined by the outcome of competition between these two dynamics. We find that appropriate synergetic effects and moderate aspiration level boost the fixation probability of aspiration-driven dynamics most effectively. Our work may be helpful in understanding the cooperative behavior induced by the coexistence of imitation dynamics and aspiration dynamics in the society.

  5. Alternating event processes during lifetimes: population dynamics and statistical inference.

    Science.gov (United States)

    Shinohara, Russell T; Sun, Yifei; Wang, Mei-Cheng

    2018-01-01

    In the literature studying recurrent event data, a large amount of work has been focused on univariate recurrent event processes where the occurrence of each event is treated as a single point in time. There are many applications, however, in which univariate recurrent events are insufficient to characterize the feature of the process because patients experience nontrivial durations associated with each event. This results in an alternating event process where the disease status of a patient alternates between exacerbations and remissions. In this paper, we consider the dynamics of a chronic disease and its associated exacerbation-remission process over two time scales: calendar time and time-since-onset. In particular, over calendar time, we explore population dynamics and the relationship between incidence, prevalence and duration for such alternating event processes. We provide nonparametric estimation techniques for characteristic quantities of the process. In some settings, exacerbation processes are observed from an onset time until death; to account for the relationship between the survival and alternating event processes, nonparametric approaches are developed for estimating exacerbation process over lifetime. By understanding the population dynamics and within-process structure, the paper provide a new and general way to study alternating event processes.

  6. Stochastic population dynamics in spatially extended predator-prey systems

    Science.gov (United States)

    Dobramysl, Ulrich; Mobilia, Mauro; Pleimling, Michel; Täuber, Uwe C.

    2018-02-01

    Spatially extended population dynamics models that incorporate demographic noise serve as case studies for the crucial role of fluctuations and correlations in biological systems. Numerical and analytic tools from non-equilibrium statistical physics capture the stochastic kinetics of these complex interacting many-particle systems beyond rate equation approximations. Including spatial structure and stochastic noise in models for predator-prey competition invalidates the neutral Lotka-Volterra population cycles. Stochastic models yield long-lived erratic oscillations stemming from a resonant amplification mechanism. Spatially extended predator-prey systems display noise-stabilized activity fronts that generate persistent correlations. Fluctuation-induced renormalizations of the oscillation parameters can be analyzed perturbatively via a Doi-Peliti field theory mapping of the master equation; related tools allow detailed characterization of extinction pathways. The critical steady-state and non-equilibrium relaxation dynamics at the predator extinction threshold are governed by the directed percolation universality class. Spatial predation rate variability results in more localized clusters, enhancing both competing species’ population densities. Affixing variable interaction rates to individual particles and allowing for trait inheritance subject to mutations induces fast evolutionary dynamics for the rate distributions. Stochastic spatial variants of three-species competition with ‘rock-paper-scissors’ interactions metaphorically describe cyclic dominance. These models illustrate intimate connections between population dynamics and evolutionary game theory, underscore the role of fluctuations to drive populations toward extinction, and demonstrate how space can support species diversity. Two-dimensional cyclic three-species May-Leonard models are characterized by the emergence of spiraling patterns whose properties are elucidated by a mapping onto a complex

  7. Spatial dispersal of bacterial colonies induces a dynamical transition from local to global quorum sensing

    Science.gov (United States)

    Yusufaly, Tahir I.; Boedicker, James Q.

    2016-12-01

    Bacteria communicate using external chemical signals called autoinducers (AI) in a process known as quorum sensing (QS). QS efficiency is reduced by both limitations of AI diffusion and potential interference from neighboring strains. There is thus a need for predictive theories of how spatial community structure shapes information processing in complex microbial ecosystems. As a step in this direction, we apply a reaction-diffusion model to study autoinducer signaling dynamics in a single-species community as a function of the spatial distribution of colonies in the system. We predict a dynamical transition between a local quorum sensing (LQS) regime, with the AI signaling dynamics primarily controlled by the local population densities of individual colonies, and a global quorum sensing (GQS) regime, with the dynamics being dependent on collective intercolony diffusive interactions. The crossover between LQS to GQS is intimately connected to a trade-off between the signaling network's latency, or speed of activation, and its throughput, or the total spatial range over which all the components of the system communicate.

  8. Identifying consumer-resource population dynamics using paleoecological data.

    Science.gov (United States)

    Einarsson, Árni; Hauptfleisch, Ulf; Leavitt, Peter R; Ives, Anthony R

    2016-02-01

    Ecologists have long been fascinated by cyclic population fluctuations, because they suggest strong interactions between exploiter and victim species. Nonetheless, even for populations showing high-amplitude fluctuations, it is often hard to identify which species are the key drivers of the dynamics, because data are generally only available for a single species. Here, we use a paleoecological approach to investigate fluctuations in the midge population in Lake Mývatn, Iceland, which ranges over several orders of magnitude in irregular, multigeneration cycles. Previous circumstantial evidence points to consumer-resource interactions between midges and their primary food, diatoms, as the cause of these high-amplitude fluctuations. Using a pair of sediment cores from the lake, we reconstructed 26 years of dynamics of midges using egg remains and of algal groups using diagnostic pigments. We analyzed these data using statistical methods that account for both the autocorrelated nature of paleoecological data and measurement error caused by the mixing of sediment layers. The analyses revealed a signature of consumer-resource interactions in the fluctuations of midges and diatoms: diatom abundance (as inferred from biomarker pigment diatoxanthin) increased when midge abundance was low, and midge abundance (inferred from egg capsules) decreased when diatom abundance was low. Similar patterns were not found for pigments characterizing the other dominant primary producer group in the lake (cyanobacteria), subdominant algae (cryptophytes), or ubiquitous but chemically unstable biomarkers of total algal abundance (chlorophyll a); however, a significant but weaker pattern was found for the chemically stable indicator of total algal populations (β-carotene) to which diatoms are the dominant contributor. These analyses provide the first paleoecological evaluation of specific trophic interactions underlying high amplitude population fluctuations in lakes.

  9. Bacterial enteropathogens associated with diarrhea in a rural population of Haiti

    Directory of Open Access Journals (Sweden)

    Jackson JC

    2011-09-01

    Full Text Available John C Jackson, Anthony L Farone, Mary B Farone Biology Department, Middle Tennessee State University, Murfreesboro, Tennessee, USA Purpose: Diarrheal disease is one of the leading causes of morbidity in developing countries. To further understand the epidemiology of diarrheal disease among a rural population surrounding Robillard, Haiti, fecal swabs from patients with diarrhea were screened for the presence of enteropathogenic bacteria. Patients and methods: Fecal swabs were collected from 34 patients with signs and symptoms of diarrhea and stored in BBLTM Cary-Blair transport medium (Becton, Dickinson and Company, Sparks, MD until transit to the USA. Swab material was inoculated on to different enrichment and selective agars for incubation. Fermenting and nonfermenting bacteria that grew on the enteric selection media were identified by the BBLTM CrystalTM Enteric/Nonferementing Identification system (Becton, Dickinson and Company. Organisms identified as Escherichia coli were further screened for the presence of virulence factors by polymerase chain reaction (PCR. Results: Of 34 patients, no Campylobacter, Shigella, Salmonella, or Vibrio spp. were isolated from swabs transported to the USA for culture. Of 73 E. coli isolates cultured from the swabs, one enteropathogenic strain of E. coli was identified by multiplex PCR. Escherichia fergusonii and Cronobacter sakazakii, both potential gastrointestinal pathogens, were also isolated from patient stools. Conclusion: This study was undertaken to determine if bacterial enteropathogens could be detected in the stools of patients suffering from diarrhea or dysentery and, in the absence of sufficient facilities, rectal swabs could be transported to the USA for culture. Although several genera of overt enteropathogens were not detected, one enteropathogenic E. coli and other pathogenic enterobacteriaceae were successfully cultured and identified. Keywords: Escherichia, Cronobacter, diarrheagenic, stool

  10. Time to antibiotic therapy and outcome in bacterial meningitis: a Danish population-based cohort study.

    Science.gov (United States)

    Bodilsen, Jacob; Dalager-Pedersen, Michael; Schønheyder, Henrik Carl; Nielsen, Henrik

    2016-08-09

    Community-acquired bacterial meningitis (CABM) is a life-threatening disease and timing of antibiotic therapy remains crucial. We aimed to analyse the impact of antibiotic timing on the outcome of CABM in a contemporary cohort. We conducted a population-based cohort study based on chart reviews of all adult cases (>16 years of age) of CABM in North Denmark from 1998 to 2014 excluding patients given pre-hospital parenteral antibiotics. We used modified Poisson regression analyses to compute the adjusted risk ratio (adj. RR) with 95 % confidence intervals (CIs) for in-hospital mortality and unfavourable outcome at discharge by time after arrival to hospital to adequate antibiotic therapy. We identified 195 adults with CABM of whom 173 patients were eligible for further analyses. The median door-to-antibiotic time was 2.0 h (interquartile range (IQR) 1.0-5.5). We observed increased adjusted risk ratios for in-hospital mortality of 1.6 (95 % CI 0.8-3.2) and an unfavourable outcome at discharge of 1.5 (95 % CI 1.0-2.2, p = 0.03) when treatment delays exceeded 6 h versus treatment within 2 h of admission. These findings corresponded to adjusted risk ratios of in-hospital mortality of 1.1 per hour of delay (95 % CI 0.8-1.5) and an unfavourable outcome at discharge of 1.1 per hour of delay (95 % CI 1.0-1.3) within the first 6 h of admission. Some patients (31 %) were diagnosed after admission and had more delays in antibiotic therapy and correspondingly increased in-hospital mortality (30 vs 14 %, p = 0.01) and unfavourable outcome (62 vs 37 %, p = 0.002). Delay in antibiotic therapy was associated with unfavourable outcome at discharge.

  11. Effects of rainfall on Culex mosquito population dynamics.

    Science.gov (United States)

    Valdez, L D; Sibona, G J; Diaz, L A; Contigiani, M S; Condat, C A

    2017-05-21

    The dynamics of a mosquito population depends heavily on climatic variables such as temperature and precipitation. Since climate change models predict that global warming will impact on the frequency and intensity of rainfall, it is important to understand how these variables affect the mosquito populations. We present a model of the dynamics of a Culex quinquefasciatus mosquito population that incorporates the effect of rainfall and use it to study the influence of the number of rainy days and the mean monthly precipitation on the maximum yearly abundance of mosquitoes M max . Additionally, using a fracturing process, we investigate the influence of the variability in daily rainfall on M max . We find that, given a constant value of monthly precipitation, there is an optimum number of rainy days for which M max is a maximum. On the other hand, we show that increasing daily rainfall variability reduces the dependence of M max on the number of rainy days, leading also to a higher abundance of mosquitoes for the case of low mean monthly precipitation. Finally, we explore the effect of the rainfall in the months preceding the wettest season, and we obtain that a regimen with high precipitations throughout the year and a higher variability tends to advance slightly the time at which the peak mosquito abundance occurs, but could significantly change the total mosquito abundance in a year. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Population dynamics of minimally cognitive individuals. Part 2: Dynamics of time-dependent knowledge

    Energy Technology Data Exchange (ETDEWEB)

    Schmieder, R.W.

    1995-07-01

    The dynamical principle for a population of interacting individuals with mutual pairwise knowledge, presented by the author in a previous paper for the case of constant knowledge, is extended to include the possibility that the knowledge is time-dependent. Several mechanisms are presented by which the mutual knowledge, represented by a matrix K, can be altered, leading to dynamical equations for K(t). The author presents various examples of the transient and long time asymptotic behavior of K(t) for populations of relatively isolated individuals interacting infrequently in local binary collisions. Among the effects observed in the numerical experiments are knowledge diffusion, learning transients, and fluctuating equilibria. This approach will be most appropriate to small populations of complex individuals such as simple animals, robots, computer networks, agent-mediated traffic, simple ecosystems, and games. Evidence of metastable states and intermittent switching leads them to envision a spectroscopy associated with such transitions that is independent of the specific physical individuals and the population. Such spectra may serve as good lumped descriptors of the collective emergent behavior of large classes of populations in which mutual knowledge is an important part of the dynamics.

  13. Exploiting Fast-Variables to Understand Population Dynamics and Evolution

    Science.gov (United States)

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

    2017-11-01

    We describe a continuous-time modelling framework for biological population dynamics that accounts for demographic noise. In the spirit of the methodology used by statistical physicists, transitions between the states of the system are caused by individual events while the dynamics are described in terms of the time-evolution of a probability density function. In general, the application of the diffusion approximation still leaves a description that is quite complex. However, in many biological applications one or more of the processes happen slowly relative to the system's other processes, and the dynamics can be approximated as occurring within a slow low-dimensional subspace. We review these time-scale separation arguments and analyse the more simple stochastic dynamics that result in a number of cases. We stress that it is important to retain the demographic noise derived in this way, and emphasise this point by showing that it can alter the direction of selection compared to the prediction made from an analysis of the corresponding deterministic model.

  14. Population dynamics in Asia and the Pacific: implications for development.

    Science.gov (United States)

    1994-03-01

    This article is an excerpt from a recently published article on interactions between population and development in the "Economic and Social Survey of Asia and the Pacific, 1993." Topics include the dynamics of change (growth, age structure, sex composition, migration); implications for specific development issues (population and education, population and health, population and employment, and population and the environment); and policy approaches (slowing growth, spatial distribution, and the role of women). The Asian focus is on population policy and fertility declines. Different conditions specific to each country and varying degrees of program success give rise to country-specific differences in rates of growth and declines in fertility. Population compositions and pressures on spatial distribution differ among countries. Development demands differ for education, health, employment, and environmental controls. A common feature is that population is integrated into social and economic development policies. The links between population and the environment are recognized and will be integrated into policy as knowledge emerges. The ESCAP region has about 58% of world population, and fertility has declined to 3.1 children per woman. Fertility declines do not result in demonstrable changes in the rate of population growth, because the proportion of reproductive age women has increased and will continue to do so until 2010. Reductions in fertility are balanced by mortality declines. The annual rate of increase has gradually slowed, however the absolute size is still huge. The goal of the Bali Declaration of 1992 is to reach replacement level fertility of 2.2 children per woman by 2010 in the ESCAP region. The UN median variant projects 2.4 children per woman by 2010. The countries unlikely to reach replacement level fertility are India, the Philippines, Vietnam, Bangladesh, and Pakistan. Age structure will determine the need for services. For example, South Asia will

  15. Potential Environmental Factors Affecting Oil-Degrading Bacterial Populations in Deep and Surface Waters of the Northern Gulf of Mexico.

    Science.gov (United States)

    Liu, Jiqing; Bacosa, Hernando P; Liu, Zhanfei

    2016-01-01

    Understanding bacterial community dynamics as a result of an oil spill is important for predicting the fate of oil released to the environment and developing bioremediation strategies in the Gulf of Mexico. In this study, we aimed to elucidate the roles of temperature, water chemistry (nutrients), and initial bacterial community in selecting oil degraders through a series of incubation experiments. Surface (2 m) and bottom (1537 m) waters, collected near the Deepwater Horizon site, were amended with 200 ppm light Louisiana sweet crude oil and bacterial inoculums from surface or bottom water, and incubated at 4 or 24°C for 50 days. Bacterial community and residual oil were analyzed by pyrosequencing and gas chromatography-mass spectrometry (GC-MS), respectively. The results showed that temperature played a key role in selecting oil-degrading bacteria. Incubation at 4°C favored the development of Cycloclasticus, Pseudoalteromonas , Sulfitobacter , and Reinekea , while 24°C incubations enhanced Oleibacter, Thalassobius, Phaeobacter, and Roseobacter. Water chemistry and the initial community also had potential roles in the development of hydrocarbon-degrading bacterial communities. Pseudoalteromonas , Oleibacter , and Winogradskyella developed well in the nutrient-enriched bottom water, while Reinekea and Thalassobius were favored by low-nutrient surface water. We revealed that the combination of 4°C, crude oil and bottom inoculum was a key factor for the growth of Cycloclasticus , while the combination of surface inoculum and bottom water chemistry was important for the growth of Pseudoalteromonas . Moreover, regardless of the source of inoculum, bottom water at 24°C was a favorable condition for Oleibacter. Redundancy analysis further showed that temperature and initial community explained 57 and 19% of the variation observed, while oil and water chemistry contributed 14 and 10%, respectively. Overall, this study revealed the relative roles of temperature, water

  16. Inoculation Effect of N2-Fixer and P-Solubilizer into a Mixture of Fresh Manure and Phosphate Rock Formulated as Organonitrofos Fertilizer on Bacterial and Fungal Populations

    Directory of Open Access Journals (Sweden)

    Sutopo Ghani Nugroho

    2013-03-01

    Full Text Available Microbial N2-fixer and P-solubilizer were innoculated in a mixture of fresh manure and phosphate rock formulated as an Organonitrophos fertilizer. The population dynamics of bacteria and fungi growing during the composting process were observed. The inoculation treatments consisted of: K = mixture of 20% phosphate rock and 80% of fresh manure + decomposers (control, N = mixture of 20% phosphate rock and 80% of fresh manure + decomposers + N2-fixer (Azotobacter and Azospirillum sp. , P = mixture of 20% phosphate rock and 80% of fresh manure + decomposers + P-solubilizer (A. niger and P. fluorescens, and NP = mixture of 20% phosphate rock and 80% of fresh manure + decomposers + N2-fixer + P-solubilizer. The results showed that inoculation of microbial N2-fixer and combination inoculation of N2-fixer and P-solubilizer increased the total bacterial population compared to that of the control as well as the only inoculation of microbial P-solubilizer on the 14th day of observation in which the bacteria reached the highest population. On all the observation days, the population of fungi in the inoculation of microbial P-solubilizer treatment increased significantly compared to that of the control. However, there was no difference between the populations of fungi in the inoculation of N2-fixer and combination inoculation of N2-fixer and Psolubilizer. The genus of fungy identified in the compost of the mixture of fresh manure and phosphate rock were Chytridium sp., Aspergillus sp., Rhizopus sp., and Fusarium sp.

  17. Plasmodium vivax population structure and transmission dynamics in Sabah Malaysia.

    Science.gov (United States)

    Abdullah, Noor Rain; Barber, Bridget E; William, Timothy; Norahmad, Nor Azrina; Satsu, Umi Rubiah; Muniandy, Prem Kumar; Ismail, Zakiah; Grigg, Matthew J; Jelip, Jenarun; Piera, Kim; von Seidlein, Lorenz; Yeo, Tsin W; Anstey, Nicholas M; Price, Ric N; Auburn, Sarah

    2013-01-01

    Despite significant progress in the control of malaria in Malaysia, the complex transmission dynamics of P. vivax continue to challenge national efforts to achieve elimination. To assess the impact of ongoing interventions on P. vivax transmission dynamics in Sabah, we genotyped 9 short tandem repeat markers in a total of 97 isolates (8 recurrences) from across Sabah, with a focus on two districts, Kota Marudu (KM, n = 24) and Kota Kinabalu (KK, n = 21), over a 2 year period. STRUCTURE analysis on the Sabah-wide dataset demonstrated multiple sub-populations. Significant differentiation (F ST  = 0.243) was observed between KM and KK, located just 130 Km apart. Consistent with low endemic transmission, infection complexity was modest in both KM (mean MOI  = 1.38) and KK (mean MOI  = 1.19). However, population diversity remained moderate (H E  = 0.583 in KM and H E  = 0.667 in KK). Temporal trends revealed clonal expansions reflecting epidemic transmission dynamics. The haplotypes of these isolates declined in frequency over time, but persisted at low frequency throughout the study duration. A diverse array of low frequency isolates were detected in both KM and KK, some likely reflecting remnants of previous expansions. In accordance with clonal expansions, high levels of Linkage Disequilibrium (I A (S) >0.5 [PSabah's shrinking P. vivax population appears to have rendered this low endemic setting vulnerable to epidemic expansions. Migration may play an important role in the introduction of new parasite strains leading to epidemic expansions, with important implications for malaria elimination.

  18. [On the relation between encounter rate and population density: Are classical models of population dynamics justified?].

    Science.gov (United States)

    Nedorezov, L V

    2015-01-01

    A stochastic model of migrations on a lattice and with discrete time is considered. It is assumed that space is homogenous with respect to its properties and during one time step every individual (independently of local population numbers) can migrate to nearest nodes of lattice with equal probabilities. It is also assumed that population size remains constant during certain time interval of computer experiments. The following variants of estimation of encounter rate between individuals are considered: when for the fixed time moments every individual in every node of lattice interacts with all other individuals in the node; when individuals can stay in nodes independently, or can be involved in groups in two, three or four individuals. For each variant of interactions between individuals, average value (with respect to space and time) is computed for various values of population size. The samples obtained were compared with respective functions of classic models of isolated population dynamics: Verhulst model, Gompertz model, Svirezhev model, and theta-logistic model. Parameters of functions were calculated with least square method. Analyses of deviations were performed using Kolmogorov-Smirnov test, Lilliefors test, Shapiro-Wilk test, and other statistical tests. It is shown that from traditional point of view there are no correspondence between the encounter rate and functions describing effects of self-regulatory mechanisms on population dynamics. Best fitting of samples was obtained with Verhulst and theta-logistic models when using the dataset resulted from the situation when every individual in the node interacts with all other individuals.

  19. Periodic matrix models for seasonal dynamics of structured populations with application to a seabird population.

    Science.gov (United States)

    Cushing, J M; Henson, Shandelle M

    2018-02-03

    For structured populations with an annual breeding season, life-stage interactions and behavioral tactics may occur on a faster time scale than that of population dynamics. Motivated by recent field studies of the effect of rising sea surface temperature (SST) on within-breeding-season behaviors in colonial seabirds, we formulate and analyze a general class of discrete-time matrix models designed to account for changes in behavioral tactics within the breeding season and their dynamic consequences at the population level across breeding seasons. As a specific example, we focus on egg cannibalism and the daily reproductive synchrony observed in seabirds. Using the model, we investigate circumstances under which these life history tactics can be beneficial or non-beneficial at the population level in light of the expected continued rise in SST. Using bifurcation theoretic techniques, we study the nature of non-extinction, seasonal cycles as a function of environmental resource availability as they are created upon destabilization of the extinction state. Of particular interest are backward bifurcations in that they typically create strong Allee effects in population models which, in turn, lead to the benefit of possible (initial condition dependent) survival in adverse environments. We find that positive density effects (component Allee effects) due to increased adult survival from cannibalism and the propensity of females to synchronize daily egg laying can produce a strong Allee effect due to a backward bifurcation.

  20. Diversity of endophytic bacterial populations and their interaction with Xylella fastidiosa in citrus plants

    NARCIS (Netherlands)

    Araujo, W.L.; Marcon, J.; jr. Maccheroni, W.; Elsas, van J.D.; Vuurde, van J.W.L.; Azevedo, de J.L.

    2002-01-01

    Citrus variegated chlorosis (CVC) is caused by Xylella fastidiosa, a phytopathogenic bacterium that can infect all Citrus sinensis cultivars. The endophytic bacterial communities of healthy, resistant, and CVC-affected citrus plants were studied by using cultivation as well as

  1. Microbiological studies in schirmacher oasis, Antarctica: Effect of temperature on bacterial populations

    Digital Repository Service at National Institute of Oceanography (India)

    Matondkar, S.G.P.

    and mesophiles. Pulses in the bacterial cycle were also found in the Basis as a function of daily and seasonal variations in air and soil temperature. Requirement of growth temperature of individual bacterium is the best physiological marker to workout...

  2. Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection.

    Science.gov (United States)

    Guthke, Reinhard; Möller, Ulrich; Hoffmann, Martin; Thies, Frank; Töpfer, Susanne

    2005-04-15

    The immune response to bacterial infection represents a complex network of dynamic gene and protein interactions. We present an optimized reverse engineering strategy aimed at a reconstruction of this kind of interaction networks. The proposed approach is based on both microarray data and available biological knowledge. The main kinetics of the immune response were identified by fuzzy clustering of gene expression profiles (time series). The number of clusters was optimized using various evaluation criteria. For each cluster a representative gene with a high fuzzy-membership was chosen in accordance with available physiological knowledge. Then hypothetical network structures were identified by seeking systems of ordinary differential equations, whose simulated kinetics could fit the gene expression profiles of the cluster-representative genes. For the construction of hypothetical network structures singular value decomposition (SVD) based methods and a newly introduced heuristic Network Generation Method here were compared. It turned out that the proposed novel method could find sparser networks and gave better fits to the experimental data. Reinhard.Guthke@hki-jena.de.

  3. Do farming practices influence population dynamics of rodents?

    DEFF Research Database (Denmark)

    Massawe, A W; Rwamugira, W; Leirs, Herwig

    2007-01-01

    A capture-mark-recapture study was conducted in crop fields in Morogoro, Tanzania, to investigate how the population dynamics of multimammate field rats, Mastomys natalensis, was influenced by the commonly practised land preparation methods and cropping systems. Two land preparation methods (trac...... practices. In maize fields in Tanzania, the crop is most susceptible to damage by M. natalensis in the first 2 weeks after planting, and therefore, lower densities of rodents will result into lower crop damage in tractor ploughed fields....

  4. Spatial dynamics of a periodic population model with dispersal

    International Nuclear Information System (INIS)

    Jin Yu; Zhao Xiaoqiang

    2009-01-01

    This paper is devoted to the study of spatial dynamics of a class of periodic integro-differential equations which describe the population dispersal process via a dispersal kernel. By appealing to the theory of asymptotic speeds of spread and travelling waves for monotonic periodic semiflows, we establish the existence of the spreading speed c * and the nonexistence of continuous periodic travelling wave solutions with wave speed c * . We also prove the existence of left-continuous periodic travelling waves with wave speed c ≥ c * . In the autonomous case, the continuity of monotonic wave profiles with wave speed c ≥ c * is obtained

  5. Bacterial meningitis in diabetes patients: a population-based prospective study

    Science.gov (United States)

    van Veen, Kiril E. B.; Brouwer, Matthijs C.; van der Ende, Arie; van de Beek, Diederik

    2016-01-01

    Diabetes mellitus is associated with increased infection rates. We studied clinical features and outcome of community-acquired bacterial meningitis in diabetes patients. Patients were selected from a nationwide, prospective cohort on community-acquired bacterial meningitis performed from March 2006 to October 2014. Data on patient history, symptoms and signs on admission, treatment, and outcome were prospectively collected. A total of 183 of 1447 episodes (13%) occurred in diabetes patients. The incidence of bacterial meningitis in diabetes patients was 3.15 per 100,000 patients per year and the risk of acquiring bacterial meningitis was 2.2-fold higher for diabetes patients. S. pneumoniae was the causative organism in 139 of 183 episodes (76%) and L. monocytogenes in 11 of 183 episodes (6%). Outcome was unfavourable in 82 of 183 episodes (45%) and in 43 of 183 episodes (23%) the patient died. Diabetes was associated with death with an odds ratio of 1.63 (95% CI 1.12–2.37, P = 0.011), which remained after adjusting for known predictors of death in a multivariable analysis (OR 1.98 [95% CI 1.13–3.48], P = 0.017). In conclusion, diabetes is associated with a 2-fold higher risk of acquiring bacterial meningitis. Diabetes is a strong independent risk factor for death in community-acquired adult bacterial meningitis. PMID:27845429

  6. Bacterial meningitis in solid organ transplant recipients: a population-based prospective study.

    Science.gov (United States)

    van Veen, K E B; Brouwer, M C; van der Ende, A; van de Beek, D

    2016-10-01

    Solid organ transplant (SOT) recipients are at risk of infections of the central nervous system. However, the incidence and clinical course of bacterial meningitis in SOT recipients are unclear. We studied occurrence, disease course, and prognosis of bacterial meningitis in SOT recipients in the Netherlands. All patients with a medical history of solid organ transplantation were selected from our nationwide prospective cohort study on community-acquired bacterial meningitis in patients >16 years old, performed from March 1, 2006 to October 31, 2014. Data on patient history, symptoms and signs on admission, treatment, and outcome were collected prospectively. For transplant recipients, additional information was collected retrospectively. We identified 6 SOT recipients, all receiving renal transplants. The annual incidence of bacterial meningitis was 7-fold higher (95% confidence interval [CI] 2.94-17.02, P bacterial meningitis (fever, neck stiffness, and change in mental status). Seizures were common, occurring in 33% of patients. Streptococcus pneumoniae and Listeria monocytogenes were identified in 2 patients each, and Escherichia coli and Pseudomonas aeruginosa were both identified once. Four of 6 patients (67%) had an unfavorable functional outcome. Bacterial meningitis is a rare but devastating complication of solid organ transplantation. SOT recipients are at high risk for developing meningitis, and recognition of this condition may be difficult, owing to atypical clinical manifestation. © 2016 The Authors. Transplant Infectious Disease Published by John Wiley & Sons Ltd.

  7. Outward migration may alter population dynamics and income inequality

    Science.gov (United States)

    Shayegh, Soheil

    2017-11-01

    Climate change impacts may drive affected populations to migrate. However, migration decisions in response to climate change could have broader effects on population dynamics in affected regions. Here, I model the effect of climate change on fertility rates, income inequality, and human capital accumulation in developing countries, focusing on the instrumental role of migration as a key adaptation mechanism. In particular, I investigate how climate-induced migration in developing countries will affect those who do not migrate. I find that holding all else constant, climate change raises the return on acquiring skills, because skilled individuals have greater migration opportunities than unskilled individuals. In response to this change in incentives, parents may choose to invest more in education and have fewer children. This may ultimately reduce local income inequality, partially offsetting some of the damages of climate change for low-income individuals who do not migrate.

  8. State-dependent neutral delay equations from population dynamics.

    Science.gov (United States)

    Barbarossa, M V; Hadeler, K P; Kuttler, C

    2014-10-01

    A novel class of state-dependent delay equations is derived from the balance laws of age-structured population dynamics, assuming that birth rates and death rates, as functions of age, are piece-wise constant and that the length of the juvenile phase depends on the total adult population size. The resulting class of equations includes also neutral delay equations. All these equations are very different from the standard delay equations with state-dependent delay since the balance laws require non-linear correction factors. These equations can be written as systems for two variables consisting of an ordinary differential equation (ODE) and a generalized shift, a form suitable for numerical calculations. It is shown that the neutral equation (and the corresponding ODE--shift system) is a limiting case of a system of two standard delay equations.

  9. Host-Parasite Interactions and Population Dynamics of Rock Ptarmigan.

    Science.gov (United States)

    Stenkewitz, Ute; Nielsen, Ólafur K; Skírnisson, Karl; Stefánsson, Gunnar

    2016-01-01

    evidence that E. muta through time-lag in prevalence with respect to host population size and by showing significant relations with host body condition, mortality, and fecundity could destabilize ptarmigan population dynamics in Iceland.

  10. Evolutionary dynamics for persistent cooperation in structured populations

    Science.gov (United States)

    Li, Yan; Liu, Xinsheng; Claussen, Jens Christian; Guo, Wanlin

    2015-06-01

    The emergence and maintenance of cooperative behavior is a fascinating topic in evolutionary biology and social science. The public goods game (PGG) is a paradigm for exploring cooperative behavior. In PGG, the total resulting payoff is divided equally among all participants. This feature still leads to the dominance of defection without substantially magnifying the public good by a multiplying factor. Much effort has been made to explain the evolution of cooperative strategies, including a recent model in which only a portion of the total benefit is shared by all the players through introducing a new strategy named persistent cooperation. A persistent cooperator is a contributor who is willing to pay a second cost to retrieve the remaining portion of the payoff contributed by themselves. In a previous study, this model was analyzed in the framework of well-mixed populations. This paper focuses on discussing the persistent cooperation in lattice-structured populations. The evolutionary dynamics of the structured populations consisting of three types of competing players (pure cooperators, defectors, and persistent cooperators) are revealed by theoretical analysis and numerical simulations. In particular, the approximate expressions of fixation probabilities for strategies are derived on one-dimensional lattices. The phase diagrams of stationary states, and the evolution of frequencies and spatial patterns for strategies are illustrated on both one-dimensional and square lattices by simulations. Our results are consistent with the general observation that, at least in most situations, a structured population facilitates the evolution of cooperation. Specifically, here we find that the existence of persistent cooperators greatly suppresses the spreading of defectors under more relaxed conditions in structured populations compared to that obtained in well-mixed populations.

  11. Population Dynamics in the Capitalist World-Economy

    Directory of Open Access Journals (Sweden)

    Daniela Danna

    2015-08-01

    Full Text Available World-systems analysis has given scant attention to population dynamics. Overlooked are large-scale macrohistorical population trends and their microhistorical foundation on procreative decisions-decisions which are taken by a historically changing subject of procreation: local elders or other authorities, head(s of the household, couples, and women. The discipline of demography is also not as helpful as it could be, given its basis in modernization theory, which fails to recognize intentionality in reproduction in pre-capitalist societies. It assumes a model of "demographic transition" from a state of "natural fertility" to a state of conscious family planning, while also treating mortality as independent of fertility Marxism recognized the importance of population as a source of labor for profit and capital accumulation. With its tools Sydney Coontz developed a demand for labor theory explaining in particular the decrease in the birth rate in England and the United States at the turn of the century This theory was f urther developed by anthropologists of the "mode of product ion and population pat terns " who, with other authors, offer useful theories and insights to advance world-historical research on population. This article explores connections between population dy namics and world-systems analysis. I explore six key questions at different levels of analysis, including: 1 Are there world-systems ' imperatives concerning human reproduction?; 2 Do human reproduction imperatives differ across world-systems.'?; 3 How do the (eventual systems requirements get transmitted to households and individuals'?; 4 Why do people have children.'?; 5 Who is the subject of procreation decisions'?; and 6 How is the number of offspring chosen? Finally, I offer guidelines for applying the six questions to the capitalist world-economy.

  12. Dynamics of Bacterial and Fungal Communities during the Outbreak and Decline of an Algal Bloom in a Drinking Water Reservoir.

    Science.gov (United States)

    Zhang, Haihan; Jia, Jingyu; Chen, Shengnan; Huang, Tinglin; Wang, Yue; Zhao, Zhenfang; Feng, Ji; Hao, Huiyan; Li, Sulin; Ma, Xinxin

    2018-02-18

    The microbial communities associated with algal blooms play a pivotal role in organic carbon, nitrogen and phosphorus cycling in freshwater ecosystems. However, there have been few studies focused on unveiling the dynamics of bacterial and fungal communities during the outbreak and decline of algal blooms in drinking water reservoirs. To address this issue, the compositions of bacterial and fungal communities were assessed in the Zhoucun drinking water reservoir using 16S rRNA and internal transcribed spacer (ITS) gene Illumina MiSeq sequencing techniques. The results showed the algal bloom was dominated by Synechococcus, Microcystis, and Prochlorothrix. The bloom was characterized by a steady decrease of total phosphorus (TP) from the outbreak to the decline period (p water bacterial and fungal community structure. During the bloom, the dominant bacterial genus were Acinetobacter sp., Limnobacter sp., Synechococcus sp., and Roseomonas sp. The relative size of the fungal community also changed with algal bloom and its composition mainly contained Ascomycota, Basidiomycota and Chytridiomycota. Heat map profiling indicated that algal bloom had a more consistent effect upon fungal communities at genus level. Redundancy analysis (RDA) also demonstrated that the structure of water bacterial communities was significantly correlated to conductivity and ammonia nitrogen. Meanwhile, water temperature, Fe and ammonia nitrogen drive the dynamics of water fungal communities. The results from this work suggested that water bacterial and fungal communities changed significantly during the outbreak and decline of algal bloom in Zhoucun drinking water reservoir. Our study highlights the potential role of microbial diversity as a driving force for the algal bloom and biogeochemical cycling of reservoir ecology.

  13. Population dynamics of two antilisterial cheese surface consortia revealed by temporal temperature gradient gel electrophoresis

    Directory of Open Access Journals (Sweden)

    Hasler Madlen

    2010-03-01

    Full Text Available Abstract Background Surface contamination of smear cheese by Listeria spp. is of major concern for the industry. Complex smear ecosystems have been shown to harbor antilisterial potential but the microorganisms and mechanisms involved in the inhibition mostly remain unclear, and are likely related to complex interactions than to production of single antimicrobial compounds. Bacterial biodiversity and population dynamics of complex smear ecosystems exhibiting antilisterial properties in situ were investigated by Temporal temperature gradient gel electrophoresis (TTGE, a culture independent technique, for two microbial consortia isolated from commercial Raclette type cheeses inoculated with defined commercial ripening cultures (F or produced with an old-young smearing process (M. Results TTGE revealed nine bacterial species common to both F and M consortia, but consortium F exhibited a higher diversity than consortium M, with thirteen and ten species, respectively. Population dynamics were studied after application of the consortia on fresh-produced Raclette cheeses. TTGE analyses revealed a similar sequential development of the nine species common to both consortia. Beside common cheese surface bacteria (Staphylococcus equorum, Corynebacterium spp., Brevibacterium linens, Microbacterium gubbeenense, Agrococcus casei, the two consortia contained marine lactic acid bacteria (Alkalibacterium kapii, Marinilactibacillus psychrotolerans that developed early in ripening (day 14 to 20, shortly after the growth of staphylococci (day 7. A decrease of Listeria counts was observed on cheese surface inoculated at day 7 with 0.1-1 × 102 CFU cm-2, when cheeses were smeared with consortium F or M. Listeria counts went below the detection limit of the method between day 14 and 28 and no subsequent regrowth was detected over 60 to 80 ripening days. In contrast, Listeria grew to high counts (105 CFU cm-2 on cheeses smeared with a defined surface culture

  14. A bacterial population analysis of granular sludge from an anaerobic digester treating a maize-processing waste

    Energy Technology Data Exchange (ETDEWEB)

    Howgrave-Graham, A.R.; Wallis, F.M. (Natal Univ., Pietermaritzburg (ZA). Dept. of Microbiology and Plant Pathology); Steyn, P.L. (Pretoria Univ. (South Africa))

    1991-01-01

    Microbial population studies were conducted on a dense granular sludge, with excellent settling, thickening and nutrient removal properties, from a South African clarigester treating effluent from a factory producing glucose and other carbohydrates from maize. The bacterial population comprised a heterogeneous group including acetogens, enterobacteria, sulphate-reducers, spirochaetes, heterofermentative lactobacilli and methanogens. The presence of these bacteria and lack of propionic acid and butyric acid bacteria suggests that the microbial activity of this anaerobic digester involved acetate and lactate metabolism rather than propionate or butyrate catabolism as a source of precursors for methane production. (author).

  15. Bacterial and Archaeal Community Dynamics at CO2-RICH Shallow-Sea Hydrothermal Vents (panarea, Italy)

    Science.gov (United States)

    Schubotz, F.; Huang, C.; Meyerdierks, A.; Amend, J.; Price, R. E.; Amann, R.; Hinrichs, K.; Summons, R. E.

    2013-12-01

    Shallow marine hydrothermal vents are highly dynamic systems with unique habitats that can support both chemosynthetic and photosynthetic communities at steep temperature and geochemical gradients. Here, we present a combined organic geochemical and microbiological approach to describe the microbial community composition and their metabolism at the CO2-rich shallow hydrothermal vents off Panarea Island, in Sicily. We investigated two contrasting hydrothermal environments: Hot Lake, a depression filled with hydrothermal fluids diffusing gradually out of the seafloor, with temperatures ranging from 40 to 70°C, and Blackpoint, a site with vigorous venting of hydrothermal gasses and fluids with temperatures as high as 135°C. At Hot Lake, Bacteria dominate the microbial community composition in the sediments. 16S rRNA clone libraries revealed Bacteriodetes-, Epsilonproteobacteria- and Deltaproteobacteria-related sequences as the most abundant members. Bacterial intact polar membrane lipids (IPLs) were dominated by the non-phosphorous containing ornithine lipids throughout all depths, indicating an important role of this aminolipid at elevated temperatures and/or low pH. At Hot Lake, archaeal IPLs were comprised mainly of glycosidic tetraethers and increased up to 20% of total IPLs with increasing temperature and depth. At the same site, archaeal 16S rRNA clone libraries were mainly comprised of Euryarchaea-affiliated sequences; crenarchaeotal sequences were only found in deeper sediment layers with temperatures of ca. 70°C. In contrast to Hot Lake, Archaea dominated sediments at the much hotter site at Blackpoint. Here, novel methylated H-shaped archaeal tetraethers, with multiple sugars as head groups, were the most abundant membrane lipids. Reports on these lipids in cultures are very limited, but their abundant occurrence at elevated temperatures suggests an important role in membrane homeostastis in thermophilic Archaea. Stable carbon isotope values of -35‰ to

  16. Bacterial community dynamics over successional stages of Australian biological soil crusts

    Science.gov (United States)

    Chilton, Angela; Woodhouse, Jason; Neilan, Brett

    2015-04-01

    A key aspect for successful ecological rehabilitation is understanding the naturally occurring ecosystem and landscape function which is to be restored. This allows for recovery indicators to be identified and criteria to be developed to assess progress and outcomes. In arid rangelands, environmental stresses result in characteristically heterogeneous landscapes where biological soil crusts (BSCs) cover large expanses of inter-plant areas. Here, BSCs perform crucial roles in nutrient cycling and re-distribution, affect hydrological patterns and stabilise the soil surface. They also serve as a large reservoir of microbial and avascular plant biodiversity. The recognition of these important roles has resulted in increased global arid rehabilitation efforts employing BSCs. Within Australia, research has focused on the macro components of BSCs including lichens and mosses, however, there have been insufficient studies examining the BSC bacterial communities and their dynamics over different successional stages. This project surveyed the bacterial community of crust-free soil and three successional stages of undisturbed BSCs from New South Wales (NSW), Australia, in order to provide reference standards of naturally occurring Australian BSCs. Visual assessments were conducted and BSCs were categorised as Early, Mid or Late stage depending on colour, thickness, topography and presence of lichens and mosses. The crust-free soil and different stages were sampled within three 50 m2 plots of the same edaphic conditions near the town of Cobar, NSW. High throughput sequencing using the Illumina MiSeq platform was performed targeting the V2 region of the 16S rRNA gene. Preliminary analysis has revealed a clear distinction between the crust-free and crusted soil while Canonical Analysis of Principal Co-ordinates (CAP) suggests the presence of two distinct BSC microbial communities despite three stages being sampled. Across all sample types, the dominant phyla were Actinobacteria

  17. The model of fungal population dynamics affected by nystatin

    Science.gov (United States)

    Voychuk, Sergei I.; Gromozova, Elena N.; Sadovskiy, Mikhail G.

    Fungal diseases are acute problems of the up-to-day medicine. Significant increase of resistance of microorganisms to the medically used antibiotics and a lack of new effective drugs follows in a growth of dosage of existing chemicals to solve the problem. Quite often such approach results in side effects on humans. Detailed study of fungi-antibiotic dynamics can identify new mechanisms and bring new ideas to overcome the microbial resistance with a lower dosage of antibiotics. In this study, the dynamics of the microbial population under antibiotic treatment was investigated. The effects of nystatin on the population of Saccharomyces cerevisiae yeasts were used as a model system. Nystatin effects were investigated both in liquid and solid media by viability tests. Dependence of nystatin action on osmotic gradient was evaluated in NaCl solutions. Influences of glucose and yeast extract were additionally analyzed. A "stepwise" pattern of the cell death caused by nystatin was the most intriguing. This pattern manifested in periodical changes of the stages of cell death against stages of resistance to the antibiotic. The mathematical model was proposed to describe cell-antibiotic interactions and nystatin viability effects in the liquid medium. The model implies that antibiotic ability to cause a cells death is significantly affected by the intracellular compounds, which came out of cells after their osmotic barriers were damaged

  18. Representation of dynamical stimuli in populations of threshold neurons.

    Directory of Open Access Journals (Sweden)

    Tatjana Tchumatchenko

    2011-10-01

    Full Text Available Many sensory or cognitive events are associated with dynamic current modulations in cortical neurons. This raises an urgent demand for tractable model approaches addressing the merits and limits of potential encoding strategies. Yet, current theoretical approaches addressing the response to mean- and variance-encoded stimuli rarely provide complete response functions for both modes of encoding in the presence of correlated noise. Here, we investigate the neuronal population response to dynamical modifications of the mean or variance of the synaptic bombardment using an alternative threshold model framework. In the variance and mean channel, we provide explicit expressions for the linear and non-linear frequency response functions in the presence of correlated noise and use them to derive population rate response to step-like stimuli. For mean-encoded signals, we find that the complete response function depends only on the temporal width of the input correlation function, but not on other functional specifics. Furthermore, we show that both mean- and variance-encoded signals can relay high-frequency inputs, and in both schemes step-like changes can be detected instantaneously. Finally, we obtain the pairwise spike correlation function and the spike triggered average from the linear mean-evoked response function. These results provide a maximally tractable limiting case that complements and extends previous results obtained in the integrate and fire framework.

  19. Survival and Population Dynamics of the Marabou Stork in an Isolated Population, Swaziland

    Science.gov (United States)

    Monadjem, Ara; Kane, Adam; Botha, Andre; Dalton, Desire; Kotze, Antoinette

    2012-01-01

    Investigating the ecology of long lived birds is particularly challenging owing to the time scales involved. Here an analysis is presented of a long term study of the survival and population dynamics of the marabou stork (Leptoptilos crumeniferus), a wide ranging scavenging bird from Sub-Saharan Africa. Using resightings data of tagged nestlings and free flying birds we show that the stork population can be divided into three general life stages with unique survival probabilities and fecundities. Fecundity of the storks is inversely related to rainfall during their breeding season. Corroborative evidence for a metapopulation structure is discussed highlighting the impact of the Swaziland birds on the ecology of the species in the broader region. The importance of tag loss or illegibility over time is highlighted. Clearly, any attempt at conserving a species will require a detailed understanding of its population structure, of the sort examined here. PMID:23029517

  20. Bacterial Meningitis in Patients using Immunosuppressive Medication: a Population-based Prospective Nationwide Study.

    Science.gov (United States)

    van Veen, Kiril E B; Brouwer, Matthijs C; van der Ende, Arie; van de Beek, Diederik

    2017-06-01

    We studied occurrence, presentation, disease course, effect of adjunctive dexamethasone, and prognosis of bacterial meningitis in patients using immunosuppressive medication. Patients were selected from our nationwide, prospective cohort on community-acquired bacterial meningitis performed from March 1, 2006 through October 31, 2014. Eighty-seven of 1447 episodes (6 %) of bacterial meningitis occurred in patients using immunosuppressive medication, and consisted of corticosteroids in 82 %. Patients with bacterial meningitis using immunosuppressive medication were less likely to present with headache (P = 0.02) or neck stiffness (P = 0.005), as compared those not on immunosuppressive medication. In 46 % of episodes CSF leukocyte count was below 1000/mm 3 . CSF cultures revealed S. pneumoniae in 41 % and L. monocytogenes in 40 % of episodes. Outcome was unfavorable in 39 of 87 episodes (45 %) and death occurred in 22 of 87 episodes (25 %). Adjunctive dexamethasone was administered in 52 of 87 (60 %) episodes, and mortality tended to be lower in those on adjunctive dexamethasone therapy as compared to those without dexamethasone therapy (10 of 52 [19 %] vs 12 of 35 [34 %], P = 0.14). We conclude that bacterial meningitis in patients using immunosuppressive medication is likely to present with atypical clinical and laboratory features, and is often caused by atypical bacteria, mainly L. monocytogenes. Adjunctive dexamethasone is widely prescribed in these patients and was not associated with harm in this study.

  1. Plasmodium vivax Population Structure and Transmission Dynamics in Sabah Malaysia

    Science.gov (United States)

    Abdullah, Noor Rain; Barber, Bridget E.; William, Timothy; Norahmad, Nor Azrina; Satsu, Umi Rubiah; Muniandy, Prem Kumar; Ismail, Zakiah; Grigg, Matthew J.; Jelip, Jenarun; Piera, Kim; von Seidlein, Lorenz; Yeo, Tsin W.; Anstey, Nicholas M.; Price, Ric N.; Auburn, Sarah

    2013-01-01

    Despite significant progress in the control of malaria in Malaysia, the complex transmission dynamics of P. vivax continue to challenge national efforts to achieve elimination. To assess the impact of ongoing interventions on P. vivax transmission dynamics in Sabah, we genotyped 9 short tandem repeat markers in a total of 97 isolates (8 recurrences) from across Sabah, with a focus on two districts, Kota Marudu (KM, n = 24) and Kota Kinabalu (KK, n = 21), over a 2 year period. STRUCTURE analysis on the Sabah-wide dataset demonstrated multiple sub-populations. Significant differentiation (F ST  = 0.243) was observed between KM and KK, located just 130 Km apart. Consistent with low endemic transmission, infection complexity was modest in both KM (mean MOI  = 1.38) and KK (mean MOI  = 1.19). However, population diversity remained moderate (H E  = 0.583 in KM and H E  = 0.667 in KK). Temporal trends revealed clonal expansions reflecting epidemic transmission dynamics. The haplotypes of these isolates declined in frequency over time, but persisted at low frequency throughout the study duration. A diverse array of low frequency isolates were detected in both KM and KK, some likely reflecting remnants of previous expansions. In accordance with clonal expansions, high levels of Linkage Disequilibrium (I A S >0.5 [Ppopulation appears to have rendered this low endemic setting vulnerable to epidemic expansions. Migration may play an important role in the introduction of new parasite strains leading to epidemic expansions, with important implications for malaria elimination. PMID:24358203

  2. Hydrogeochemistry and coal-associated bacterial populations from a methanogenic coal bed

    Science.gov (United States)

    Barnhart, Elliott P.; Weeks, Edwin P.; Jones, Elizabeth J.P.; Ritter, Daniel J.; McIntosh, Jennifer C.; Clark, Arthur C.; Ruppert, Leslie F.; Cunningham, Alfred B.; Vinson, David S.; Orem, William H.; Fields, Matthew W.

    2016-01-01

    Biogenic coalbed methane (CBM), a microbially-generated source of natural gas trapped within coal beds, is an important energy resource in many countries. Specific bacterial populations and enzymes involved in coal degradation, the potential rate-limiting step of CBM formation, are relatively unknown. The U.S. Geological Survey (USGS) has established a field site, (Birney test site), in an undeveloped area of the Powder River Basin (PRB), with four wells completed in the Flowers-Goodale coal bed, one in the overlying sandstone formation, and four in overlying and underlying coal beds (Knoblach, Nance, and Terret). The nine wells were positioned to characterize the hydraulic conductivity of the Flowers-Goodale coal bed and were selectively cored to investigate the hydrogeochemistry and microbiology associated with CBM production at the Birney test site. Aquifer-test results indicated the Flowers-Goodale coal bed, in a zone from about 112 to 120 m below land surface at the test site, had very low hydraulic conductivity (0.005 m/d) compared to other PRB coal beds examined. Consistent with microbial methanogenesis, groundwater in the coal bed and overlying sandstone contain dissolved methane (46 mg/L average) with low δ13C values (−67‰ average), high alkalinity values (22 meq/kg average), relatively positive δ13C-DIC values (4‰ average), and no detectable higher chain hydrocarbons, NO3−, or SO42−. Bioassay methane production was greatest at the upper interface of the Flowers-Goodale coal bed near the overlying sandstone. Pyrotag analysis identified Aeribacillus as a dominant in situbacterial community member in the coal near the sandstone and statistical analysis indicated Actinobacteria predominated coal core samples compared to claystone or sandstone cores. These bacteria, which previously have been correlated with hydrocarbon-containing environments such as oil reservoirs, have demonstrated the ability to produce biosurfactants to break down

  3. Changes in the bacterial populations of the highly alkaline saline soil of the former lake Texcoco (Mexico) following flooding.

    Science.gov (United States)

    Valenzuela-Encinas, César; Neria-González, Isabel; Alcántara-Hernández, Rocio J; Estrada-Alvarado, Isabel; Zavala-Díaz de la Serna, Francisco Javier; Dendooven, Luc; Marsch, Rodolfo

    2009-07-01

    Flooding an extreme alkaline-saline soil decreased alkalinity and salinity, which will change the bacterial populations. Bacterial 16S rDNA libraries were generated of three soils with different electrolytic conductivity (EC), i.e. soil with EC 1.7 dS m(-1) and pH 7.80 (LOW soil), with EC 56 dS m(-1) and pH 10.11 (MEDIUM soil) and with EC 159 dS m(-1) and pH 10.02 (HIGH soil), using universal bacterial oligonucleotide primers, and 463 clone 16S rDNA sequences were analyzed phylogenetically. Library proportions and clone identification of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Cyanobacteria, Bacteroidetes, Firmicutes and Cloroflexi showed that the bacterial communities were different. Species and genera of the Rhizobiales, Rhodobacterales and Xanthomonadales orders of the alpha- and gamma-subdivision of Proteobacteria were found at the three sites. Species and genera of the Rhodospirillales, Sphingobacteriales, Clostridiales, Oscillatoriales and Caldilineales were found only in the HIGH soil, Sphingomonadales, Burkholderiales and Pseudomonadales in the MEDIUM soil, Myxococcales in the LOW soil, and Actinomycetales in the MEDIUM and LOW soils. It was found that the largest diversity at the order and species level was found in the MEDIUM soil as bacteria of both the HIGH and LOW soils were found in it.

  4. A dynamic regression analysis tool for quantitative assessment of bacterial growth written in Python.

    Science.gov (United States)

    Hoeflinger, Jennifer L; Hoeflinger, Daniel E; Miller, Michael J

    2017-01-01

    Herein, an open-source method to generate quantitative bacterial growth data from high-throughput microplate assays is described. The bacterial lag time, maximum specific growth rate, doubling time and delta OD are reported. Our method was validated by carbohydrate utilization of lactobacilli, and visual inspection revealed 94% of regressions were deemed excellent. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. DMPD: Cellular reprogramming by gram-positive bacterial components: a review. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 16885502 Cellular reprogramming by gram-positive bacterial components: a review. Bu...(.csml) Show Cellular reprogramming by gram-positive bacterial components: a review. PubmedID 16885502 Title Cellular reprogramming...ckley JM, Wang JH, Redmond HP. J Leukoc Biol. 2006 Oct;80(4):731-41. Epub 2006 Aug 2. (.png) (.svg) (.html)

  6. World Trade, disease and Florida's animal populations. The changing dynamics.

    Science.gov (United States)

    Coffman, L M

    2000-01-01

    One of Florida's three leading economic industries is agriculture. Agriculture feeds and enhances the lives of millions of people in Florida, the United States, and the entire world. Agriculture in Florida results in more than $6 billion in farm cash receipts, employment for more than 60,000 people a month, more than $18 billion in farm-related economic activity and stretches from the farm gate to the state's supermarkets with an impact of nearly $45 billion. The domestic and wild animal populations of Florida, our unique relationship to the Caribbean, Atlantic Ocean, Gulf of Mexico, Central and South America, as well as tourism, diverse human population growth and immigration, all add to the complexity of an environment capable of establishing many animals, animal pests and diseases not native to the United States. Never before have the dynamics of disease control involved as much challenge and diversity. Is the balance at risk, or is the risk over-balanced? Can science, economics and politics blend to maintain this balance? How will the balance affect world trade, disease control and the animal populations of Florida?

  7. Transmission dynamics of gram-negative bacterial pathogens in the anesthesia work area.

    Science.gov (United States)

    Loftus, Randy W; Brown, Jeremiah R; Patel, Hetal M; Koff, Matthew D; Jensen, Jens T; Reddy, Sundara; Ruoff, Kathryn L; Heard, Stephen O; Dodds, Thomas M; Beach, Michael L; Yeager, Mark P

    2015-04-01

    Gram-negative organisms are a major health care concern with increasing prevalence of infection and community spread. Our primary aim was to characterize the transmission dynamics of frequently encountered gram-negative bacteria in the anesthesia work area environment (AWE). Our secondary aim was to examine links between these transmission events and 30-day postoperative health care-associated infections (HCAIs). Gram-negative isolates obtained from the AWE (patient nasopharynx and axilla, anesthesia provider hands, and the adjustable pressure-limiting valve and agent dial of the anesthesia machine) at 3 major academic medical centers were identified as possible intraoperative bacterial transmission events by class of pathogen, temporal association, and phenotypic analysis (analytical profile indexing). The top 5 frequently encountered genera were subjected to antibiotic disk diffusion sensitivity to identify epidemiologically related transmission events. Complete multivariable logistic regression analysis and binomial tests of proportion were then used to examine the relative contributions of reservoirs of origin and within- and between-case modes of transmission, respectively, to epidemiologically related transmission events. Analyses were conducted with and without the inclusion of duplicate transmission events of the same genera occurring in a given study unit (first and second case of the day in each operating room observed) to examine the potential effect of statistical dependency. Transmitted isolates were compared by pulsed-field gel electrophoresis to disease-causing bacteria for 30-day postoperative HCAIs. The top 5 frequently encountered gram-negative genera included Acinetobacter, Pseudomonas, Brevundimonas, Enterobacter, and Moraxella that together accounted for 81% (767/945) of possible transmission events. For all isolates, 22% (167/767) of possible transmission events were identified by antibiotic susceptibility patterns as epidemiologically related

  8. Subversion of actin dynamics by EspM effectors of attaching and effacing bacterial pathogens.

    Science.gov (United States)

    Arbeloa, Ana; Bulgin, Richard R; MacKenzie, Georgina; Shaw, Robert K; Pallen, Mark J; Crepin, Valerie F; Berger, Cedric N; Frankel, Gad

    2008-07-01

    Rho GTPases are common targets of bacterial toxins and type III secretion system effectors. IpgB1 and IpgB2 of Shigella and Map of enteropathogenic (EPEC) and enterohemorrhagic (EHEC) Escherichia coli were recently grouped together on the basis that they share a conserved WxxxE motif. In this study, we characterized six WxxxE effectors from attaching and effacing pathogens: TrcA and EspM1 of EPEC strain B171, EspM1 and EspM2 of EHEC strain Sakai and EspM2 and EspM3 of Citrobacter rodentium. We show that EspM2 triggers formation of global parallel stress fibres, TrcA and EspM1 induce formation of localized parallel stress fibres and EspM3 triggers formation of localized radial stress fibres. Using EspM2 and EspM3 as model effectors, we report that while substituting the conserved Trp with Ala abolished activity, conservative Trp to Tyr or Glu to Asp substitutions did not affect stress-fibre formation. We show, using dominant negative constructs and chemical inhibitors, that the activity of EspM2 and EspM3 is RhoA and ROCK-dependent. Using Rhotekin pull-downs, we have shown that EspM2 and EspM3 activate RhoA; translocation of EspM2 and EspM3 triggered phosphorylation of cofilin. These results suggest that the EspM effectors modulate actin dynamics by activating the RhoA signalling pathway.

  9. Bacterial meningitis in hematopoietic stem cell transplant recipients: a population-based prospective study

    NARCIS (Netherlands)

    van Veen, K. E. B.; Brouwer, M. C.; van der Ende, A.; van de Beek, D.

    2016-01-01

    We performed a nationwide prospective cohort study on the epidemiology and clinical features of community-acquired bacterial meningitis. Patients with a medical history of autologous or allogeneic hematopoietic stem cell transplantation (HSCT) were identified from the cohort performed from March

  10. Selection of bacterial populations in the mycosphere of Laccaria proxima : is type III secretion involved?

    NARCIS (Netherlands)

    Warmink, Jan Aaldrik; van Elsas, Jan Dirk

    The bacterial communities in the Laccaria proxima mycosphere (soil from beneath fruiting bodies) and the corresponding bulk soil were compared by cultivation-dependent and cultivation-independent methods. To assess the distribution of type III secretion systems (TTSS), a PCR-based system for the

  11. Characterization of Bacterial and Fungal Community Dynamics by High-Throughput Sequencing (HTS) Metabarcoding during Flax Dew-Retting.

    Science.gov (United States)

    Djemiel, Christophe; Grec, Sébastien; Hawkins, Simon

    2017-01-01

    Flax dew-retting is a key step in the industrial extraction of fibers from flax stems and is dependent upon the production of a battery of hydrolytic enzymes produced by micro-organisms during this process. To explore the diversity and dynamics of bacterial and fungal communities involved in this process we applied a high-throughput sequencing (HTS) DNA metabarcoding approach (16S rRNA/ITS region, Illumina Miseq) on plant and soil samples obtained over a period of 7 weeks in July and August 2014. Twenty-three bacterial and six fungal phyla were identified in soil samples and 11 bacterial and four fungal phyla in plant samples. Dominant phyla were Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes (bacteria) and Ascomycota, Basidiomycota, and Zygomycota (fungi) all of which have been previously associated with flax dew-retting except for Bacteroidetes and Basidiomycota that were identified for the first time. Rare phyla also identified for the first time in this process included Acidobacteria, CKC4, Chlorobi, Fibrobacteres, Gemmatimonadetes, Nitrospirae and TM6 (bacteria), and Chytridiomycota (fungi). No differences in microbial communities and colonization dynamics were observed between early and standard flax harvests. In contrast, the common agricultural practice of swath turning affects both bacterial and fungal community membership and structure in straw samples and may contribute to a more uniform retting. Prediction of community function using PICRUSt indicated the presence of a large collection of potential bacterial enzymes capable of hydrolyzing backbones and side-chains of cell wall polysaccharides. Assignment of functional guild (functional group) using FUNGuild software highlighted a change from parasitic to saprophytic trophic modes in fungi during retting. This work provides the first exhaustive description of the microbial communities involved in flax dew-retting and will provide a valuable benchmark in future studies aiming to evaluate

  12. Characterization of Bacterial and Fungal Community Dynamics by High-Throughput Sequencing (HTS Metabarcoding during Flax Dew-Retting

    Directory of Open Access Journals (Sweden)

    Christophe Djemiel

    2017-10-01

    Full Text Available Flax dew-retting is a key step in the industrial extraction of fibers from flax stems and is dependent upon the production of a battery of hydrolytic enzymes produced by micro-organisms during this process. To explore the diversity and dynamics of bacterial and fungal communities involved in this process we applied a high-throughput sequencing (HTS DNA metabarcoding approach (16S rRNA/ITS region, Illumina Miseq on plant and soil samples obtained over a period of 7 weeks in July and August 2014. Twenty-three bacterial and six fungal phyla were identified in soil samples and 11 bacterial and four fungal phyla in plant samples. Dominant phyla were Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes (bacteria and Ascomycota, Basidiomycota, and Zygomycota (fungi all of which have been previously associated with flax dew-retting except for Bacteroidetes and Basidiomycota that were identified for the first time. Rare phyla also identified for the first time in this process included Acidobacteria, CKC4, Chlorobi, Fibrobacteres, Gemmatimonadetes, Nitrospirae and TM6 (bacteria, and Chytridiomycota (fungi. No differences in microbial communities and colonization dynamics were observed between early and standard flax harvests. In contrast, the common agricultural practice of swath turning affects both bacterial and fungal community membership and structure in straw samples and may contribute to a more uniform retting. Prediction of community function using PICRUSt indicated the presence of a large collection of potential bacterial enzymes capable of hydrolyzing backbones and side-chains of cell wall polysaccharides. Assignment of functional guild (functional group using FUNGuild software highlighted a change from parasitic to saprophytic trophic modes in fungi during retting. This work provides the first exhaustive description of the microbial communities involved in flax dew-retting and will provide a valuable benchmark in future studies aiming

  13. Microbial population dynamics in continuous anaerobic digester systems during start up, stable conditions and recovery after starvation.

    Science.gov (United States)

    de Jonge, Nadieh; Moset, Veronica; Møller, Henrik Bjarne; Nielsen, Jeppe Lund

    2017-05-01

    The evolution and population dynamics of complex anaerobic microbial communities in anaerobic digesters were investigated during stable operation and recovery after prolonged starvation. Three thermophilic reactor systems fed with cattle manure were operated continuously in parallel for 167days. Significant changes in the microbial communities were observed for both the bacterial and archaeal populations as the reactor systems were subjected to changing feeding regimes. The ecosystems developed from being relatively similar in structure to more specialised communities, with large population shifts within the acetogenic and methanogenic communities, which appeared to shift towards the hydrogenotrophic methanogenesis pathway. All reactor systems showed signs of adaptation to a harsher environment under high VFA, H 2 S and ammonia concentrations, but remained at a lower degree of stability after 45days of recovery compared to stable period of operation before starvation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Isolation, Characterization and Application of Bacterial Population From Agricultural Soil at Sohag Province, Egypt

    Directory of Open Access Journals (Sweden)

    Bahig, A. E.

    2008-01-01

    Full Text Available Forty soil samples of agriculture soil were collected from two different sites in Sohag province, Egypt, during hot and cold seasons. Twenty samples were from soil irrigated with canal water (site A and twenty samples were from soil irrigated with wastewater (site B. This study aimed to compare the incidence of plasmids in bacteria isolated from soil and to investigate the occurrence of metal and antibiotic resistance bacteria, and consequently to select the potential application of these bacteria in bioremediation. The total bacterial count (CFU/gm in site (B was higher than that in site (A. Moreover, the CFU values in summer were higher than those values in winter at both sites. A total of 771 bacterial isolates were characterized as Bacillus, Micrococcus, Staphylococcus, Pseudomonas, Eschershia, Shigella, Xanthomonas, Acetobacter, Citrobacter, Enterobacter, Moraxella and Methylococcus. Minimum inhibitory concentrations (MICs of Pb+2, Cu+2, Zn+2, Hg+2, Co+2, Cd+2, Cr+3, Te+2, As+2 and Ni+2 for plasmid-possessed bacteria were determined and the highest MICs were 1200 µg/mL for lead, 800 µg/mL for both Cobalt and Arsenate, 1200 µg/mL for Nickel, 1000 µg/ml for Copper and less than 600 µg/mL for other metals. Bacterial isolates from both sites A and B showed multiple heavy metal resistance. A total of 337 bacterial isolates contained plasmids and the incidence of plasmids was approximately 25-50% higher in bacteria isolated from site (B than that from site (A. These isolates were resistance to different antibiotics. Approximately, 61% of the bacterial isolates were able to assimilate insecticide, carbaryl, as a sole source of carbon and energy. However, the Citrobacter AA101 showed the best growth on carbaryl.

  15. Effect of phosphate-solubilizing bacteria on phosphorus dynamics and the bacterial community during composting of sugarcane industry waste.

    Science.gov (United States)

    Estrada-Bonilla, German A; Lopes, Cintia M; Durrer, Ademir; Alves, Paulo R L; Passaglia, Nicolle; Cardoso, Elke J B N

    2017-07-01

    Sugarcane processing generates a large quantity of residues, such as filter cake and ashes, which are sometimes composted prior to their amendment in soil. However, important issues still have to be addressed on this subject, such as the description of bacterial succession that occurs throughout the composting process and the possibilities of using phosphate-solubilizing bacteria (PSB) during the process to improve phosphorus (P) availability in the compost end product. Consequently, this study evaluated the bacterial diversity and P dynamics during the composting process when inoculated with Pseudomonas aeruginosa PSBR12 and Bacillus sp. BACBR01. To characterize the bacterial community structure during composting, and to compare PSB-inoculated compost with non-inoculated compost, partial sequencing of the bacterial 16S rRNA gene and sequential P fractionation were used. The data indicated that members of the order Lactobacillales prevailed in the early stages of composting for up to 30 days, mostly due to initial changes in pH and the C/N ratio. This dominant bacterial group was then slowly replaced by Bacillales during a composting process of up to 60 days. In addition, inoculation of PSB reduced the levels of Ca-bound P by 21% and increased the labile organic P fraction. In PSB-inoculated compost, Ca-P compound solubilization occurred concomitantly with an increase of the genus Bacillus. The bacterial succession and the final community is described in compost from sugarcane residues and the possible use of these inoculants to improve P availability in the final compost is validated. Copyright © 2017 Elsevier GmbH. All rights reserved.

  16. Artificial bee colony algorithm with dynamic multi-population

    Science.gov (United States)

    Zhang, Ming; Ji, Zhicheng; Wang, Yan

    2017-07-01

    To improve the convergence rate and make a balance between the global search and local turning abilities, this paper proposes a decentralized form of artificial bee colony (ABC) algorithm with dynamic multi-populations by means of fuzzy C-means (FCM) clustering. Each subpopulation periodically enlarges with the same size during the search process, and the overlapping individuals among different subareas work for delivering information acting as exploring the search space with diffusion of solutions. Moreover, a Gaussian-based search equation with redefined local attractor is proposed to further accelerate the diffusion of the best solution and guide the search towards potential areas. Experimental results on a set of benchmarks demonstrate the competitive performance of our proposed approach.

  17. Mean-field games with logistic population dynamics

    KAUST Repository

    Gomes, Diogo A.

    2013-12-01

    In its standard form, a mean-field game can be defined by coupled system of equations, a Hamilton-Jacobi equation for the value function of agents and a Fokker-Planck equation for the density of agents. Traditionally, the latter equation is adjoint to the linearization of the former. Since the Fokker-Planck equation models a population dynamic, we introduce natural features such as seeding and birth, and nonlinear death rates. In this paper we analyze a stationary meanfield game in one dimension, illustrating various techniques to obtain regularity of solutions in this class of systems. In particular we consider a logistic-type model for birth and death of the agents which is natural in problems where crowding affects the death rate of the agents. The introduction of these new terms requires a number of new ideas to obtain wellposedness. In a forthcoming publication we will address higher dimensional models. ©2013 IEEE.

  18. Dynamical criticality in the collective activity of a neural population

    Science.gov (United States)

    Mora, Thierry

    The past decade has seen a wealth of physiological data suggesting that neural networks may behave like critical branching processes. Concurrently, the collective activity of neurons has been studied using explicit mappings to classic statistical mechanics models such as disordered Ising models, allowing for the study of their thermodynamics, but these efforts have ignored the dynamical nature of neural activity. I will show how to reconcile these two approaches by learning effective statistical mechanics models of the full history of the collective activity of a neuron population directly from physiological data, treating time as an additional dimension. Applying this technique to multi-electrode recordings from retinal ganglion cells, and studying the thermodynamics of the inferred model, reveals a peak in specific heat reminiscent of a second-order phase transition.

  19. On signals of phase transitions in salmon population dynamics

    Science.gov (United States)

    Krkošek, Martin; Drake, John M.

    2014-01-01

    Critical slowing down (CSD) reflects the decline in resilience of equilibria near a bifurcation and may reveal early warning signals (EWS) of ecological phase transitions. We studied CSD in the recruitment dynamics of 120 stocks of three Pacific salmon (Oncorhynchus spp.) species in relation to critical transitions in fishery models. Pink salmon (Oncorhynchus gorbuscha) exhibited increased variability and autocorrelation in populations that had a growth parameter, r, close to zero, consistent with EWS of extinction. However, models and data for sockeye salmon (Oncorhynchus nerka) indicate that portfolio effects from heterogeneity in age-at-maturity may obscure EWS. Chum salmon (Oncorhynchus keta) show intermediate results. The data do not reveal EWS of Ricker-type bifurcations that cause oscillations and chaos at high r. These results not only provide empirical support for CSD in some ecological systems, but also indicate that portfolio effects of age structure may conceal EWS of some critical transitions. PMID:24759855

  20. On the stochastic approach to marine population dynamics

    Directory of Open Access Journals (Sweden)

    Eduardo Ferrandis

    2007-03-01

    Full Text Available The purpose of this article is to deepen and structure the statistical basis of marine population dynamics. The starting point is the correspondence between the concepts of mortality, survival and lifetime distribution. This is the kernel of the possibilities that survival analysis techniques offer to marine population dynamics. A rigorous definition of survival and mortality based on their properties and their probabilistic versions is briefly presented. Some well established models for lifetime distribution, which generalise the usual simple exponential distribution, might be used with their corresponding survivals and mortalities. A critical review of some published models is also made, including original models proposed in the way opened by Caddy (1991 and Sparholt (1990, which allow for a continuously decreasing natural mortality. Considering these elements, the pure death process dealt with in the literature is used as a theoretical basis for the evolution of a marine cohort. The elaboration of this process is based on Chiang´s study of the probability distribution of the life table (Chiang, 1960 and provides specific structured models for stock evolution as a Markovian process. These models may introduce new ideas in the line of thinking developed by Gudmundsson (1987 and Sampson (1990 in order to model the evolution of a marine cohort by stochastic processes. The suitable approximation of these processes by means of Gaussian processes may allow theoretical and computational multivariate Gaussian analysis to be applied to the probabilistic treatment of fisheries issues. As a consequence, the necessary catch equation appears as a stochastic integral with respect to the mentioned Markovian process of the stock. The solution of this equation is available when the mortalities are proportional, hence the use of the proportional hazards model (Cox, 1959. The assumption of these proportional mortalities leads naturally to the construction of a

  1. Evolutionary game dynamics in a growing structured population

    International Nuclear Information System (INIS)

    Poncela, Julia; Gomez-Gardenes, Jesus; Moreno, Yamir; Traulsen, Arne

    2009-01-01

    We discuss a model for evolutionary game dynamics in a growing, network-structured population. In our model, new players can either make connections to random preexisting players or preferentially attach to those that have been successful in the past. The latter depends on the dynamics of strategies in the game, which we implement following the so-called Fermi rule such that the limits of weak and strong strategy selection can be explored. Our framework allows to address general evolutionary games. With only two parameters describing the preferential attachment and the intensity of selection, we describe a wide range of network structures and evolutionary scenarios. Our results show that even for moderate payoff preferential attachment, over represented hubs arise. Interestingly, we find that while the networks are growing, high levels of cooperation are attained, but the same network structure does not promote cooperation as a static network. Therefore, the mechanism of payoff preferential attachment is different to those usually invoked to explain the promotion of cooperation in static, already-grown networks.

  2. Sonoluminescence and dynamics of cavitation bubble populations in sulfuric acid.

    Science.gov (United States)

    Thiemann, Andrea; Holsteyns, Frank; Cairós, Carlos; Mettin, Robert

    2017-01-01

    The detailed link of liquid phase sonochemical reactions and bubble dynamics is still not sufficiently known. To further clarify this issue, we image sonoluminescence and bubble oscillations, translations, and shapes in an acoustic cavitation setup at 23kHz in sulfuric acid with dissolved sodium sulfate and xenon gas saturation. The colour of sonoluminescence varies in a way that emissions from excited non-volatile sodium atoms are prominently observed far from the acoustic horn emitter ("red region"), while such emissions are nearly absent close to the horn tip ("blue region"). High-speed images reveal the dynamics of distinct bubble populations that can partly be linked to the different emission regions. In particular, we see smaller strongly collapsing spherical bubbles within the blue region, while larger bubbles with a liquid jet during collapse dominate the red region. The jetting is induced by the fast bubble translation, which is a consequence of acoustic (Bjerknes) forces in the ultrasonic field. Numerical simulations with a spherical single bubble model reproduce quantitatively the volume oscillations and fast translation of the sodium emitting bubbles. Additionally, their intermittent stopping is explained by multistability in a hysteretic parameter range. The findings confirm the assumption that bubble deformations are responsible for pronounced sodium sonoluminescence. Notably the observed translation induced jetting appears to serve as efficient mixing mechanism of liquid into the heated gas phase of collapsing bubbles, thus potentially promoting liquid phase sonochemistry in general. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Dynamical evolution of a fictitious population of binary Neptune Trojans

    Science.gov (United States)

    Brunini, Adrián

    2018-03-01

    We present numerical simulations of the evolution of a synthetic population of Binary Neptune Trojans, under the influence of the solar perturbations and tidal friction (the so-called Kozai cycles and tidal friction evolution). Our model includes the dynamical influence of the four giant planets on the heliocentric orbit of the binary centre of mass. In this paper, we explore the evolution of initially tight binaries around the Neptune L4 Lagrange point. We found that the variation of the heliocentric orbital elements due to the libration around the Lagrange point introduces significant changes in the orbital evolution of the binaries. Collisional processes would not play a significant role in the dynamical evolution of Neptune Trojans. After 4.5 × 109 yr of evolution, ˜50 per cent of the synthetic systems end up separated as single objects, most of them with slow diurnal rotation rate. The final orbital distribution of the surviving binary systems is statistically similar to the one found for Kuiper Belt Binaries when collisional evolution is not included in the model. Systems composed by a primary and a small satellite are more fragile than the ones composed by components of similar sizes.

  4. Replication, Communication, and the Population Dynamics of Scientific Discovery.

    Science.gov (United States)

    McElreath, Richard; Smaldino, Paul E

    2015-01-01

    Many published research results are false (Ioannidis, 2005), and controversy continues over the roles of replication and publication policy in improving the reliability of research. Addressing these problems is frustrated by the lack of a formal framework that jointly represents hypothesis formation, replication, publication bias, and variation in research quality. We develop a mathematical model of scientific discovery that combines all of these elements. This model provides both a dynamic model of research as well as a formal framework for reasoning about the normative structure of science. We show that replication may serve as a ratchet that gradually separates true hypotheses from false, but the same factors that make initial findings unreliable also make replications unreliable. The most important factors in improving the reliability of research are the rate of false positives and the base rate of true hypotheses, and we offer suggestions for addressing each. Our results also bring clarity to verbal debates about the communication of research. Surprisingly, publication bias is not always an obstacle, but instead may have positive impacts-suppression of negative novel findings is often beneficial. We also find that communication of negative replications may aid true discovery even when attempts to replicate have diminished power. The model speaks constructively to ongoing debates about the design and conduct of science, focusing analysis and discussion on precise, internally consistent models, as well as highlighting the importance of population dynamics.

  5. Effects of Exogenous Yeast and Bacteria on the Microbial Population Dynamics and Outcomes of Olive Fermentations.

    Science.gov (United States)

    Zaragoza, Jose; Bendiks, Zachary; Tyler, Charlotte; Kable, Mary E; Williams, Thomas R; Luchkovska, Yelizaveta; Chow, Elaine; Boundy-Mills, Kyria; Marco, Maria L

    2017-01-01

    In this study, we examined Sicilian-style green olive fermentations upon the addition of Saccharomyces cerevisiae UCDFST 09-448 and/or Pichia kudriazevii UCDFST09-427 or the lactic acid bacteria (LAB) Lactobacillus plantarum AJ11R and Leuconostoc pseudomesenteroides BGM3R. Olives containing S. cerevisiae UCDFST 09-448, a strain able to hydrolyze pectin, but not P. kudriazevii UCDFST 09-427, a nonpectinolytic strain, exhibited excessive tissue damage within 4 weeks. DNA sequencing of fungal internal transcribed spacer (ITS) regions and comparisons to a yeast-specific ITS sequence database remarkably showed that neither S. cerevisiae UCDFST 09-448 nor P. kudriazevii UCDFST 09-427 resulted in significant changes to yeast species diversity. Instead, Candida boidinii constituted the majority (>90%) of the total yeast present, independent of whether S. cerevisiae or P. kudriazevii was added. By comparison, Lactobacillus species were enriched in olives inoculated with potential starter LAB L. plantarum AJ11R and L. pseudomesenteroides BGM3R according to community 16S rRNA gene sequence analysis. The bacterial diversity of those olives was significantly reduced and resembled control fermentations incubated for a longer period of time. Importantly, microbial populations were highly dynamic at the strain level, as indicated by the large variations in AJ11R and BGM3R cell numbers over time and reductions in the numbers of yeast isolates expressing polygalacturonase activity. These findings show the distinct effects of exogenous spoilage and starter microbes on indigenous communities in plant-based food fermentations that result in very different impacts on product quality. IMPORTANCE Food fermentations are subject to tremendous selective pressures resulting in the growth and persistence of a limited number of bacterial and fungal taxa. Although these foods are vulnerable to spoilage by unintended contamination of certain microorganisms, or alternatively, can be

  6. Bacterial community dynamics during cold storage of minced meat packaged under modified atmosphere and supplemented with different preservatives.

    Science.gov (United States)

    Stoops, J; Ruyters, S; Busschaert, P; Spaepen, R; Verreth, C; Claes, J; Lievens, B; Van Campenhout, L

    2015-06-01

    Since minced meat is very susceptible for microbial growth, characterisation of the bacterial community dynamics during storage is important to optimise preservation strategies. The purpose of this study was to investigate the effect of different production batches and the use of different preservatives on the composition of the bacterial community in minced meat during 9 days of cold storage under modified atmosphere (66% O2, 25% CO2 and 9% N2). To this end, both culture-dependent (viable aerobic and anaerobic counts) and culture-independent (454 pyrosequencing) analyses were performed. Initially, microbial counts of fresh minced meat showed microbial loads between 3.5 and 5.0 log cfu/g. The observed microbial diversity was relatively high, and the most abundant bacteria differed among the samples. During storage an increase of microbial counts coincided with a dramatic decrease in bacterial diversity. At the end of the storage period, most samples showed microbial counts above the spoilage level of 7 log cfu/g. A relatively similar bacterial community was obtained regardless of the manufacturing batch and the preservative used, with Lactobacillus algidus and Leuconostoc sp. as the most dominant microorganisms. This suggests that both bacteria played an important role in the spoilage of minced meat packaged under modified atmosphere. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Programming microbial population dynamics by engineered cell-cell communication.

    Science.gov (United States)

    Song, Hao; Payne, Stephen; Tan, Cheemeng; You, Lingchong

    2011-07-01

    A major aim of synthetic biology is to program novel cellular behavior using engineered gene circuits. Early endeavors focused on building simple circuits that fulfill simple functions, such as logic gates, bistable toggle switches, and oscillators. These gene circuits have primarily focused on single-cell behaviors since they operate intracellularly. Thus, they are often susceptible to cell-cell variations due to stochastic gene expression. Cell-cell communication offers an efficient strategy to coordinate cellular behavior at the population level. To this end, we review recent advances in engineering cell-cell communication to achieve reliable population dynamics, spanning from communication within single species to multispecies, from one-way sender-receiver communication to two-way communication in synthetic microbial ecosystems. These engineered systems serve as well-defined model systems to better understand design principles of their naturally occurring counterparts and to facilitate novel biotechnology applications. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Effects of constant immigration on the dynamics and persistence of stable and unstable Drosophila populations

    Science.gov (United States)

    Dey, Snigdhadip; Joshi, Amitabh

    2013-01-01

    Constant immigration can stabilize population size fluctuations but its effects on extinction remain unexplored. We show that constant immigration significantly reduced extinction in fruitfly populations with relatively stable or unstable dynamics. In unstable populations with oscillations of amplitude around 1.5 times the mean population size, persistence and constancy were unrelated. Low immigration enhanced persistence without affecting constancy whereas high immigration increased constancy without enhancing persistence. In relatively stable populations with erratic fluctuations of amplitude close to the mean population size, both low and high immigration enhanced persistence. In these populations, the amplitude of fluctuations relative to mean population size went down due to immigration, and their dynamics were altered to low-period cycles. The effects of immigration on the population size distribution and intrinsic dynamics of stable versus unstable populations differed considerably, suggesting that the mechanisms by which immigration reduced extinction risk depended on underlying dynamics in complex ways. PMID:23470546

  9. Molecular characterization of bacterial populations of different soils Caracterização molecular de populações bacterianas de diferentes solos

    Directory of Open Access Journals (Sweden)

    Rodrigo Matheus Pereira

    2006-12-01

    Full Text Available Until recently, few studies were carried out in Brazil about diversity of bacterial soil communities. Aiming to characterize the bacterial population in the soil through 16S rRNA analysis, two types of soil have been analyzed: one of them characterized by intensive use where tomato, beans and corn were cultivated (CS; the other analyzed soil was under forest (FS, unchanged by man; both located in Guaíra, São Paulo State, Brazil. Using specific primers, 16S rRNA genes from metagenomic DNA in both soils were amplified by PCR, amplicons were cloned and 139 clones from two libraries were partially sequenced. The use of 16S rRNA analysis allowed identification of several bacterial populations in the soil belonging to the following phyla: Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria Verrucomicrobia in addition to the others that were not classified, beyond Archaea domain. Differences between FS and CS libraries were observed in size phyla. A larger number of phyla and, consequently, a greater bacterial diversity were found in the under-forest soil. These data were confirmed by the analyses of genetic diversity that have been carried out. The characterization of bacterial communities of soil has made its contribution by providing facts for further studies on the dynamics of bacterial populations in different soil conditions in Brazil.Até o momento poucos estudos foram realizados no Brasil a respeito da diversidade de comunidades bacterianas no solo. Com o objetivo de caracterizar as populações bacterianas presentes no solo através da análise do gene 16S rRNA, foram analisados dois solos: um caracterizado pelo uso intensivo, principalmente para a produção de tomate, feijão e milho (CS; e outro sob floresta (FS, não modificado pelo homem, ambos do município de Guaíra, no estado de São Paulo, Brasil. Usando oligonucleotídeos específicos, de genes 16S rRNA do DNA metagenomico de ambos os solos foram amplificados

  10. Population dynamics of caribou herds in southwestern Alaska

    Directory of Open Access Journals (Sweden)

    Patrick Valkenburg

    2003-04-01

    Full Text Available The five naturally occurring and one transplanted caribou (Rangifer tarandus granti herd in southwestern Alaska composed about 20% of Alaska's caribou population in 2001. All five of the naturally occurring herds fluctuated considerably in size between the late 1800s and 2001 and for some herds the data provide an indication of long-term periodic (40-50 year fluctuations. At the present time, the Unimak (UCH and Southern Alaska Peninsula (SAP are recovering from population declines, the Northern Alaska Peninsula Herd (NAP appears to be nearing the end of a protracted decline, and the Mulchatna Herd (MCH appears to now be declining after 20 years of rapid growth. The remaining naturally occurring herd (Kilbuck has virtually disappeared. Nutrition had a significant effect on the size of 4-month-old and 10-month-old calves in the NAP and the Nushagak Peninsula Herd (NPCH and probably also on population growth in at least 4 (SAP, NAP, NPCH, and MCH of the six caribou herds in southwestern Alaska. Predation does not appear to be sufficient to keep caribou herds in southwestern Alaska from expanding, probably because rabies is endemic in red foxes (Vulpes vulpes and is periodically transferred to wolves (Canis lupus and other canids. However, we found evidence that pneumonia and hoof rot may result in significant mortality of caribou in southwestern Alaska, whereas there is no evidence that disease is important in the dynamics of Interior herds. Cooperative conservation programs, such as the Kilbuck Caribou Management Plan, can be successful in restraining traditional harvest and promoting growth in caribou herds. In southwestern Alaska we also found evidence that small caribou herds can be swamped and assimilated by large herds, and fidelity to traditional calving areas can be lost.

  11. Bacterial meningitis in alcoholic patients: A population-based prospective study.

    Science.gov (United States)

    van Veen, Kiril E B; Brouwer, Matthijs C; van der Ende, Arie; van de Beek, Diederik

    2017-04-01

    To study clinical features and outcome of community-acquired bacterial meningitis in alcoholic patients. Patients with a history of alcoholism were selected from our nationwide, prospective cohort on community-acquired bacterial meningitis performed from March 2006 to October 2014. Data on patient history, symptoms and signs on admission, treatment, and outcome were prospectively collected. Of 1359 included episodes, 88 episodes (6%) occurred in 88 alcoholic patients. Seizures as presenting symptom were present in 18% alcoholic patients, and 23% presented with co-existing pneumonia. Causative organisms were Streptococcus pneumoniae in 76%, Listeria monocytogenes in 8%, and Neisseria meningitidis in 6% of patients. A high rate of systemic complications occurred with respiratory failure in 40% and endocarditis in 9% of patients. Outcome was unfavorable in 58% of alcoholic patients, and 25% died. Alcoholism was associated with unfavorable outcome in a multivariate analysis (OR 1.96; 95% CI 1.12-3.46; P = 0.019), but not with death (OR 0.76; 95% CI 0.35-1.68; P = 0.762). Alcoholic bacterial meningitis patients often have an unfavorable outcome, which appears to result from a high rate of systemic complications, mainly respiratory failure. Seizures are common in alcoholic patients and warrant caution of development of an alcohol withdrawal syndrome. Copyright © 2017. Published by Elsevier Ltd.

  12. A new method for determining the metabolic activity of specific bacterial populations in soil using tritiated leucine and immunomagnetic separation

    DEFF Research Database (Denmark)

    Sengeløv, Gitte; Sørensen, Søren Johannes; Frette, Lone

    2000-01-01

    A new assay, using immunomagnetic separation and uptake of tritiated leucine ([3H]-Leu), was developed for measuring the in situ metabolic activity of specific bacterial populations in soil. Such assays are needed to assess the role individual species play in diverse microbial soil communities...... reduced this unspecific binding, resulting in metabolic activity of the target cells. As expected, a linear relationship...... between activity and temperature was observed, demonstrating the sensitivity of the assay. The method was applied to compare activities of the target strain in bulk soil and in the rhizosphere of barley. Contrary to what was anticipated, no significant difference in metabolic activity was observed....

  13. Phase control of light amplification with dynamically irreversible pathways of population transfer in a Λ system

    International Nuclear Information System (INIS)

    Yuan Shi; Wu Jinhui; Gao Jinyue; Pan Chunliu

    2002-01-01

    We use the relative phase of two coherent fields for the control of light amplification with dynamically irreversible pathways of population transfer in a Λ system. The population inversion and gain with dynamically irreversible pathways of population transfer are shown as the relative phase is varied. We support our results by numerical calculation and analytical explanation

  14. Exploring the links between population dynamics of total and active bacteria and the variables influencing a full-scale membrane bioreactor (MBR).

    Science.gov (United States)

    Gómez-Silván, C; Arévalo, J; González-López, J; Rodelas, B

    2014-06-01

    Long-term dynamics of total and active bacterial populations in a full-scale membrane bioreactor (MBR) treating urban wastewater were monitored during nine months by temperature-gradient gel electrophoresis (TGGE) of partial 16S-rRNA genes, amplified from community DNA and RNA templates. The bacterial community, dominated by Alphaproteobacteria, displayed the required characteristics for a successful and steady contaminant removal under real operating conditions. The evolution of population dynamics showed that a fully-stable microbial community was not developed even after technical stabilization and steady performance of the MBR were achieved. Non-metric multidimensional scaling and BIO-ENV demonstrated that the trends of the populations were often mostly explained by temperature, followed by the concentration of volatile suspended solids and C/N ratio of the influent. These variables were mainly responsible for triggering the shifts between functionally redundant populations. These conclusions contribute to the prediction of the complex profiles of adaptation and response of bacterial populations under changing conditions. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Target-directed Dynamic Combinatorial Chemistry: A Study on Potentials and Pitfalls as Exemplified on a Bacterial Target.

    Science.gov (United States)

    Frei, Priska; Pang, Lijuan; Silbermann, Marleen; Eriş, Deniz; Mühlethaler, Tobias; Schwardt, Oliver; Ernst, Beat

    2017-08-25

    Target-directed dynamic combinatorial chemistry (DCC) is an emerging technique for the efficient identification of inhibitors of pharmacologically relevant targets. In this contribution, we present an application for a bacterial target, the lectin FimH, a crucial virulence factor of uropathogenic E. coli being the main cause of urinary tract infections. A small dynamic library of acylhydrazones was formed from aldehydes and hydrazides and equilibrated at neutral pH in presence of aniline as nucleophilic catalyst. The major success factors turned out to be an accordingly adjusted ratio of scaffolds and fragments, an adequate sample preparation prior to HPLC analysis, and the data processing. Only then did the ranking of the dynamic library constituents correlate well with affinity data. Furthermore, as a support of DCC applications especially to larger libraries, a new protocol for improved hit identification was established. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Usefulness of inflammatory biomarkers in discriminating between bacterial and aseptic meningitis in hospitalized children from a population with low vaccination coverage

    Science.gov (United States)

    Wysocki, Jacek; Avonts, Dirk; Januszkiewicz-Lewandowska, Danuta; Michalak, Michal

    2016-01-01

    Introduction Neisseria meningitidis and Streptococcus pneumoniae are the most frequent pathogens responsible for meningitis beyond the neonatal period. Aseptic meningitis is a disabling condition, but bacterial meningitis if left untreated is 100% fatal. The aim of the study was to analyze the usefulness of biochemical and hematological parameters in distinguishing between bacterial and non-bacterial meningitis in children with meningitis from a population with low rates of vaccination against S. pneumoniae and N. meningitidis. Material and methods This study is a retrospective chart review of children hospitalized with meningitis. In patients with aseptic and bacterial meningitis the following parameters were compared: C-reactive protein, D-dimers, fibrinogen, glucose level, and leukocyte level, and in cerebrospinal fluid, protein, glucose, and leukocyte concentrations were analyzed. Number of points in the Bacterial Meningitis Score (BMS) was calculated. The predictive value of each parameter to distinguish between bacterial and aseptic meningitis was evaluated. Results In total, 129 patients were included in the study: 65 diagnosed with bacterial meningitis and 64 with aseptic meningitis. Bacterial and aseptic meningitis were statistically significantly different based on each analyzed parameter (p meningitis 42 (66%) scored 0 points in the BMS, while all the children with bacterial meningitis had at least one point. Conclusions In children with meningitis inflammatory biomarkers differ statistically significantly depending on the etiology – bacterial or aseptic. Serum concentration of C-reactive protein higher than 80 mg/dl is a useful marker of bacterial etiology of meningitis. A high Bacterial Meningitis Score is indicative for bacterial meningitis. PMID:27186188

  17. Mucosa-associated bacterial microbiome of the gastrointestinal tract of weaned pigs and dynamics linked to dietary calcium-phosphorus.

    Directory of Open Access Journals (Sweden)

    Evelyne Mann

    Full Text Available Dietary composition largely influences pig's gastrointestinal microbiota and represents a useful prophylactic tool against enteric disturbances in young pigs. Despite the importance for host-microbe interactions and bacterial colonization, dietary responses of the mucosa-associated bacterial communities are less well investigated. In the present study, we characterized the mucosa-associated bacterial communities at the Pars non-glandularis of the stomach, ileum and colon, and identified shifts in these communities in response to different dietary calcium-phosphorus (Ca-P contents (100% versus 190% of the Ca and P requirements in combination with two basal diets (wheat-barley- or corn-based in weaned pigs. Pyrosequencing of 16S rRNA genes from 93 mucosal samples yielded 447,849 sequences, clustering into 997 operational taxonomic units (OTUs at 97% similarity level. OTUs were assigned to 198 genera belonging to 14 different phyla. Correlation-based networks revealed strong interactions among OTUs at the various gastrointestinal sites. Our data describe a previously not reported high diversity and species richness at the Pars non-glandularis of the stomach in weaned pigs. Moreover, high versus adequate Ca-P content significantly promoted Lactobacillus by 14.9% units (1.4 fold change at the gastric Pars non-glandularis (P = 0.035. Discriminant analysis revealed dynamic changes in OTU composition in response to dietary cereals and Ca-P contents at all gastrointestinal sites which were less distinguishable at higher taxonomic levels. Overall, this study revealed a distinct mucosa-associated bacterial community at the different gut sites, and a strong effect of high Ca-P diets on the gastric community, thereby markedly expanding our comprehension on mucosa-associated microbiota and their diet-related dynamics in weaned pigs.

  18. Mucosa-associated bacterial microbiome of the gastrointestinal tract of weaned pigs and dynamics linked to dietary calcium-phosphorus.

    Science.gov (United States)

    Mann, Evelyne; Schmitz-Esser, Stephan; Zebeli, Qendrim; Wagner, Martin; Ritzmann, Mathias; Metzler-Zebeli, Barbara U

    2014-01-01

    Dietary composition largely influences pig's gastrointestinal microbiota and represents a useful prophylactic tool against enteric disturbances in young pigs. Despite the importance for host-microbe interactions and bacterial colonization, dietary responses of the mucosa-associated bacterial communities are less well investigated. In the present study, we characterized the mucosa-associated bacterial communities at the Pars non-glandularis of the stomach, ileum and colon, and identified shifts in these communities in response to different dietary calcium-phosphorus (Ca-P) contents (100% versus 190% of the Ca and P requirements) in combination with two basal diets (wheat-barley- or corn-based) in weaned pigs. Pyrosequencing of 16S rRNA genes from 93 mucosal samples yielded 447,849 sequences, clustering into 997 operational taxonomic units (OTUs) at 97% similarity level. OTUs were assigned to 198 genera belonging to 14 different phyla. Correlation-based networks revealed strong interactions among OTUs at the various gastrointestinal sites. Our data describe a previously not reported high diversity and species richness at the Pars non-glandularis of the stomach in weaned pigs. Moreover, high versus adequate Ca-P content significantly promoted Lactobacillus by 14.9% units (1.4 fold change) at the gastric Pars non-glandularis (P = 0.035). Discriminant analysis revealed dynamic changes in OTU composition in response to dietary cereals and Ca-P contents at all gastrointestinal sites which were less distinguishable at higher taxonomic levels. Overall, this study revealed a distinct mucosa-associated bacterial community at the different gut sites, and a strong effect of high Ca-P diets on the gastric community, thereby markedly expanding our comprehension on mucosa-associated microbiota and their diet-related dynamics in weaned pigs.

  19. Dynamics of bacterial communities in soils of rainforest fragments under restoration processes

    Science.gov (United States)

    Vasconcellos, Rafael; Zucchi, Tiago; Taketani, Rodrigo; Andreote, Fernando; Cardoso, Elke

    2014-05-01

    The Brazilian Atlantic Forest ("Mata Atlântica") has been largely studied due to its valuable and unique biodiversity. Unfortunately, this priceless ecosystem has been widely deforested and only 10% of its original area still remains. Many projects have been successfully implemented to restore its fauna and flora but there is a lack of information on how the soil bacterial communities respond to this process. Thus, our aim was to evaluate the influence of soil attributes and seasonality on soil bacterial communities of rainforest fragments under restoration processes. Soil samples from a native site and two ongoing restoration fragments with different ages of implementation (10 and 20 years) were collected and assayed by using culture-independent approaches. Our findings demonstrate that seasonality barely altered the bacterial distribution whereas soil chemical attributes and plant diversity highly influenced the bacterial community structure during the restoration process. Moreover, the strict relationship observed for two bacterial groups, Solibacteriaceae and Verrucomicrobia, one with the youngest (10 years) and the other with the oldest (native) site suggests their use as bioindicators of soil quality and soil recovery of forest fragments under restoration.

  20. Bacterial community dynamics in an anaerobic plug-flow type bioreactor treating swine manure.

    Science.gov (United States)

    Roy, Caroline S; Talbot, Guylaine; Topp, Edward; Beaulieu, Carole; Palin, Marie-France; Massé, Daniel I

    2009-01-01

    A plug-flow type anaerobic reactor consisting of eight sequential compartments was used to study shifts in a bacterial community adapted to degrade swine manure at 25 degrees C. The investigation was carried out during the first 6 months of reactor operation. The reactor successfully separated the hydrolysis/acidogenesis stage from the methanogenesis stage. Bacterial 16S rDNA- and rRNA-based fingerprints obtained through amplicon length heterogeneity PCR (LH-PCR) were analyzed with a view to characterizing the bacterial community structure and the metabolically active community, respectively. Multivariate statistical tools showed that the rDNA-based fingerprints described a more temporal than compartmentalized distribution of similar bacterial communities. By contrast, the rRNA-based multivariate analyses described a distribution that was linked more to reactor performance parameters, especially during short time periods. Diversity indices calculated from fingerprint data were used to assess overall diversity shifts. The decrease in rRNA-based diversity observed through the reactor compartments was greater than the decrease in rDNA-based diversity. This finding indicates that the analysis of metabolically active bacteria diversity was more discriminative than the analysis based on the mere presence of bacteria. The observed decrease in diversity suggests that the bacterial community became specialized in degrading less diversified substrates through the compartments. All these findings suggest that rRNA-based analyses are more appropriate for monitoring reactor performance.

  1. Temporal Sampling of White Band Disease Infected Corals Reveals Complex and Dynamic Bacterial Communities

    Science.gov (United States)

    Gignoux-Wolfsohn, S.; Vollmer, S. V.; Aronson, F. M.

    2016-02-01

    White band disease (WBD) is a coral disease that is currently decimating populations of the endangered staghorn coral, Acropora cervicornis and elkhorn coral, A. palmata across the Caribbean. Since it was first reported in 1979, WBD has killed 95% of these critical reef-building Caribbean corals. WBD is infectious; it can be transmitted through the water column or by a corallivorous snail. While previous research shows that WBD is likely caused by bacteria, identification of a specific pathogen or pathogens has remained elusive. Much of the difficulty of understanding the etiology of the disease comes from a lack of information about how existing bacterial communities respond to disease and separating initial from secondary colonizers. In order to address this lack of information, we performed a fully-crossed tank infection experiment. We exposed healthy corals from two different sites to disease and healthy (control) homogenates from both sites, replicating genotype across tanks. We sampled every coral at three time points: before inoculation with the homogenate, after inoculation, and when the coral showed signs of disease. We then performed 16S rRNA gene sequencing on the Illumina HiSeq 2000. We saw significant differences between time points and disease state. Interestingly, at the first time point (time one) we observed differences between genotypes: every fragment from some genotypes was dominated by Endozoicomonas, while other genotypes were not dominated by one family. At time two we saw an increase in abundance of Alteromonadaceae and Flavobacteriaceae in all corals, and a larger increase in disease-exposed corals. At time three, we saw another increase in Flavobacteriaceae abundance in diseased corals, as well as an introduction of Francisella to diseased corals. While Flavobacteriaceae and Francisella were proposed as potential pathogens, their increase at time three suggests they may be secondary colonizers or opportunists. In genotypes that were

  2. A framework for studying transient dynamics of population projection matrix models

    DEFF Research Database (Denmark)

    Stott, Iain; Townley, Stuart; Hodgson, David James

    2011-01-01

    Empirical models are central to effective conservation and population management, and should be predictive of real-world dynamics. Available modelling methods are diverse, but analysis usually focuses on long-term dynamics that are unable to describe the complicated short-term time series that ca...... of transient population density, but criticises the utility of established indices of convergence times. Our findings should guide further development of analyses of transient population dynamics using PPMs or other empirical modelling techniques....

  3. Fine-scale population dynamics in a marine fish species inferred from dynamic state-space models.

    Science.gov (United States)

    Rogers, Lauren A; Storvik, Geir O; Knutsen, Halvor; Olsen, Esben M; Stenseth, Nils C

    2017-07-01

    Identifying the spatial scale of population structuring is critical for the conservation of natural populations and for drawing accurate ecological inferences. However, population studies often use spatially aggregated data to draw inferences about population trends and drivers, potentially masking ecologically relevant population sub-structure and dynamics. The goals of this study were to investigate how population dynamics models with and without spatial structure affect inferences on population trends and the identification of intrinsic drivers of population dynamics (e.g. density dependence). Specifically, we developed dynamic, age-structured, state-space models to test different hypotheses regarding the spatial structure of a population complex of coastal Atlantic cod (Gadus morhua). Data were from a 93-year survey of juvenile (age 0 and 1) cod sampled along >200 km of the Norwegian Skagerrak coast. We compared two models: one which assumes all sampled cod belong to one larger population, and a second which assumes that each fjord contains a unique population with locally determined dynamics. Using the best supported model, we then reconstructed the historical spatial and temporal dynamics of Skagerrak coastal cod. Cross-validation showed that the spatially structured model with local dynamics had better predictive ability. Furthermore, posterior predictive checks showed that a model which assumes one homogeneous population failed to capture the spatial correlation pattern present in the survey data. The spatially structured model indicated that population trends differed markedly among fjords, as did estimates of population parameters including density-dependent survival. Recent biomass was estimated to be at a near-record low all along the coast, but the finer scale model indicated that the decline occurred at different times in different regions. Warm temperatures were associated with poor recruitment, but local changes in habitat and fishing pressure may

  4. Bacterial community dynamics and activity in relation to dissolved organic matter availability during sea-ice formation in a mesocosm experiment.

    Science.gov (United States)

    Eronen-Rasimus, Eeva; Kaartokallio, Hermanni; Lyra, Christina; Autio, Riitta; Kuosa, Harri; Dieckmann, Gerhard S; Thomas, David N

    2014-02-01

    The structure of sea-ice bacterial communities is frequently different from that in seawater. Bacterial entrainment in sea ice has been studied with traditional microbiological, bacterial abundance, and bacterial production methods. However, the dynamics of the changes in bacterial communities during the transition from open water to frozen sea ice is largely unknown. Given previous evidence that the nutritional status of the parent water may affect bacterial communities during ice formation, bacterial succession was studied in under ice water and sea ice in two series of mesocosms: the first containing seawater from the North Sea and the second containing seawater enriched with algal-derived dissolved organic matter (DOM). The composition and dynamics of bacterial communities were investigated with terminal restriction fragment length polymorphism (T-RFLP), and cloning alongside bacterial production (thymidine and leucine uptake) and abundance measurements (measured by flow cytometry). Enriched and active sea-ice bacterial communities developed in ice formed in both unenriched and DOM-enriched seawater (0-6 days). γ-Proteobacteria dominated in the DOM-enriched samples, indicative of their capability for opportunistic growth in sea ice. The bacterial communities in the unenriched waters and ice consisted of the classes Flavobacteria, α- and γ-Proteobacteria, which are frequently found in natural sea ice in polar regions. Furthermore, the results indicate that seawater bacterial communities are able to adapt rapidly to sudden environmental changes when facing considerable physicochemical stress such as the changes in temperature, salinity, nutrient status, and organic matter supply during ice formation. © 2014 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  5. Quantitative analysis of ruminal bacterial populations involved in lipid metabolism in dairy cows fed different vegetable oils

    DEFF Research Database (Denmark)

    Vargas-Bello-Pérez, E.; Cancino-Padilla, N.; Romero, J.

    2016-01-01

    Vegetable oils are used to increase energy density of dairy cow diets, although they can provoke changes in rumen bacteria populations and have repercussions on the biohydrogenation process. The aim of this study was to evaluate the effect of two sources of dietary lipids: soybean oil (SO......, an unsaturated source) and hydrogenated palm oil (HPO, a saturated source) on bacterial populations and the fatty acid profile of ruminal digesta. Three non-lactating Holstein cows fitted with ruminal cannulae were used in a 3×3 Latin square design with three periods consisting of 21 days. Dietary treatments...... parameters, whereas HPO can increase load of ruminal P. bryantii. Also, results observed in our targeted bacteria may have depended on the saturation degree of dietary oils....

  6. Single-bacterium nanomechanics in biomedicine: unravelling the dynamics of bacterial cells

    International Nuclear Information System (INIS)

    Aguayo, S; Bozec, L; Donos, N; Spratt, D

    2015-01-01

    The use of the atomic force microscope (AFM) in microbiology has progressed significantly throughout the years since its first application as a high-resolution imaging instrument. Modern AFM setups are capable of characterizing the nanomechanical behaviour of bacterial cells at both the cellular and molecular levels, where elastic properties and adhesion forces of single bacterium cells can be examined under different experimental conditions. Considering that bacterial and biofilm-mediated infections continue to challenge the biomedical field, it is important to understand the biophysical events leading towards bacterial adhesion and colonization on both biological and non-biological substrates. The purpose of this review is to present the latest findings concerning the field of single-bacterium nanomechanics, and discuss future trends and applications of nanoindentation and single-cell force spectroscopy techniques in biomedicine. (topical review)

  7. Population dynamics and monitoring applied to decision-making

    Directory of Open Access Journals (Sweden)

    Conroy, M. J.

    2004-06-01

    influence diagrams to capture the stochastic, temporal processes of managing cheetah population in Kenya. The model predicts likely anagement decisions made by various actors within these countries, (e.g., the President, the Environmental Protection Agency, and rural residents and the resulting probability of cheetah extinction following these decisions. By approaching the problem in both its political and ecological contexts one avoids consideration of decisions that, while beneficial from a purely conservation point of view, are unlikely to be implemented because of conflicting political objectives. Haas’s analysis demonstrates both the promise and challenges of this type of modeling, and he offers suggestions for overcoming inherent technical difficulties such as model calibration. The second paper, by Simon Hoyle and Mark Maunder (Hoyle & Maunder, 2004, uses a Bayesian approach to model population dynamics and the effects of commercial fishing bycatch for the eastern Pacific Ocean spotted dolphin (Stenella attenuata. Their paper provides a good example of why Bayesian analysis is particularly suited to many management problems. Namely, because it allows the integration of disparate pieces of monitoring data in the simultaneous estimation of population parameters; allows forincorporation of expert judgment and data from other systems and species; and provides for explicit consideration of uncertainty in decision–making. Alternative management scenarios can then be explored via forward simulations. In the third paper, Chris Fonnesbeck and Mike Conroy (Fonnesbeck & Conroy, 2004 present an integrated approach for estimating parameters and predicting abundance of American black duck (Anas rubripes populations. They also employ a ayesian approach and overcome some of the computational challenges by using Markov chain–Monte Carlo methods. Ring–recovery and harvest data are used to estimate fall age ratios under alternative reproductive models. These in turn are used to

  8. Effect of immobilization of a bacterial consortium on diuron dissipation and community dynamics.

    Science.gov (United States)

    Bazot, Stéphane; Lebeau, Thierry

    2009-09-01

    This work intended to study the relationship between diuron herbicide dissipation and the population dynamics of co-cultivated Delftia acidovorans WDL34 (WDL34) and Arthrobacter sp. N4 (N4) for different cell formulations: free cells or immobilization in Ca-alginate beads of one or both strains. GFP-tagged WDL34 and N4 Gram staining allowed analyzing the cell growth and distribution of each strain in both beads and culture medium in the course of the time. Compared to the free cell co-culture of WDL34 and N4, immobilization of WDL34 in Ca-alginate beads co-cultivated with free N4 increased the dissipation rate of diuron by 53% (0.141 mg ml(-1) h(-1)). In that case, immobilization strongly modified the final equilibrium among both strains (highest total N4 to WDL34 ratio). Our results demonstrated that the inoculant formulation played a major role in the cell growth of each cultivated strain possibly increasing diuron dissipation. This optimized cell formulation may allow improving water and soil treatment.

  9. Effects of triclosan on bacterial community composition and 'Vibrio' populations in natural seawater microcosms

    Directory of Open Access Journals (Sweden)

    Keri Ann Lydon

    2017-05-01

    Full Text Available Pharmaceuticals and personal care products, including antimicrobials, can be found at trace levels in treated wastewater effluent. Impacts of chemical contaminants on coastal aquatic microbial community structure and pathogen abundance are unknown despite the potential for selection through antimicrobial resistance. In particular, 'Vibrio', a marine bacterial genus that includes several human pathogens, displays resistance to the ubiquitous antimicrobial compound triclosan. Here we demonstrated through use of natural seawater microcosms that triclosan (at a concentration of ~5 ppm can induce a significant 'Vibrio' growth response (68–1,700 fold increases in comparison with no treatment controls for three distinct coastal ecosystems: Looe Key Reef (Florida Keys National Marine Sanctuary, Doctors Arm Canal (Big Pine Key, FL, and Clam Bank Landing (North Inlet Estuary, Georgetown, SC. Additionally, microbial community analysis by 16 S rRNA gene sequencing for Looe Key Reef showed distinct changes in microbial community structure with exposure to 5 ppm triclosan, with increases observed in the relative abundance of 'Vibrio'naceae (17-fold, Pseudoalteromonadaceae (65-fold, Alteromonadaceae (108-fold, Colwelliaceae (430-fold, and Oceanospirillaceae (1,494-fold. While the triclosan doses tested were above concentrations typically observed in coastal surface waters, results identify bacterial families that are potentially resistant to triclosan and/or adapted to use triclosan as a carbon source. The results further suggest the potential for selection of 'Vibrio' in coastal environments, especially sediments, where triclosan may accumulate at high levels.

  10. Bacterial and archaeal populations at two shallow hydrothermal vents off Panarea Island (Eolian Islands, Italy).

    Science.gov (United States)

    Maugeri, Teresa Luciana; Lentini, Valeria; Gugliandolo, Concetta; Italiano, Francesco; Cousin, Sylvie; Stackebrandt, Erko

    2009-01-01

    The aim of this study was to investigate the microbial community thriving at two shallow hydrothermal vents off Panarea Island (Italy). Physico-chemical characteristics of thermal waters were examined in order to establish the effect of the vents on biodiversity of both Bacteria and Archaea. Water and adjacent sediment samples were collected at different times from two vents, characterised by different depth and temperature, and analysed to evaluate total microbial abundances, sulphur-oxidising and thermophilic aerobic bacteria. Total microbial abundances were on average of the order of 10(5) cells ml(-1), expressed as picoplanktonic size fraction. Picophytoplanktonic cells accounted for 0.77-3.83% of the total picoplanktonic cells. The contribution of bacterial and archaeal taxa to prokaryotic community diversity was investigated by PCR-DGGE fingerprinting method. The number of bands derived from bacterial DNA was highest in the DGGE profiles of water sample from the warmest and deepest site (site 2). In contrast, archaeal richness was highest in the water of the coldest and shallowest site (site 1). Sulphur-oxidising bacteria were detected by both culture-dependent and -independent methods. The primary production at the shallow hydrothermal system of Panarea is supported by a complex microbial community composed by phototrophs and chemolithotrophs.

  11. Population structure of the bacterial pathogen Xylella fastidiosa among street trees in Washington D.C.

    Directory of Open Access Journals (Sweden)

    Jordan Lee Harris

    Full Text Available Bacterial leaf scorch, associated with the bacterial pathogen Xylella fastidiosa, is a widely established and problematic disease of landscape ornamentals in Washington D.C. A multi-locus sequence typing analysis was performed using 10 housekeeping loci for X. fastidiosa strains in order to better understand the epidemiology of leaf scorch disease in this municipal environment. Samples were collected from 7 different tree species located throughout the District of Columbia, consisting of 101 samples of symptomatic and asymptomatic foliage from 84 different trees. Five strains of the bacteria were identified. Consistent with prior data, these strains were host specific, with only one strain associated with members of the red oak family, one strain associated with American elm, one strain associated with American sycamore, and two strains associated with mulberry. Strains found for asymptomatic foliage were the same as strains from the symptomatic foliage on individual trees. Cross transmission of the strains was not observed at sites with multiple species of infected trees within an approx. 25 m radius of one another. X. fastidiosa strain specificity observed for each genus of tree suggests a highly specialized host-pathogen relationship.

  12. Evaluation of gastrointestinal bacterial population for the production of holocellulose enzymes for biomass deconstruction.

    Science.gov (United States)

    Asem, Dhaneshwaree; Leo, Vincent Vineeth; Passari, Ajit Kumar; Tonsing, Mary Vanlalhruaii; Joshi, J Beslin; Uthandi, Sivakumar; Hashem, Abeer; Abd Allah, Elsayed Fathi; Singh, Bhim Pratap

    2017-01-01

    The gastrointestinal (GI) habitat of ruminant and non-ruminant animals sustains a vast ensemble of microbes that are capable of utilizing lignocellulosic plant biomass. In this study, an indigenous swine (Zovawk) and a domesticated goat (Black Bengal) were investigated to isolate bacteria having plant biomass degrading enzymes. After screening and enzymatic quantification of eighty-one obtained bacterial isolates, Serratia rubidaea strain DBT4 and Aneurinibacillus aneurinilyticus strain DBT87 were revealed as the most potent strains, showing both cellulase and xylanase production. A biomass utilization study showed that submerged fermentation (SmF) of D2 (alkaline pretreated pulpy biomass) using strain DBT4 resulted in the most efficient biomass deconstruction with maximum xylanase (11.98 U/mL) and FPase (0.5 U/mL) activities (55°C, pH 8). The present study demonstrated that bacterial strains residing in the gastrointestinal region of non-ruminant swine are a promising source for lignocellulose degrading microorganisms that could be used for biomass conversion.

  13. Evaluation of gastrointestinal bacterial population for the production of holocellulose enzymes for biomass deconstruction.

    Directory of Open Access Journals (Sweden)

    Dhaneshwaree Asem

    Full Text Available The gastrointestinal (GI habitat of ruminant and non-ruminant animals sustains a vast ensemble of microbes that are capable of utilizing lignocellulosic plant biomass. In this study, an indigenous swine (Zovawk and a domesticated goat (Black Bengal were investigated to isolate bacteria having plant biomass degrading enzymes. After screening and enzymatic quantification of eighty-one obtained bacterial isolates, Serratia rubidaea strain DBT4 and Aneurinibacillus aneurinilyticus strain DBT87 were revealed as the most potent strains, showing both cellulase and xylanase production. A biomass utilization study showed that submerged fermentation (SmF of D2 (alkaline pretreated pulpy biomass using strain DBT4 resulted in the most efficient biomass deconstruction with maximum xylanase (11.98 U/mL and FPase (0.5 U/mL activities (55°C, pH 8. The present study demonstrated that bacterial strains residing in the gastrointestinal region of non-ruminant swine are a promising source for lignocellulose degrading microorganisms that could be used for biomass conversion.

  14. Population structure of the bacterial pathogen Xylella fastidiosa among street trees in Washington D.C.

    Science.gov (United States)

    Harris, Jordan Lee; Balci, Yilmaz

    2015-01-01

    Bacterial leaf scorch, associated with the bacterial pathogen Xylella fastidiosa, is a widely established and problematic disease of landscape ornamentals in Washington D.C. A multi-locus sequence typing analysis was performed using 10 housekeeping loci for X. fastidiosa strains in order to better understand the epidemiology of leaf scorch disease in this municipal environment. Samples were collected from 7 different tree species located throughout the District of Columbia, consisting of 101 samples of symptomatic and asymptomatic foliage from 84 different trees. Five strains of the bacteria were identified. Consistent with prior data, these strains were host specific, with only one strain associated with members of the red oak family, one strain associated with American elm, one strain associated with American sycamore, and two strains associated with mulberry. Strains found for asymptomatic foliage were the same as strains from the symptomatic foliage on individual trees. Cross transmission of the strains was not observed at sites with multiple species of infected trees within an approx. 25 m radius of one another. X. fastidiosa strain specificity observed for each genus of tree suggests a highly specialized host-pathogen relationship.

  15. Evolution in an Afternoon: Rapid Natural Selection and Adaptation of Bacterial Populations

    Science.gov (United States)

    Delpech, Roger

    2009-01-01

    This paper describes a simple, rapid and low-cost technique for growing bacteria (or other microbes) in an environmental gradient, in order to determine the tolerance of the microbial population to varying concentrations of sodium chloride ions, and suggests how the evolutionary response of a microbial population to the selection pressure of the…

  16. Population dynamics of potato cyst nematodes and associated damage to potato

    NARCIS (Netherlands)

    Schans, J.

    1993-01-01

    Population dynamics of potato cyst nematodes (PCN; Globoderarostochiensis (Woll.) Skarbilovich and G. pallida Stone) and their interactions with potato plants are insufficiently understood to explain variations of population

  17. Density dependence and population dynamics of black rhinos (Diceros bicornis michaeli) in Kenya's rhino sanctuaries

    NARCIS (Netherlands)

    Ouma, B.O.; Amin, R.; Langevelde, van F.; Leader-Williams, N.

    2010-01-01

    Density-dependent feedback mechanisms provide insights into the population dynamics and interactions of large herbivores with their ecosystem. Sex ratio also has particularly important implications for growth rates of many large mammal populations through its influence on reproductive potential.

  18. Analysis of Bacillus thuringiensis Population Dynamics and Its Interaction With Pseudomonas fluorescens in Soil

    Science.gov (United States)

    Rojas-Ruiz, Norma Elena; Sansinenea-Royano, Estibaliz; Cedillo-Ramirez, Maria Lilia; Marsch-Moreno, Rodolfo; Sanchez-Alonso, Patricia; Vazquez-Cruz, Candelario

    2015-01-01

    Background: Bacillus thuringiensis is the most successful biological control agent, however, studies so far have shown that B. thuringiensis is very sensitive to environmental factors such as soil moisture and pH. Ultraviolet light from the sun had been considered as the main limiting factor for its persistence in soil and it has recently been shown that the antagonism exerted by other native soil organisms, such as Pseudomonas fluorescens, is a determining factor in the persistence of this bacterium under in vitro culture conditions. Objectives: The aim of the present investigation was to analyze the population dynamics of B. thuringiensis and its interaction with P. fluorescens using microbiological and molecular methods in soil, under different conditions, and to determinate the effect of nutrients and moisture on its interaction. Materials and Methods: The monitoring was performed by microbiological methods, such as viable count of bacteria, and molecular methods such as Polymerase Chain Reaction (PCR) and hybridization, using the direct extraction of DNA from populations of inoculated soil. Results: The analysis of the interaction between B. thuringiensis and P. fluorescens in soil indicated that the disappearance of B. thuringiensis IPS82 is not dependent on the moisture but the composition of nutrients that may be affecting the secretion of toxic compounds in the environment of P. fluorescens. The results showed that the recovered cells were mostly spores and not vegetative cells in all proved treatments. The molecular methods were effective for monitoring bacterial population inoculated in soil. Conclusions: Bacillus thuringiensis is very sensitive to the interaction of P. fluorescens, however is capable to survive in soil due to its capacity of sporulate. Some of the cells in the form of spores germinated and folded slightly and remained in a constant cycle of sporulation and germination. This confirms that B. thuringiensis IPS82 can germinate, grow and

  19. Molecular assessment of bacterial community dynamics and functional endpoints during sediment bioaccumulation test

    NARCIS (Netherlands)

    Diepens, N.J.; Dimitrov, M.R.; Koelmans, A.A.; Smidt, H.

    2015-01-01

    Whole sediment toxicity tests play an important role in environmental risk assessment of organic chemicals. It is not clear, however, to what extent changing microbial community composition and associated functions affect sediment test results. We assessed the development of bacterial communities in

  20. Storm-scale dynamics of bacterial community composition in throughfall and stemflow

    Science.gov (United States)

    Van Stan, J. T., II; Teachey, M. E.; Pound, P.; Ottesen, E. A.

    2017-12-01

    Transport of bacteria between ecosystem spheres can significantly affect microbially-mediated biogeochemical processes. During rainfall, there is a large, temporally-concentrated exchange of bacteria between the forest phyllosphere and the pedosphere by rain dripping from canopy surfaces, as throughfall (TF), and draining to the stem, as stemflow (SF). Many phyllosphere bacteria possibly transported by TF and SF have been linked to important litter and soil processes (like cyanobacteria and actinobacteria). Despite this, no work has applied high throughput DNA sequencing to assess the community composition of bacteria transported by TF and SF. We characterized bacterial community composition for TF and SF from an epiphyte-laden (Tillandsia usneoides L., Spanish moss) southern live oak (Quercus virginiana) forest in southeastern Georgia (USA) to address two hypotheses: that bacterial community composition will differ between (1) TF and SF, and (2) TF sampled beneath bare and epiphyte-laden canopy. Variability in family-level bacterial abundance, Bray-Curtis dissimilarity, and Shannon diversity index was greater between storms than between net rainfall fluxes. In fact, TF and SF bacterial communities were relatively similar for individual storms and may be driven by pre-storm atmospheric deposition rather than the communities affixed to leaves, bark, and epiphyte surfaces.

  1. Selective labelling and eradication of antibiotic-tolerant bacterial populations in Pseudomonas aeruginosa biofilms

    DEFF Research Database (Denmark)

    Chua, Song Lin; Yam, Joey Kuok Hoong; Hao, Piliang

    2016-01-01

    subpopulations, with colistin-tolerant cells using type IV pili to migrate onto the top of the colistin-killed biofilm. The colistin-tolerant cells employ quorum sensing (QS) to initiate the formation of new colistin-tolerant subpopulations, highlighting multicellular behaviour in antibiotic tolerance......Drug resistance and tolerance greatly diminish the therapeutic potential of antibiotics against pathogens. Antibiotic tolerance by bacterial biofilms often leads to persistent infections, but its mechanisms are unclear. Here we use a proteomics approach, pulsed stable isotope labelling with amino...... acids (pulsed-SILAC), to quantify newly expressed proteins in colistin-tolerant subpopulations of Pseudomonas aeruginosa biofilms (colistin is a 'last-resort' antibiotic against multidrug-resistant Gram-negative pathogens). Migration is essential for the formation of colistin-tolerant biofilm...

  2. Application of quantitative real-time PCR for enumeration of total bacterial, archaeal, and yeast populations in kimchi.

    Science.gov (United States)

    Park, Eun-Jin; Chang, Ho-Won; Kim, Kyoung-Ho; Nam, Young-Do; Roh, Seong Woon; Bae, Jin-Woo

    2009-12-01

    Kimchi is a Korean traditional fermented food made of brined vegetables, with a variety of spices. Various microorganisms are associated with the kimchi fermentation process. This study was undertaken in order to apply quantitative real-time PCR targeting the 16S and 26S rRNA genes for the investigation of dynamics of bacterial, archaeal, and yeast communities during fermentation of various types of kimchi. Although the total bacterial and archaeal rRNA gene copy numbers increased during kimchi fermentation, the number of yeasts was not significantly altered. In 1 ng of bulk DNA, the mean number of rRNA gene copies for all strains of bacteria was 5.45 x 10(6) which was 360 and 50 times greater than those for archaea and yeast, respectively. The total gene copy number for each group of microorganisms differed among the different types of kimchi, although the relative ratios among them were similar. The common dominance of bacteria in the whole microbial communities of various types of kimchi suggests that bacteria play a principal role in the kimchi fermentation process.

  3. Relationship of nutrient dynamics and bacterial community structure at the water-sediment interface using a benthic chamber experiment.

    Science.gov (United States)

    Ki, Bo-Min; Huh, In Ae; Choi, Jung-Hyun; Cho, Kyung-Suk

    2018-01-05

    The relationships between nutrient dynamics and the bacterial community at the water-sediment interface were investigated using the results of nutrient release fluxes, bacterial communities examined by 16S rRNA pyrosequencing and canonical correlation analysis (CCA) accompanied by lab-scale benthic chamber experiment. The nutrient release fluxes from the sediments into the water were as follows: -3.832 to 12.157 mg m -2 d -1 for total phosphorus, 0.049 to 9.993 mg m -2 d -1 for PO 4 -P, -2.011 to 41.699 mg m -2 d -1 for total nitrogen, -7.915 to -0.074 mg m -2 d -1 for NH 3 -N, and -17.940 to 1.209 mg m -2 d -1 for NO 3 -N. To evaluate the relationship between the bacterial communities and environmental variables, CCA was conducted in three representative conditions: in the overlying water, in the sediment at a depth of 0-5 cm, and in the sediment at a depth of 5-15 cm. CCA results showed that environmental variables such as nutrient release fluxes (TN, NH 4 , NO 3 , TP, and PO 4 ) and water chemical parameters (pH, DO, COD, and temperature) were highly correlated with the bacterial communities. From the results of the nutrient release fluxes and the bacterial community, this study proposed the hypothesis for bacteria involved in the nutrient dynamics at the interface between water and sediment. In the sediment, sulfate-reducing bacteria (SRB) such as Desulfatibacillum, Desulfobacterium, Desulfomicrobium, and Desulfosalsimonas are expected to contribute to the decomposition of organic matter, and release of ammonia (NH 4 + ) and phosphate (PO 4 3- ). The PO 4 3- released into the water layer was observed by the positive fluxes of PO 4 3- . The NH 4 + released from the sediment was rapidly oxidized by the methane-oxidizing bacteria (MOB). This study observed in the water layer dominantly abundant MOB of Methylobacillus, Methylobacter, Methylocaldum, and Methylophilus. The nitrate (NO 3 - ) accumulation caused by the oxidation environment of the water layer

  4. Effects of demographic structure on key properties of stochastic density-independent population dynamics.

    Science.gov (United States)

    Vindenes, Yngvild; Sæther, Bernt-Erik; Engen, Steinar

    2012-12-01

    The development of stochastic demography has largely been based on age structured populations, although other types of demographic structure, especially permanent and dynamic heterogeneity, are likely common in natural populations. The combination of stochasticity and demographic structure is a challenge for analyses of population dynamics and extinction risk, because the population structure will fluctuate around the stable structure and the population size shows transient fluctuations. However, by using a diffusion approximation for the total reproductive value, density-independent dynamics of structured populations can be described with only three population parameters: the expected population growth rate, the environmental variance and the demographic variance. These parameters depend on population structure via the state-specific vital rates and transition rates. Once they are found, the diffusion approximation represents a substantial reduction in model complexity. Here, we review and compare the key population parameters across a wide range of demographic structure, from the case of no structure to the most general case of dynamic heterogeneity, and for both discrete and continuous types. We focus on the demographic variance, but also show how environmental stochasticity can be included. This study brings together results from recent models, each considering a specific type of population structure, and places them in a general framework for structured populations. Comparison across different types of demographic structure reveals that the reproductive value is an essential concept for understanding how population structure affects stochastic dynamics and extinction risk. Copyright © 2011 Elsevier Inc. All rights reserved.

  5. Second Cancers After Fractionated Radiotherapy: Stochastic Population Dynamics Effects

    Science.gov (United States)

    Sachs, Rainer K.; Shuryak, Igor; Brenner, David; Fakir, Hatim; Hahnfeldt, Philip

    2007-01-01

    When ionizing radiation is used in cancer therapy it can induce second cancers in nearby organs. Mainly due to longer patient survival times, these second cancers have become of increasing concern. Estimating the risk of solid second cancers involves modeling: because of long latency times, available data is usually for older, obsolescent treatment regimens. Moreover, modeling second cancers gives unique insights into human carcinogenesis, since the therapy involves administering well characterized doses of a well studied carcinogen, followed by long-term monitoring. In addition to putative radiation initiation that produces pre-malignant cells, inactivation (i.e. cell killing), and subsequent cell repopulation by proliferation can be important at the doses relevant to second cancer situations. A recent initiation/inactivation/proliferation (IIP) model characterized quantitatively the observed occurrence of second breast and lung cancers, using a deterministic cell population dynamics approach. To analyze ifradiation-initiated pre-malignant clones become extinct before full repopulation can occur, we here give a stochastic version of this I I model. Combining Monte Carlo simulations with standard solutions for time-inhomogeneous birth-death equations, we show that repeated cycles of inactivation and repopulation, as occur during fractionated radiation therapy, can lead to distributions of pre-malignant cells per patient with variance >> mean, even when pre-malignant clones are Poisson-distributed. Thus fewer patients would be affected, but with a higher probability, than a deterministic model, tracking average pre-malignant cell numbers, would predict. Our results are applied to data on breast cancers after radiotherapy for Hodgkin disease. The stochastic IIP analysis, unlike the deterministic one, indicates: a) initiated, pre-malignant cells can have a growth advantage during repopulation, not just during the longer tumor latency period that follows; b) weekend

  6. Diversity of bacterial communities in the midgut of Bactrocera cucurbitae (Diptera: Tephritidae) populations and their potential use as attractants.

    Science.gov (United States)

    Hadapad, Ashok B; Prabhakar, Chandra S; Chandekar, Snehal C; Tripathi, Jyoti; Hire, Ramesh S

    2016-06-01

    The microbiota plays an important role in insect development and fitness. Understanding the gut microbiota composition is essential for the development of pest management strategies. Midgut bacteria were isolated from nine wild B. cucurbitae populations collected from different agroecological zones of India. These isolates were further studied for attractant potential of fruit fly adults, and the chemical constituents in the supernatants of gut bacteria were analysed. Twenty-six bacterial isolates belonging to the families Enterobacteriaceae, Bacillaceae, Micrococcaceae and Staphylococcaceae were isolated and identified on the basis of 16S rRNA gene sequence analysis. The dominant species in the midgut of melon fly were from the genera Enterobacter (34.6%), Klebsiella (19.2%), Citrobacter (7.7%), Bacillus (15.4%) and Providencia (7.7%), and 3.8% each of Micrococcus, Staphylococcus, Leclercia and Exiguobacterium. Bactrocera cucurbitae and B. dorsalis adults were significantly attracted to bacterial whole cell cultures and their supernatants in the fruit fly attraction bioassays. Bacillus cereus, Enterobacter, Klebsiella, Citrobacter and Providencia species attracted both male and females of Bactrocera species. The supernatants of Klebsiella, Citrobacter and Providencia species attracted a significantly greater number of females than males. The most abundant chemical constituents in supernatants of K. oxytoca and C. freundii were 3-methyl-1-butanol, 2-phenylethanol, butyl isocyanatoacetate, 2-methyl-1-propanol and 3-hydroxy-2-butanone, as identified by gas chromatography-mass spectrometry. The bacterial endosymbionts associated with melon fly exhibited attractant potential which could facilitate eco-friendly insect control strategies. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

  7. Dynamics of bacterial endospores, and microbial activities in soils and sediments

    DEFF Research Database (Denmark)

    Tamez-Hidalgo, Paulina

    between being considered slow growers, dormant or even immortal. Despite discussions about minimum energy requirements and metabolic categories, there is a paraphyletic group of Bacteria (the Firmicutes or low-GC Gram positive) able to create the toughest dormant forms on Earth, the endospores. Bacterial...... endospore is a great advantage to persist in environments in spite of the physicochemical conditions. Bacterial endospores can remained dormant for extraordinarily prolonged periods. Despite their apparent metabolic inactivity, endospores are constantly monitoring the nutritional status......, and together they comprise the largest portion of life’s genetic diversity. Prokaryotic communities face recurrent nutrient exhaustion periods that can be prolonged up to centuries, until a season with nutrient deposition arrives. Thus, they have developed the ability to lower their metabolism to the limit...

  8. Geographic coupling of juvenile and adult habitat shapes spatial population dynamics of a coral reef fish

    NARCIS (Netherlands)

    Huijbers, C.M.; Nagelekerken, I.; Debrot, A.O.; Jongejans, E.

    2013-01-01

    Marine spatial population dynamics are often addressed with a focus on larval dispersal, without taking into account movement behavior of individuals in later life stages. Processes occurring during demersal life stages may also drive spatial population dynamics if habitat quality is perceived

  9. A short-time scale colloidal system reveals early bacterial adhesion dynamics.

    Directory of Open Access Journals (Sweden)

    Christophe Beloin

    2008-07-01

    Full Text Available The development of bacteria on abiotic surfaces has important public health and sanitary consequences. However, despite several decades of study of bacterial adhesion to inert surfaces, the biophysical mechanisms governing this process remain poorly understood, due, in particular, to the lack of methodologies covering the appropriate time scale. Using micrometric colloidal surface particles and flow cytometry analysis, we developed a rapid multiparametric approach to studying early events in adhesion of the bacterium Escherichia coli. This approach simultaneously describes the kinetics and amplitude of early steps in adhesion, changes in physicochemical surface properties within the first few seconds of adhesion, and the self-association state of attached and free-floating cells. Examination of the role of three well-characterized E. coli surface adhesion factors upon attachment to colloidal surfaces--curli fimbriae, F-conjugative pilus, and Ag43 adhesin--showed clear-cut differences in the very initial phases of surface colonization for cell-bearing surface structures, all known to promote biofilm development. Our multiparametric analysis revealed a correlation in the adhesion phase with cell-to-cell aggregation properties and demonstrated that this phenomenon amplified surface colonization once initial cell-surface attachment was achieved. Monitoring of real-time physico-chemical particle surface properties showed that surface-active molecules of bacterial origin quickly modified surface properties, providing new insight into the intricate relations connecting abiotic surface physicochemical properties and bacterial adhesion. Hence, the biophysical analytical method described here provides a new and relevant approach to quantitatively and kinetically investigating bacterial adhesion and biofilm development.

  10. The bacterial community inhabiting temperate deciduous forests is vertically stratified and undergoes seasonal dynamics

    Czech Academy of Sciences Publication Activity Database

    López-Mondéjar, Rubén; Voříšková, Jana; Větrovský, Tomáš; Baldrian, Petr

    2015-01-01

    Roč. 87, č. 1 (2015), s. 43-50 ISSN 0038-0717 R&D Projects: GA MŠk(CZ) EE2.3.30.0003; GA MŠk(CZ) ED1.1.00/02.0109; GA MŠk LD12048; GA MŠk LD12050 Institutional support: RVO:61388971 Keywords : Bacterial community * Deciduous forest * Forest soil Subject RIV: EE - Microbiology, Virology Impact factor: 4.152, year: 2015

  11. Effects of gamma-irradiation before and after cooking on bacterial population and sensory quality of Dakgalbi

    International Nuclear Information System (INIS)

    Yoon, Young Min; Park, Jong-Heum; Lee, Ji-Hye; Park, Jae-Nam; Park, Jin-Kyu; Sung, Nak-Yun; Song, Beom-Seok; Kim, Jae-Hun; Yoon, Yohan; Gao, Meixu; Yook, Hong-Sun; Lee, Ju-Woon

    2012-01-01

    The purpose of this study was to compare the effect of gamma irradiation on the total bacterial population and the sensory quality of Dakgalbi irradiated before and after cooking. Fresh chicken meat was cut into small pieces and used to prepare Dakgalbi. For the preparation of Dakgalbi cooked with gamma-irradiated chicken meat and sauce (IBC), raw chicken meat and Dakgalbi sauce were irradiated and then stir-fried. For the preparation of Dakgalbi irradiated after cooking with raw chicken meat and sauce (IAC), raw chicken meat and Dakgalbi sauce were first cooked and subsequently irradiated. Under the accelerated storage condition of 35 °C for 7 days, bacteria in IBC were below the detection limit (1 log CFU/g) on day 1 but were detected on day 2 and gradually increased hereafter. In IAC, on the other hand, bacteria were not detected at all. Evaluation of sensory quality also decreased on both samples. However, IAC showed a better trend. Our results indicate that IAC protocol was a more effective method for reducing bacterial growth in Dakgalbi. - Highlights: ► We compared the microbial safety and sensory property of Dakgalbi irradiated before and after cooking. ► Dakgalbi irradiated after cooking can be more effective processing method on microbial safety. ► Sensory property decreased on both Dakgalbis by irradiation-induced off-flavor. ► Dakgalbi irradiated after cooking showed a better tendency on the sensory evaluation.

  12. Population dynamics of soil bacteria in some areas of Midnapore coastal belt, West Bengal, India.

    Science.gov (United States)

    Azmi, Syed Afrin; Chatterjee, Soumendranath

    2016-06-01

    In this present study the population dynamics of the soil bacteria of some coastal villages, namely Padima, Jatimati, Chanpabani, Palsandapur, Bhagibaharampur, Duttapur, Gangadharpur, Gobindabasan, Somaibasan of Digha, West Bengal, India, was determined. In these villages the aerobic heterotrophic, Gram-negative, spore-forming, starch-hydrolyzing, Pseudomonas, nitrate-reducing, denitrifying, asymbiotic N 2 fixing, nitrifying, phosphate-solubilizing bacterial populations ranged from 1.22 to 2.67 × 10 6 , 0.09-1.63 × 10 5 , 1.53-3.68 × 10 5 , 2.22-4.06 × 10 5 , 0.02-0.04 × 10 5 , 0.35-1.33 × 10 5 , 0.07-0.82 × 10 5 , 0.58-2.50 × 10 5 , 0.13-2.35 × 10 5 , 0.05-1.9 × 10 5 cfu/g dry soil, respectively. The organic carbon content of the soil samples ranged from 0.61 to 0.93 %. The available nitrogen and phosphate in the soils of the study area varied from 11.2 to 29.5 and 230.8-503.09 mg/kg, respectively. The one-way ANOVA revealed significant variations (p < 0.05) in the microbial diversity with respect to different locations of the study site. Shannon-Wiener and Simpson Index of the study areas ranged from 1.56 to 1.88 and 3.85-5.73, respectively. Jatimati showed comparatively higher diversity index among the villages of the study area. From principal component analysis, three components were extracted having the Eigen values of 3.541, 1.603 and 1.391, respectively. Agglometric hierarchial cluster analysis in respect of the number of different bacterial groups in different places of the study area showed that the denitrifying, nitrate reducing, asymbiotic nitrogen-fixing and spore-forming bacteria formed a cluster while Pseudomonas differed from them forming another cluster and nitrifying, Gram negative, phosphate-solubilising and starch-hydrolyzing bacteria formed another different cluster. This variation of the soil bacteria might be dependent on the microhabitat present in different locations of the study area.

  13. An individual-based approach to explain plasmid invasion in bacterial populations

    DEFF Research Database (Denmark)

    Seoane, Jose Miguel; Yankelevich, Tatiana; Dechesne, Arnaud

    2011-01-01

    , together with contact mechanics arising from cellular growth and division, are the two main processes determining the emergent inability of the pWW0 TOL plasmid to fully invade spatially structured Pseudomonas putida populations. We have also shown that pWW0 conjugation occurs mainly at advanced stages...... observe, however, that transient periods of elevated plasmid transfer in newly formed transconjugant cells are offset by unfavorable cell-to-cell contact mechanics, which ultimately precludes the pWWO TOL plasmid from fully invading tightly packed multicellular P. putida populations such as microcolonies...

  14. The Effects of Vaccination and Immunity on Bacterial Infection Dynamics In Vivo

    Science.gov (United States)

    Coward, Chris; Restif, Olivier; Dybowski, Richard; Grant, Andrew J.; Maskell, Duncan J.; Mastroeni, Pietro

    2014-01-01

    Salmonella enterica infections are a significant global health issue, and development of vaccines against these bacteria requires an improved understanding of how vaccination affects the growth and spread of the bacteria within the host. We have combined in vivo tracking of molecularly tagged bacterial subpopulations with mathematical modelling to gain a novel insight into how different classes of vaccines and branches of the immune response protect against secondary Salmonella enterica infections of the mouse. We have found that a live Salmonella vaccine significantly reduced bacteraemia during a secondary challenge and restrained inter-organ spread of the bacteria in the systemic organs. Further, fitting mechanistic models to the data indicated that live vaccine immunisation enhanced both the bacterial killing in the very early stages of the infection and bacteriostatic control over the first day post-challenge. T-cell immunity induced by this vaccine is not necessary for the enhanced bacteriostasis but is required for subsequent bactericidal clearance of Salmonella in the blood and tissues. Conversely, a non-living vaccine while able to enhance initial blood clearance and killing of virulent secondary challenge bacteria, was unable to alter the subsequent bacterial growth rate in the systemic organs, did not prevent the resurgence of extensive bacteraemia and failed to control the spread of the bacteria in the body. PMID:25233077

  15. Study of the interactions between endolysin and bacterial peptidoglycan on S. aureus by dynamic force spectroscopy

    Science.gov (United States)

    Liu, Jianli; Zhang, Xuejie; Yang, Hang; Yuan, Jinghe; Wei, Hongping; Yu, Junping; Fang, Xiaohong

    2015-09-01

    The cell wall binding domain (CBD) of bacteriophage lysins can recognize target bacteria with extraordinary specificity through binding to bacterial peptidoglycan, thus it is a promising new probe to identify the corresponding bacterial pathogen. In this work, we used atomic force microscopy (AFM) based single-molecule force spectroscopy to investigate the interaction between the CBD of lysin PlyV12 (PlyV12C) and pathogenic bacterium Staphylococcus aureus (S. aureus). The binding forces of PlyV12C with S. aureus have been measured, and the dissociation process of their binding complex has been characterized. Furthermore, we compared the interactions of PlyV12C-S. aureus and antibody-S. aureus. It is revealed that PlyV12C has a comparable affinity to bacterial peptidoglycans as that of the S. aureus antibody. The results provide new information on the binding properties of lysin CBD with bacterium, and the application of lysin CBD in bacterium detection.

  16. The effects of vaccination and immunity on bacterial infection dynamics in vivo.

    Directory of Open Access Journals (Sweden)

    Chris Coward

    2014-09-01

    Full Text Available Salmonella enterica infections are a significant global health issue, and development of vaccines against these bacteria requires an improved understanding of how vaccination affects the growth and spread of the bacteria within the host. We have combined in vivo tracking of molecularly tagged bacterial subpopulations with mathematical modelling to gain a novel insight into how different classes of vaccines and branches of the immune response protect against secondary Salmonella enterica infections of the mouse. We have found that a live Salmonella vaccine significantly reduced bacteraemia during a secondary challenge and restrained inter-organ spread of the bacteria in the systemic organs. Further, fitting mechanistic models to the data indicated that live vaccine immunisation enhanced both the bacterial killing in the very early stages of the infection and bacteriostatic control over the first day post-challenge. T-cell immunity induced by this vaccine is not necessary for the enhanced bacteriostasis but is required for subsequent bactericidal clearance of Salmonella in the blood and tissues. Conversely, a non-living vaccine while able to enhance initial blood clearance and killing of virulent secondary challenge bacteria, was unable to alter the subsequent bacterial growth rate in the systemic organs, did not prevent the resurgence of extensive bacteraemia and failed to control the spread of the bacteria in the body.

  17. Temporal Dynamics of Bacterial and Fungal Colonization on Plastic Debris in the North Sea.

    Science.gov (United States)

    De Tender, Caroline; Devriese, Lisa I; Haegeman, Annelies; Maes, Sara; Vangeyte, Jürgen; Cattrijsse, André; Dawyndt, Peter; Ruttink, Tom

    2017-07-05

    Despite growing evidence that biofilm formation on plastic debris in the marine environment may be essential for its biodegradation, the underlying processes have yet to be fully understood. Thus, far, bacterial biofilm formation had only been studied after short-term exposure or on floating plastic, yet a prominent share of plastic litter accumulates on the seafloor. In this study, we explored the taxonomic composition of bacterial and fungal communities on polyethylene plastic sheets and dolly ropes during long-term exposure on the seafloor, both at a harbor and an offshore location in the Belgian part of the North Sea. We reconstructed the sequence of events during biofilm formation on plastic in the harbor environment and identified a core bacteriome and subsets of bacterial indicator species for early, intermediate, and late stages of biofilm formation. Additionally, by implementing ITS2 metabarcoding on plastic debris, we identified and characterized for the first time fungal genera on plastic debris. Surprisingly, none of the plastics exposed to offshore conditions displayed the typical signature of a late stage biofilm, suggesting that biofilm formation is severely hampered in the natural environment where most plastic debris accumulates.

  18. Elucidation of the tidal influence on bacterial populations in a monsoon influenced estuary through simultaneous observations

    Digital Repository Service at National Institute of Oceanography (India)

    Khandeparker, L.; Eswaran, R.; Gardade, L.; Kuchi, N.; Mapari, K.E.; Naik, S.D.; Anil, A.C.

    on plankton and suspended matter for their persistence (Islam et al. 2007). The interaction between microorganisms (pathogens) and particulate matter is most prevalent in estuarine environments due to the formation of suspended sediment (Flocs) at the marine..., 00157-11. Hsieh, J. L., Fries, J. S., & Noble, R. T. (2008). Dynamics and predictive modeling of Vibrio spp. in the Neuse River Estuary, North Carolina, USA. Environmental Microbiology, 10, 57-64. Huq, A., Xu, B., Chowdhury, M. A., Islam, M. S...

  19. Dynamic of population-dynamics in a medically important snail species Lymnaea (Radix Luteola (Lamarck

    Directory of Open Access Journals (Sweden)

    T. K. Misra

    1993-09-01

    Full Text Available The life-cycle parameters of the snail Lymnaea (Radix luteola and the factors influencing the same have been studied under laboratory conditions. Ins each month, from July 1990 to June 1991, a batch of 100 zero-day old individual were considered for studies. The snails of April batch survived for 19.42 days while those in December batch survived for 87.45 days. The May batch individual though survived for 65.67 days gained maximum shell size (15.84 mm in length and body weight (419.87 mg. All individuals of April batch died prior to attainment of sexual maturity. In the remaining 11 batches the snails became sexually mature between 32 and 53 days. At this stage, they were with varying shell lengths, 9.3 mm to 13,11 mm in respect to batches. The reproduction period varied from 1-67 days. An individual laid, on an average, 0,25 (March batch to 443.67 (May batch eggs in its life-span. A batch of such snails would leave 24312, 22520, 720268, 80408, 76067, 418165, 214, 9202, 0, 0, 2459386 and 127894 individuals at the end of 352nd day. Since the environmental conditions were almost similar the 'dynamic' of population dynamics seems to be involved with the 'strain' of the snail individuals of the batches concerned.

  20. Antimicrobial activity of endophytic bacterial populations isolated from medical plants of Iran.

    Science.gov (United States)

    Beiranvand, Maryam; Amin, Mansour; Hashemi-Shahraki, Abdolrazag; Romani, Bizhan; Yaghoubi, Sajad; Sadeghi, Parisa

    2017-02-01

    Endophytic actinobacteria colonize inside the plant tissues without causing damages to the host plant. Since these microorganisms colonize in the different parts of plants and can stop plant disease, they have been applied as biological agents for controlling human diseases. The aim of this study was molecular identification and measuring the antimicrobial activity of endophytic Actinomycete s isolated from medicinal plants of Iran. The total of 23 medicinal plant samples were collected, sterilized, and crushed. Small pieces of the crushed samples were then cultured directly on three selective media. Grown colonies were identified by 16S rRNA gene sequencing method. Each isolate was cultured in TSB medium and then antimicrobial compound was extracted using ethyl acetate and tested against the target bacteria. Sixteen out of 23 bacterial isolates (69%) exhibited antimicrobial activity against the selected pathogenic bacteria, such as Bacillus cereus, Staphylococcus aureus, Bacillus subtilis, Klebsiella pneumoniae, Citrobacter freundii, Proteus mirabilis, Shigella flexneri and Escherichia coli. Our Study showed a high phylogenetic diversity and the potent antibiotic activity of endophytic bacteria in medicinal plants of Iran.

  1. Antimicrobial activity of endophytic bacterial populations isolated from medical plants of Iran

    Science.gov (United States)

    Beiranvand, Maryam; Amin, Mansour; Hashemi-Shahraki, Abdolrazag; Romani, Bizhan; Yaghoubi, Sajad; Sadeghi, Parisa

    2017-01-01

    Background and Objectives: Endophytic actinobacteria colonize inside the plant tissues without causing damages to the host plant. Since these microorganisms colonize in the different parts of plants and can stop plant disease, they have been applied as biological agents for controlling human diseases. The aim of this study was molecular identification and measuring the antimicrobial activity of endophytic Actinomycetes isolated from medicinal plants of Iran. Materials and Methods: The total of 23 medicinal plant samples were collected, sterilized, and crushed. Small pieces of the crushed samples were then cultured directly on three selective media. Grown colonies were identified by 16S rRNA gene sequencing method. Each isolate was cultured in TSB medium and then antimicrobial compound was extracted using ethyl acetate and tested against the target bacteria. Results: Sixteen out of 23 bacterial isolates (69%) exhibited antimicrobial activity against the selected pathogenic bacteria, such as Bacillus cereus, Staphylococcus aureus, Bacillus subtilis, Klebsiella pneumoniae, Citrobacter freundii, Proteus mirabilis, Shigella flexneri and Escherichia coli. Conclusion: Our Study showed a high phylogenetic diversity and the potent antibiotic activity of endophytic bacteria in medicinal plants of Iran. PMID:28775818

  2. Housefly Larva Vermicomposting Efficiently Attenuates Antibiotic Resistance Genes in Swine Manure, with Concomitant Bacterial Population Changes.

    Science.gov (United States)

    Wang, Hang; Li, Hongyi; Gilbert, Jack A; Li, Haibo; Wu, Longhua; Liu, Meng; Wang, Liling; Zhou, Qiansheng; Yuan, Junxiang; Zhang, Zhijian

    2015-11-01

    Manure from swine treated with antimicrobials as feed additives is a major source for the expansion of the antibiotic resistance gene (ARG) reservoir in the environment. Vermicomposting via housefly larvae (Musca domestica) can be efficiently used to treat manure and regenerate biofertilizer, but few studies have investigated its effect on ARG attenuation. Here, we tracked the abundances of 9 ARGs and the composition and structure of the bacterial communities in manure samples across 6 days of full-scale manure vermicomposting. On day 6, the abundances of genes encoding tetracycline resistance [tet(M), tet(O), tet(Q), and tet(W)] were reduced (P genes encoding sulfonamide resistance (sul1 and sul2) were increased (P resistance genes were correlated (P < 0.05) with the changing concentrations of tetracyclines in the manure. The overall diversity and richness of the bacteria significantly decreased during vermicomposting, accompanied by a 100 times increase in the relative abundance of Flavobacteriaceae spp. Variations in the abundances of ARGs were correlated with the changing microbial community structure and the relative abundances of the family Ruminococcaceae, class Bacilli, or phylum Proteobacteria. Vermicomposting, as a waste management practice, can reduce the overall abundance of ARGs. More research is warranted to assess the use of this waste management practice as a measure to attenuate the dissemination of antimicrobial residues and ARGs from livestock production before vermicompost can be safely used as biofertilizer in agroecosystems. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  3. Could bacteriophages transfer antibiotic resistance genes from environmental bacteria to human-body associated bacterial populations?

    Science.gov (United States)

    Muniesa, Maite; Colomer-Lluch, Marta; Jofre, Juan

    2013-07-01

    Environments without any contact with anthropogenic antibiotics show a great abundance of antibiotic resistance genes that use to be chromosomal and are part of the core genes of the species that harbor them. Some of these genes are shared with human pathogens where they appear in mobile genetic elements. Diversity of antibiotic resistance genes in non-contaminated environments is much greater than in human and animal pathogens, and in environments contaminated with antibiotic from anthropogenic activities. This suggests the existence of some bottleneck effect for the mobilization of antibiotic resistance genes among different biomes. Bacteriophages have characteristics that make them suitable vectors between different biomes, and as well for transferring genes from biome to biome. Recent metagenomic studies and detection of bacterial genes by genomic techniques in the bacteriophage fraction of different microbiota provide indirect evidences that the mobilization of genes mediated by phages, including antibiotic resistance genes, is far more relevant than previously thought. Our hypothesis is that bacteriophages might be of critical importance for evading one of the bottlenecks, the lack of ecological connectivity that modulates the pass of antibiotic resistance genes from natural environments such as waters and soils, to animal and human microbiomes. This commentary concentrates on the potential importance of bacteriophages in transferring resistance genes from the environment to human and animal body microbiomes, but there is no doubt that transduction occurs also in body microbiomes.

  4. Uncovering potential 'herbal probiotics' in Juzen-taiho-to through the study of associated bacterial populations.

    Science.gov (United States)

    Montenegro, Diego; Kalpana, Kriti; Chrissian, Christine; Sharma, Ashutosh; Takaoka, Anna; Iacovidou, Maria; Soll, Clifford E; Aminova, Olga; Heguy, Adriana; Cohen, Lisa; Shen, Steven; Kawamura, Akira

    2015-02-01

    Juzen-taiho-to (JTT) is an immune-boosting formulation of ten medicinal herbs. It is used clinically in East Asia to boost the human immune functions. The active factors in JTT have not been clarified. But, existing evidence suggests that lipopolysaccharide (LPS)-like factors contribute to the activity. To examine this possibility, JTT was subjected to a series of analyses, including high resolution mass spectrometry, which suggested the presence of structural variants of LPS. This finding opened a possibility that JTT contains immune-boosting bacteria. As the first step to characterize the bacteria in JTT, 16S ribosomal RNA sequencing was carried out for Angelica sinensis (dried root), one of the most potent immunostimulatory herbs in JTT. The sequencing revealed a total of 519 bacteria genera in A. sinensis. The most abundant genus was Rahnella, which is widely distributed in water and plants. The abundance of Rahnella appeared to correlate with the immunostimulatory activity of A. sinensis. In conclusion, the current study provided new pieces of evidence supporting the emerging theory of bacterial contribution in immune-boosting herbs. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Microbial Diversity Analysis of the Bacterial and Archaeal Population in Present Day Stromatolites

    Science.gov (United States)

    Ortega, Maya C.

    2011-01-01

    Stromatolites are layered sedimentary structures resulting from microbial mat communities that remove carbon dioxide from their environment and biomineralize it as calcium carbonate. Although prevalent in the fossil record, stromatolites are rare in the modem world and are only found in a few locations including Highbome Cay in the Bahamas. The stromatolites found at this shallow marine site are analogs to ancient microbial mat ecosystems abundant in the Precambrian period on ancient Earth. To understand how stromatolites form and develop, it is important to identify what microorganisms are present in these mats, and how these microbes contribute to geological structure. These results will provide insight into the molecular and geochemical processes of microbial communities that prevailed on ancient Earth. Since stromatolites are formed by lithifying microbial mats that are able to mineralize calcium carbonate, understanding the biological mechanisms involved may lead to the development of carbon sequestration technologies that will be applicable in human spaceflight, as well as improve our understanding of global climate and its sustainability. The objective of my project was to analyze the archaeal and bacterial dIversity in stromatolites from Highborn Cay in the Bahamas. The first step in studying the molecular processes that the microorganisms carry out is to ascertain the microbial complexity within the mats, which includes identifying and estimating the numbers of different microbes that comprise these mats.

  6. The primary case is not enough: Variation among individuals, groups and social networks modify bacterial transmission dynamics.

    Science.gov (United States)

    Keiser, Carl N; Pinter-Wollman, Noa; Ziemba, Michael J; Kothamasu, Krishna S; Pruitt, Jonathan N

    2018-03-01

    The traits of the primary case of an infectious disease outbreak, and the circumstances for their aetiology, potentially influence the trajectory of transmission dynamics. However, these dynamics likely also depend on the traits of the individuals with whom the primary case interacts. We used the social spider Stegodyphus dumicola to test how the traits of the primary case, group phenotypic composition and group size interact to facilitate the transmission of a GFP-labelled cuticular bacterium. We also compared bacterial transmission across experimentally generated "daisy-chain" vs. "star" networks of social interactions. Finally, we compared social network structure across groups of different sizes. Groups of 10 spiders experienced more bacterial transmission events compared to groups of 30 spiders, regardless of groups' behavioural composition. Groups containing only one bold spider experienced the lowest levels of bacterial transmission regardless of group size. We found no evidence for the traits of the primary case influencing any transmission dynamics. In a second experiment, bacteria were transmitted to more individuals in experimentally induced star networks than in daisy-chains, on which transmission never exceeded three steps. In both experimental network types, transmission success depended jointly on the behavioural traits of the interacting individuals; however, the behavioural traits of the primary case were only important for transmission on star networks. Larger social groups exhibited lower interaction density (i.e. had a low ratio of observed to possible connections) and were more modular, i.e. they had more connections between nodes within a subgroup and fewer connections across subgroups. Thus, larger groups may restrict transmission by forming fewer interactions and by isolating subgroups that interacted with the primary case. These findings suggest that accounting for the traits of single exposed hosts has less power in predicting transmission

  7. Correlations between bacterial populations and process parameters in four full-scale anaerobic digesters treating sewage sludge.

    Science.gov (United States)

    Shin, Seung Gu; Koo, Taewoan; Lee, Joonyeob; Han, Gyuseong; Cho, Kyungjin; Kim, Woong; Hwang, Seokhwan

    2016-08-01

    Process parameters and bacterial populations were investigated in four full-scale anaerobic digesters treating sewage sludge. Although the four digesters were operated under similar conditions, digesters A and B had higher pH (7.2-7.4) and lipid removal efficiencies (>50%) than C and D (pH 6.1-6.4; average lipid removal acid or protein/amino acid-utilizers. In contrast, fifteen others (group II) were less abundant in A and/or B and included potentially dormant/dead cells originated from activated sludge. Despite the overall richness trend, the presence of the 25 genera in groups I/II was greater in digesters A and B (24) than in C and D (17); this observation suggests that group I bacteria might be essential in AD of sewage sludge. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Effect of antibiotics on bacterial populations: a multi-hierachical selection process [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    José Luis Martínez

    2017-01-01

    Full Text Available Antibiotics have been widely used for a number of decades for human therapy and farming production. Since a high percentage of antibiotics are discharged from the human or animal body without degradation, this means that different habitats, from the human body to river water or soils, are polluted with antibiotics. In this situation, it is expected that the variable concentration of this type of microbial inhibitor present in different ecosystems may affect the structure and the productivity of the microbiota colonizing such habitats. This effect can occur at different levels, including changes in the overall structure of the population, selection of resistant organisms, or alterations in bacterial physiology. In this review, I discuss the available information on how the presence of antibiotics may alter the microbiota and the consequences of such alterations for human health and for the activity of microbiota from different habitats.

  9. Linear superposition and prediction of bacterial promoter activity dynamics in complex conditions.

    Science.gov (United States)

    Rothschild, Daphna; Dekel, Erez; Hausser, Jean; Bren, Anat; Aidelberg, Guy; Szekely, Pablo; Alon, Uri

    2014-05-01

    Bacteria often face complex environments. We asked how gene expression in complex conditions relates to expression in simpler conditions. To address this, we obtained accurate promoter activity dynamical measurements on 94 genes in E. coli in environments made up of all possible combinations of four nutrients and stresses. We find that the dynamics across conditions is well described by two principal component curves specific to each promoter. As a result, the promoter activity dynamics in a combination of conditions is a weighted average of the dynamics in each condition alone. The weights tend to sum up to approximately one. This weighted-average property, called linear superposition, allows predicting the promoter activity dynamics in a combination of conditions based on measurements of pairs of conditions. If these findings apply more generally, they can vastly reduce the number of experiments needed to understand how E. coli responds to the combinatorially huge space of possible environments.

  10. The Impact of Mine Closures on Rural Population Dynamics: The ...

    African Journals Online (AJOL)

    The paper examines the demographic and socio-cultural impact of spontaneous population inflows into Zhombe following the closure of the Empress Mine in 1982. Data was collected using a questionnaire survey. Results of the study show that mine closures cause rural population change. The population directly grows ...

  11. DYNAMICS OF Cercospora zeina POPULATIONS IN MAIZE-BASED ...

    African Journals Online (AJOL)

    ACSS

    Type II) populations in maize (Zea mays) producing areas under Uganda conditions. Populations of the fungus ... years of study the impact of selection and genetic drift on C. zeina populations in the two Ugandan agroecologies is slow, but progressive ..... measures the probability of obtaining two different alleles at a locus ...

  12. Effective population size and evolutionary dynamics in outbred ...

    Indian Academy of Sciences (India)

    Census population size, sex-ratio and female reproductive success were monitored in 10 laboratory populations of Drosophila melanogaster selected for different ages of reproduction. With this demographic information, we estimated eigenvalue, variance and probability of allele loss effective population sizes. We conclude ...

  13. On the apllication of single specie dynamic population model | Iguda ...

    African Journals Online (AJOL)

    The Method of mathematical models of Malthus and Verhults were applied on ten years data collected from Magaram Poultry Farm to determine the nature of population growth, population decay or constant ... Keywords: Birth rate, sustainable population, overcrowding, harvesting, independent t-test and one way Anova.

  14. HRT dependent performance and bacterial community population of granular hydrogen-producing mixed cultures fed with galactose.

    Science.gov (United States)

    Kumar, Gopalakrishnan; Sivagurunathan, Periyasamy; Park, Jeong-Hoon; Park, Jong-Hun; Park, Hee-Deung; Yoon, Jeong-Jun; Kim, Sang-Hyoun

    2016-04-01

    The effects of hydraulic retention times (HRTs-6, 3 and 2 h) on H2 production, operational stability and bacterial population response in a continuously stirred tank reactor (CSTR) were evaluated using galactose. A peak hydrogen production rate (HPR) of 25.9 L H2/L-d was obtained at a 3 h HRT with an organic loading rate (OLR) of 120 g/L-d, while the maximum hydrogen yield (HY) of 2.21 mol H2/mol galactose was obtained at a 6 h HRT (60 g galactose/L-d). Butyrate was dominant and the lactate concentration increased as HRT decreased, which significantly affected the HY. Biomass concentration (VSS) decreased from 16 to 3g/L at a 2 h HRT, leading to failure. A 3 h HRT supported the favorable growth of Clostridium species, as indicated by an increase in their populations from 25.4% to 27%, while significantly reducing Bacilli populations from 61.6% to 54.2%, indicating that this was the optimal condition. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Allelic variation for broad-spectrum resistance and susceptibility to bacterial pathogens identified in a rice MAGIC population.

    Science.gov (United States)

    Bossa-Castro, Ana M; Tekete, Cheick; Raghavan, Chitra; Delorean, Emily E; Dereeper, Alexis; Dagno, Karim; Koita, Ousmane; Mosquera, Gloria; Leung, Hei; Verdier, Valérie; Leach, Jan E

    2018-02-06

    Quantitative trait loci (QTL) that confer broad-spectrum resistance (BSR), or resistance that is effective against multiple and diverse plant pathogens, have been elusive targets of crop breeding programmes. Multiparent advanced generation intercross (MAGIC) populations, with their diverse genetic composition and high levels of recombination, are potential resources for the identification of QTL for BSR. In this study, a rice MAGIC population was used to map QTL conferring BSR to two major rice diseases, bacterial leaf streak (BLS) and bacterial blight (BB), caused by Xanthomonas oryzae pathovars (pv.) oryzicola (Xoc) and oryzae (Xoo), respectively. Controlling these diseases is particularly important in sub-Saharan Africa, where no sources of BSR are currently available in deployed varieties. The MAGIC founders and lines were genotyped by sequencing and phenotyped in the greenhouse and field by inoculation with multiple strains of Xoc and Xoo. A combination of genomewide association studies (GWAS) and interval mapping analyses revealed 11 BSR QTL, effective against both diseases, and three pathovar-specific QTL. The most promising BSR QTL (qXO-2-1, qXO-4-1 and qXO-11-2) conferred resistance to more than nine Xoc and Xoo strains. GWAS detected 369 significant SNP markers with distinguishable phenotypic effects, allowing the identification of alleles conferring disease resistance and susceptibility. The BSR and susceptibility QTL will improve our understanding of the mechanisms of both resistance and susceptibility in the long term and will be immediately useful resources for rice breeding programmes. © 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  16. Dynamics of a physiologically structured population in a time-varying environment

    DEFF Research Database (Denmark)

    Heilmann, Irene Louise Torpe; Starke, Jens; Andersen, Ken Haste

    2016-01-01

    Physiologically structured population models have become a valuable tool to model the dynamics of populations. In a stationary environment such models can exhibit equilibrium solutions as well as periodic solutions. However, for many organisms the environment is not stationary, but varies more...... or less regularly. In order to understand the interaction between an external environmental forcing and the internal dynamics in a population, we examine the response of a physiologically structured population model to a periodic variation in the food resource. We explore the addition of forcing in two...... cases: (A) where the population dynamics is in equilibrium in a stationary environment, and (B) where the population dynamics exhibits a periodic solution in a stationary environment. When forcing is applied in case A, the solutions are mainly periodic. In case B the forcing signal interacts...

  17. Bacterial populations