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Sample records for bacterial populations co-existing

  1. Cheating fosters species co-existence in well-mixed bacterial communities.

    PubMed

    Leinweber, Anne; Fredrik Inglis, R; Kümmerli, Rolf

    2017-05-01

    Explaining the enormous biodiversity observed in bacterial communities is challenging because ecological theory predicts that competition between species occupying the same niche should lead to the exclusion of less competitive community members. Competitive exclusion should be particularly strong when species compete for a single limiting resource or live in unstructured habitats that offer no refuge for weaker competitors. Here, we describe the 'cheating effect', a form of intra-specific competition that can counterbalance between-species competition, thereby fostering biodiversity in unstructured habitats. Using experimental communities consisting of the strong competitor Pseudomonas aeruginosa (PA) and its weaker counterpart Burkholderia cenocepacia (BC), we show that co-existence is impossible when the two species compete for a single limiting resource, iron. However, when introducing a PA cheating mutant, which specifically exploits the iron-scavenging siderophores produced by the PA wild type, we found that biodiversity was preserved under well-mixed conditions where PA cheats could outcompete the PA wild type. Cheating fosters biodiversity in our system because it creates strong intra-specific competition, which equalizes fitness differences between PA and BC. Our study identifies cheating - typically considered a destructive element - as a constructive force in shaping biodiversity.

  2. Bacterial Vaginosis and Cervical Intraepithelial Neoplasia: Is there an Association or is Co-Existence Incidental?

    PubMed

    Sodhani, Pushpa; Gupta, Sanjay; Gupta, Ruchika; Mehrotra, Ravi

    2017-05-01

    Objectives: To determine associations, if any, of bacterial vaginosis with cervical pre-neoplastic lesions and evaluate any effects of sub-categorization of smears with bacterial vaginosis. Methods: All cervico-vaginal smears reported as positive for bacterial vaginosis over a five-year period were reviewed and sub-categorized into ‘type I (dysbacteriosis)’ and ‘type II (pure Gardenerella infection)’ smears by two cytopathologists (PS, SG). The proportion of smears with healthy flora and pre-neoplastic lesions was compared with those having bacterial vaginosis in conjunction with such changes. In addition, a comparison was also attempted between the frequencies of pre-neoplastic lesions with the two categories of bacterial vaginosis smears. Results: Bacterial vaginosis was diagnosed in 28.6% (7017 of the 24,565) of the 24,565 smears received in the Institute during the study period. Of these 7,017 smears with bacterial vaginosis, 53% (3717) were categorized as type I and 42.7% (3000) as type II by both cytopathologists. Pre-neoplastic lesions were detected in 10.2% of smears with bacterial vaginosis compared to 5.7% of those with healthy flora (P<0.0001). Of the sub-categories of bacterial vaginosis, the risk of detecting precancerous lesion was higher for type II smears (P<0.001). Conclusion: Sub-categorization of bacterial vaginosis, as performed in the Dutch coding system, may be worthwhile due to the strikingly different risk of associated preneoplasia. Creative Commons Attribution License

  3. Co-existence of periodic bursts and death of cycles in a population dynamics system

    NASA Astrophysics Data System (ADS)

    Iyengar, Sudharsana V.; Balakrishnan, Janaki; Kurths, Jürgen

    2016-09-01

    We study the dynamics of a discrete-time tritrophic model which mimics the observed periodicity in the population cycles of the larch budmoth insect which causes widespread defoliation of larch forests at high altitudes periodically. Our model employs q-deformation of numbers to model the system comprising the budmoth, one or more parasitoid species, and larch trees. Incorporating climate parameters, we introduce additional parasitoid species and show that their introduction increases the periodicity of the budmoth cycles as observed experimentally. The presence of these additional species also produces other interesting dynamical effects such as periodic bursting and oscillation quenching via oscillation death, amplitude death, and partial oscillation death which are also seen in nature. We suggest that introducing additional parasitoid species provides an alternative explanation for the collapse of the nine year budmoth outbreak cycles observed in the Swiss Alps after 1981. A detailed exploration of the parameter space of the system is performed with movies of bifurcation diagrams which enable variation of two parameters at a time. Limit cycles emerge through a Neimark-Sacker bifurcation with respect to all parameters in all the five and higher dimensional models we have studied.

  4. Molecular screening for Bartonella henselae and Borrelia burgdorferi sensu lato co-existence within Ixodes ricinus populations in central and eastern parts of Poland.

    PubMed

    Sytykiewicz, Hubert; Karbowiak, Grzegorz; Werszko, Joanna; Czerniewicz, Paweł; Sprawka, Iwona; Mitrus, Joanna

    2012-01-01

    The presented study aimed at establishing the prevalence and co-infection rates of Bartonella henselae and Borrelia burgdorferi sensu lato in Ixodes ricinus ticks collected from the central and eastern parts of Poland. The common tick individuals were gathered in the years 2008-2009. Questing ticks were sampled by dragging a white woollen flag over lower vegetation at 17 localities within diverse types of habitats: urban recreational green areas (city parks and squares), suburban forests and rural woodlands throughout the investigated regions of Poland. Detection of B. henselae in tested tick specimens was based on PCR amplification of the citrate synthase (gltA) gene, while screening for the presence of B. burgdorferi s.l. DNA was carried out by analyzing fragments of two genes: the flagellin (fla) and outer surface protein A (ospA). A total number of 1,571 I. ricinus ticks were sampled: 865 (55.1%) nymphs, 377 females (24.0%) and 329 males (20.9%). The application of PCR assays revealed that 76 (4.8%) tick samples were B. henselae-positive, B. burgdorferi s.l. DNA was detected in 194 specimens (12.3%), whereas the co-existence of these pathogens was evidenced in 22 tested ticks (1.4%). Furthermore, the occurrence of bartonellae and co-circulation of analysed microorganisms in I. ricinus was affirmed only within adult individuals, while presence of the screened spirochetes was ascertained in both nymphal and adult ticks. It should be stressed that the suburban woods of Warsaw and rural forests in Warsaw County characterized the highest prevalence levels of dual infection with investigated tick-borne pathogens, whereas the lowest co-infection rates were recorded in tick populations inhabiting rural forests in Płock County and forested areas in Korczew-Mogielnica (within the Nadbużański Landscape Park).

  5. Co-existence of zebra mussels and freshwater unionids: Population dynamics of Leptodea fragilis in a coastal wetland infested with zebra mussels

    USGS Publications Warehouse

    Nichols, S. Jerrine; Amberg, Jon

    1999-01-01

    In 1996, thousands of live Leptodea fragilis were collected from a marsh located in the western basin of Lake Erie that was infested with zebra mussels (Dreissena polymorpha). Despite the presence of zebra mussels at this site for a number of years, this L. fragilis population showed no signs of competition-induced changes in population dynamics. Biofouling was limited: fewer than 1% of the L. fragilis showed evidence of recent or past zebra mussel colonization. Successful recruitment occurred yearly, with multiple year classes collected that ranged in age from 1 to 12 years. However, age and shell length were not well correlated. Seventy-one percent of the individuals collected were 51-80 mm long, but ranged in age from 2 to 4.5 years. Three different patterns of growth or shell deposition were found. Some individuals grew rapidly, reaching 105 mm in 3.5 years, while others grew only 4.5 mm over the same time period. A few grew poorly during some years but very rapidly in others. Individuals with a shell length of 41 mm or more were sexually mature and females were more common than males. The strong recruitment and steady growth of this population showed no change between the years before and after the zebra mussel invasion, indicating that this marsh is functioning as a natural refugium from potential problems caused by zebra mussels.

  6. Co-existence of major and minor viral populations from two different origins in patients secondarily infected with dengue virus serotype 2 in Bangkok.

    PubMed

    Puiprom, Orapim; Yamashita, Akifumi; Sasayama, Mikiko; Limkittikul, Kriengsak; Boonha, Khwanchit; Jittmitraphap, Akanitt; Leaungwutiwong, Pornsawan; Kurosu, Takeshi; Ramasoota, Pongrama; Ikuta, Kazuyoshi

    2011-09-16

    Generally, RNA viruses exhibit significant genetic diversity that sometimes effect viral fitness in infected hosts and probably also pathogenesis. Dengue viruses (DENVs) consist of four antigenically distinct serotypes. All the serotypes of DENV can cause mild to severe dengue illnesses. In this study, we examined the sequence variation of DENV in plasma obtained from four patients living in Bangkok who had been secondarily infected with serotype 2 (DENV-2) in 2010. The plasma-derived RNA was directly subjected to reverse transcriptase (RT)-polymerase chain reaction (PCR) at a region including most of domain III of the envelope (E) protein gene, and the PCR products obtained were subjected to clonal sequencing. Using 19-20 clones sequenced from each patient (78 total) plus 601 corresponding sequences from a public database, phylogenetic analysis revealed that the nucleic acid sequences fell into two clusters with clearly different origins. Interestingly, all patients gave sequences indicating that they carried viral populations containing 2, 3 or 5 genetic variants that consisted of one major variant plus one or more minor variants. Three patients showed a major variant from one cluster plus one or more minor components from the other while one showed major and minor variants from a single cluster. Thus, it can be concluded that DENV belonging to two different genetic lineages were co-circulated in Bangkok in 2010. For these two genotype clusters there was also a clear difference in H or Y at the deduced amino acid position 346 (i.e. H346Y) that was consistent for our sequences and 601 sequences from the public database. Thus, one among the mixed viral genotypes introduced into human individuals seems to be variably selected as the predominant component of the carried viral population, and it is possible that the dynamics of this process could influence virus evolution and disease severity.

  7. Bacterial computing with engineered populations.

    PubMed

    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.

  8. Bacterial population autowave patterns: spontaneous symmetry bursting

    NASA Astrophysics Data System (ADS)

    Medvinsky, A. B.; Tsyganov, M. A.; Karpov, V. A.; Kresteva, I. B.; Shakhbazian, V. Yu.; Ivanitsky, G. R.

    1994-12-01

    Bacteria are known to form autowave patterns (population waves) like those formed by propagating nerve impulses, phase transitions, concentration waves in the Belousov-Zhabotinsky reaction, etc. The formation of bacterial waves is due to the ability of bacteria to drift (through chemotaxis) into the regions with higher attractant concentration. As a result, in contrast to other types of autowaves, bacterial population waves have not only a diffusion component of a bacterial flow but a chemotaxis flow as well. We present the experimental results of the study of spontaneous symmetry loss of bacterial autowave patterns. We show that this phenomenon can be simulated with a simple cellular automata model, and symmetry bursting depends on the parameters characterizing chemotactic sensitivity and motility of the cells forming the population wave. In the experiments in vivo we show that the distortion of a bacterial wave shape can be initiated by bacterial density fluctuations in the parent population that the bacterial waves flake off from.

  9. Co-existence of agricultural production systems.

    PubMed

    Jank, Bernhard; Rath, Johannes; Gaugitsch, Helmut

    2006-05-01

    Strategies and best practices for the co-existence of GM and non-GM crops need to be developed and implemented with the participation of farmers and other stakeholders. According to the principle of 'subsidiarity', decisions should be made by the lowest authority possible. When applying this concept to the case of GM crops, the affected society should determine their use and management in a regional decision-making process. Public participation is better accomplished at a lower level, and democratic deficits in decision-making on GMOs are better resolved, enabling farmers to manage or avoid GM crops. Ultimately, voluntary GMO-free zones might be a tool for sustainable co-existence and GM-free production and GMO-free zones might create a specific image for marketing regional products and services, such as tourism.

  10. Dynamics of adaptive immunity against phage in bacterial populations

    PubMed Central

    Balasubramanian, Vijay

    2017-01-01

    The CRISPR (clustered regularly interspaced short palindromic repeats) mechanism allows bacteria to adaptively defend against phages by acquiring short genomic sequences (spacers) that target specific sequences in the viral genome. We propose a population dynamical model where immunity can be both acquired and lost. The model predicts regimes where bacterial and phage populations can co-exist, others where the populations exhibit damped oscillations, 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 probability. PMID:28414716

  11. Dynamics of adaptive immunity against phage in bacterial populations

    NASA Astrophysics Data System (ADS)

    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.

  12. Population bottlenecks promote cooperation in bacterial biofilms.

    PubMed

    Brockhurst, Michael A

    2007-07-25

    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 on heterogeneous bacterial substrates

    NASA Astrophysics Data System (ADS)

    Mobius, Wolfram; Murray, Andrew W.; Nelson, David R.

    2012-02-01

    How species invade new territories and how these range expansions influence the population's genotypes are important questions in the field of population genetics. The majority of work addressing these questions focuses on homogeneous environments. Much less is known about the population dynamics and population genetics when the environmental conditions are heterogeneous in space. To better understand range expansions in two-dimensional heterogeneous environments, we employ a system of bacteria and bacteriophage, the viruses of bacteria. Thereby, the bacteria constitute the environment in which a population of bacteriophages expands. The spread of phage constitutes itself in lysis of bacteria and thus formation of clear regions on bacterial lawns, called plaques. We study the population dynamics and genetics of the expanding page for various patterns of environments.

  14. Adenoid bacterial colonization in a paediatric population.

    PubMed

    Subtil, João; Rodrigues, João Carlos; Reis, Lúcia; Freitas, Luís; Filipe, Joana; Santos, Alberto; Macor, Carlos; Duarte, Aida; Jordao, Luisa

    2017-04-01

    Adenoids play a key role in both respiratory and ear infection in children. It has also been shown that adenoidectomy improves these symptoms in this population. The main goal of the present study was to evaluate adenoid bacterial colonization and document a possible relation with infectious respiratory disease. A prospective observational study was designed to evaluate the proposed hypothesis in a paediatric population submitted to adenoidectomy by either infectious or non-infectious indications and compare these two cohorts. A total of 62 patients with ages ranging from 1 to 12 years old were enrolled in the study. Adenoid surface, adenoid core and middle meatus microbiota were compared. A close association between adenoid colonization and nasal infection was found, supporting that adenoids may function as bacterial reservoir for upper airway infection. The obtained results also contribute to explain the success of adenoidectomy in patients with infectious indications.

  15. Allee effects and species co-existence in an environment where resource abundance varies.

    PubMed

    M'Gonigle, Leithen K; Greenspoon, Philip B

    2014-11-21

    Explaining patterns of diversity has long been a central focus in ecology. One of the most challenging problems has been to understand how species occupying similar ecological niches can co-exist because, with limited resources, demographic stochasticity is expected to lead to the eventual extinction of all but one of them. The Allee effect has been widely studied for its impact on the extinction risk of rare species. Its potential role in promoting co-existence has received less attention. Here, we present a model in which two species compete for a single resource across a continuous landscape. We show that Allee effects can promote their co-existence when a simple condition is met: resources are distributed unevenly across space. Furthermore, the Allee effect can stabilize co-existence despite the reduction in population density and consequent increase in demographic stochasticity that it causes. The Allee effect might, therefore, be an important force maintaining diverse communities.

  16. Bacterial Population Genetics in a Forensic Context

    SciTech Connect

    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 augmented by phylogenetic representations

  17. Bacterial Populations Associated with Smokeless Tobacco Products

    PubMed Central

    Han, Jing; Sanad, Yasser M.; Deck, Joanna; Sutherland, John B.; Li, Zhong; Walters, Matthew J.; Duran, Norma; Holman, Matthew R.

    2016-01-01

    ABSTRACT There are an estimated 8 million users of smokeless tobacco products (STPs) in the United States, and yet limited data on microbial populations within these products exist. To better understand the potential microbiological risks associated with STP use, a study was conducted to provide a baseline microbiological profile of STPs. A total of 90 samples, representing 15 common STPs, were purchased in metropolitan areas in Little Rock, AR, and Washington, DC, in November 2012, March 2013, and July 2013. Bacterial populations were evaluated using culture, pyrosequencing, and denaturing gradient gel electrophoresis (DGGE). Moist-snuff products exhibited higher levels of bacteria (average of 1.05 × 106 CFU/g STP) and diversity of bacterial populations than snus (average of 8.33 × 101 CFU/g STP) and some chewing tobacco products (average of 2.54 × 105 CFU/g STP). The most common species identified by culturing were Bacillus pumilus, B. licheniformis, B. safensis, and B. subtilis, followed by members of the genera Oceanobacillus, Staphylococcus, and Tetragenococcus. Pyrosequencing analyses of the 16S rRNA genes identified the genera Tetragenococcus, Carnobacterium, Lactobacillus, Geobacillus, Bacillus, and Staphylococcus as the predominant taxa. Several species identified are of possible concern due to their potential to cause opportunistic infections and reported abilities to reduce nitrates to nitrites, which may be an important step in the formation of carcinogenic tobacco-specific N′-nitrosamines. This report provides a microbiological baseline to help fill knowledge gaps associated with microbiological risks of STPs and to inform potential regulations regarding manufacture and testing of STPs. IMPORTANCE It is estimated that there 8 million users of smokeless tobacco products (STPs) in the United States; however, there are limited data on microbial populations that exist within these products. The current study was undertaken to better understand the

  18. Bacterial Populations Associated with Smokeless Tobacco Products.

    PubMed

    Han, Jing; Sanad, Yasser M; Deck, Joanna; Sutherland, John B; Li, Zhong; Walters, Matthew J; Duran, Norma; Holman, Matthew R; Foley, Steven L

    2016-10-15

    There are an estimated 8 million users of smokeless tobacco products (STPs) in the United States, and yet limited data on microbial populations within these products exist. To better understand the potential microbiological risks associated with STP use, a study was conducted to provide a baseline microbiological profile of STPs. A total of 90 samples, representing 15 common STPs, were purchased in metropolitan areas in Little Rock, AR, and Washington, DC, in November 2012, March 2013, and July 2013. Bacterial populations were evaluated using culture, pyrosequencing, and denaturing gradient gel electrophoresis (DGGE). Moist-snuff products exhibited higher levels of bacteria (average of 1.05 × 10(6) CFU/g STP) and diversity of bacterial populations than snus (average of 8.33 × 10(1) CFU/g STP) and some chewing tobacco products (average of 2.54 × 10(5) CFU/g STP). The most common species identified by culturing were Bacillus pumilus, B. licheniformis, B. safensis, and B. subtilis, followed by members of the genera Oceanobacillus, Staphylococcus, and Tetragenococcus. Pyrosequencing analyses of the 16S rRNA genes identified the genera Tetragenococcus, Carnobacterium, Lactobacillus, Geobacillus, Bacillus, and Staphylococcus as the predominant taxa. Several species identified are of possible concern due to their potential to cause opportunistic infections and reported abilities to reduce nitrates to nitrites, which may be an important step in the formation of carcinogenic tobacco-specific N'-nitrosamines. This report provides a microbiological baseline to help fill knowledge gaps associated with microbiological risks of STPs and to inform potential regulations regarding manufacture and testing of STPs. It is estimated that there 8 million users of smokeless tobacco products (STPs) in the United States; however, there are limited data on microbial populations that exist within these products. The current study was undertaken to better understand the potential

  19. Dynamics of genome rearrangement in bacterial populations.

    PubMed

    Darling, Aaron E; Miklós, István; Ragan, Mark A

    2008-07-18

    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.

  20. The effects of colonization, extinction and competition on co-existence in metacommunities.

    PubMed

    Hunt, Julia J F G; Bonsall, Michael B

    2009-07-01

    1. The co-existence of competitors in heterogeneous landscapes depends on the processes of colonization, extinction and spatial scale. In this study, we explore the metapopulation dynamics of competitive interactions. 2. Rather than simply evaluating the outcome of interspecific competition in the traditional manner, we focus on both the local population dynamic effects and the regional metapopulation processes affecting species co-existence. 3. We develop a theoretical model of regional co-existence to generate a set of predictions on the patterns of colonization necessary for co-existence and the regional processes that can lead to competitive exclusion. We empirically test these predictions using metacommunity microcosms of the interaction between two bruchid beetles (Callosobruchus chinensis, Callosobruchus maculatus). 4. Using well-replicated time series of the interaction between the bruchids and statistical methods of model fitting, we show how the qualitative and quantitative pattern of interspecific competition between the bruchid beetles is shaped by the structure of the metacommunity. 5. In unlimited dispersal metacommunities, the global exclusion of the inferior competitor is shown to be influenced more by the processes associated with extinction rather than low colonization ability. In restricted dispersal metacommunities, we show how the co-existence of competitors in a spatially heterogeneous habitat (patches connected through limited dispersal) is affected by Allee effects and life-history [colonization (dispersal) - competition] trade-offs.

  1. Boundary of Phase Co-existence in Docosahexaenoic Acid System

    NASA Astrophysics Data System (ADS)

    Lor, Chai; Hirst, Linda S.

    2011-11-01

    Docosahexaenoic acid (DHA) is a highly polyunsaturated fatty acid (PUFA) that exhibits six double bonds in the hydrocarbon tail. It induces phase separation of the membrane into liquid order and liquid disorder in mixtures containing other lipids with more saturation and cholesterol. With the utilization of atomic force microscopy, phase co-existence is observed in lipid mixtures containing DHA on a single supported lipid bilayer. The boundary of phase co-existence with decreasing DHA concentration is explored. The elastic force, thickness, and roughness of the different phases are investigated.

  2. Persistence of antibiotic resistance in bacterial populations.

    PubMed

    Andersson, Dan I; Hughes, Diarmaid

    2011-09-01

    Unfortunately for mankind, it is very likely that the antibiotic resistance problem we have generated during the last 60 years due to the extensive use and misuse of antibiotics is here to stay for the foreseeable future. This view is based on theoretical arguments, mathematical modeling, experiments and clinical interventions, suggesting that even if we could reduce antibiotic use, resistant clones would remain persistent and only slowly (if at all) be outcompeted by their susceptible relatives. In this review, we discuss the multitude of mechanisms and processes that are involved in causing the persistence of chromosomal and plasmid-borne resistance determinants and how we might use them to our advantage to increase the likelihood of reversing the problem. Of particular interest is the recent demonstration that a very low antibiotic concentration can be enriching for resistant bacteria and the implication that antibiotic release into the environment could contribute to the selection for resistance. Several mechanisms are contributing to the stability of antibiotic resistance in bacterial populations and even if antibiotic use is reduced it is likely that most resistance mechanisms will persist for considerable times.

  3. Gardnerella vaginalis population dynamics in bacterial vaginosis.

    PubMed

    Hilbert, D W; Schuyler, J A; Adelson, M E; Mordechai, E; Sobel, J D; Gygax, S E

    2017-02-14

    Bacterial vaginosis (BV) is the leading cause of vaginal discharge and is associated with the facultative Gram-variable bacterium Gardnerella vaginalis, whose population structure consists of four clades. Our goal was to determine if these clades differ with regard to abundance during BV. We performed a short-term longitudinal study of BV. Patients were evaluated according to the Amsel criteria and Nugent scoring at initial diagnosis, immediately after treatment and at a 40- to 45-day follow-up visit. G. vaginalis clade abundance was determined by quantitative real-time polymerase chain reactions (qPCRs). Among all specimens, the abundance of clades 1 and 4 were higher than that of clades 2 and 3 (P < 0.001). In general, the abundance of each clade increased with the degree of vaginal dysbiosis, as determined by the Nugent score and was greater in women with Amsel 4 compared with those with Amsel 0. Only clade 1 abundance was greater when Amsel 0 or 1 specimens were compared with Amsel 2 or 3 specimens (P < 0.01). Following antimicrobial treatment, abundance of clades 1 (P < 0.001) and 4 (P < 0.05) decreased regardless of the clinical and microbiological outcome, whereas clade 2 only decreased in women who had a sustained treatment response for 40-45 days (P < 0.01). Recurrent BV was characterized by post-treatment increases of clade 1 and 2 (P < 0.01). Clades 1 and 4 predominate in vaginal specimens. Clade abundance differs with regard to the Nugent score, the Amsel criteria, and response to therapy and BV recurrence.

  4. Optimal control methods for controlling bacterial populations with persister dynamics

    NASA Astrophysics Data System (ADS)

    Cogan, N. G.

    2016-06-01

    Bacterial tolerance to antibiotics is a well-known phenomena; however, only recent studies of bacterial biofilms have shown how multifaceted tolerance really is. By joining into a structured community and offering shared protection and gene transfer, bacterial populations can protect themselves genotypically, phenotypically and physically. In this study, we collect a line of research that focuses on phenotypic (or plastic) tolerance. The dynamics of persister formation are becoming better understood, even though there are major questions that remain. The thrust of our results indicate that even without detailed description of the biological mechanisms, theoretical studies can offer strategies that can eradicate bacterial populations with existing drugs.

  5. Sarcoidosis and primary biliary cirrhosis with co-existing myositis

    PubMed Central

    Hughes, P.; McGavin, C. R.

    1997-01-01

    In a small number of cases the co-existence of primary biliary cirrhosis and sarcoidosis is assumed from clinical serological and histological findings. A case of sarcoidosis is reported in which the M2 antibody, a highly specific marker for primary biliary cirrhosis, was detected. The patient also developed a severe myositis and a possible overlap syndrome is discussed. 




 PMID:9059489

  6. Molecular population genetic analysis of emerged bacterial pathogens: selected insights.

    PubMed Central

    Musser, J. M.

    1996-01-01

    Research in bacterial population genetics has increased in the last 10 years. Population genetic theory and tools and related strategies have been used to investigate bacterial pathogens that have contributed to recent episodes of temporal variation in disease frequency and severity. A common theme demonstrated by these analyses is that distinct bacterial clones are responsible for disease outbreaks and increases in infection frequency. Many of these clones are characterized by unique combinations of virulence genes or alleles of virulence genes. Because substantial interclonal variance exists in relative virulence, molecular population genetic studies have led to the concept that the unit of bacterial pathogenicity is the clone or cell line. Continued new insights into host parasite interactions at the molecular level will be achieved by combining clonal analysis of bacterial pathogens with large-scale comparative sequencing of virulence genes. PMID:8903193

  7. Co-existence of Functionally Different Vesicular Neurotransmitter Transporters

    PubMed Central

    Münster-Wandowski, Agnieszka; Zander, Johannes-Friedrich; Richter, Karin; Ahnert-Hilger, Gudrun

    2016-01-01

    The vesicular transmitter transporters VGLUT, VGAT, VMAT2 and VAChT, define phenotype and physiological properties of neuronal subtypes. VGLUTs concentrate the excitatory amino acid glutamate, VGAT the inhibitory amino acid GABA, VMAT2 monoamines, and VAChT acetylcholine (ACh) into synaptic vesicle (SV). Following membrane depolarization SV release their content into the synaptic cleft. A strict segregation of vesicular transporters is mandatory for the precise functioning of synaptic communication and of neuronal circuits. In the last years, evidence accumulates that subsets of neurons express more than one of these transporters leading to synaptic co-release of different and functionally opposing transmitters and modulation of synaptic plasticity. Synaptic co-existence of transporters may change during pathological scenarios in order to ameliorate misbalances in neuronal activity. In addition, evidence increases that transporters also co-exist on the same vesicle providing another layer of regulation. Generally, vesicular transmitter loading relies on an electrochemical gradient ΔμH+ driven by the proton ATPase rendering the lumen of the vesicle with respect to the cytosol positive (Δψ) and acidic (ΔpH). While the activity of VGLUT mainly depends on the Δψ component, VMAT, VGAT and VAChT work best at a high ΔpH. Thus, a vesicular synergy of transporters depending on the combination may increase or decrease the filling of SV with the principal transmitter. We provide an overview on synaptic co-existence of vesicular transmitter transporters including changes in the excitatory/inhibitory balance under pathological conditions. Additionally, we discuss functional aspects of vesicular synergy of transmitter transporters. PMID:26909036

  8. Co-existence of Functionally Different Vesicular Neurotransmitter Transporters.

    PubMed

    Münster-Wandowski, Agnieszka; Zander, Johannes-Friedrich; Richter, Karin; Ahnert-Hilger, Gudrun

    2016-01-01

    The vesicular transmitter transporters VGLUT, VGAT, VMAT2 and VAChT, define phenotype and physiological properties of neuronal subtypes. VGLUTs concentrate the excitatory amino acid glutamate, VGAT the inhibitory amino acid GABA, VMAT2 monoamines, and VAChT acetylcholine (ACh) into synaptic vesicle (SV). Following membrane depolarization SV release their content into the synaptic cleft. A strict segregation of vesicular transporters is mandatory for the precise functioning of synaptic communication and of neuronal circuits. In the last years, evidence accumulates that subsets of neurons express more than one of these transporters leading to synaptic co-release of different and functionally opposing transmitters and modulation of synaptic plasticity. Synaptic co-existence of transporters may change during pathological scenarios in order to ameliorate misbalances in neuronal activity. In addition, evidence increases that transporters also co-exist on the same vesicle providing another layer of regulation. Generally, vesicular transmitter loading relies on an electrochemical gradient ΔμH(+) driven by the proton ATPase rendering the lumen of the vesicle with respect to the cytosol positive (Δψ) and acidic (ΔpH). While the activity of VGLUT mainly depends on the Δψ component, VMAT, VGAT and VAChT work best at a high ΔpH. Thus, a vesicular synergy of transporters depending on the combination may increase or decrease the filling of SV with the principal transmitter. We provide an overview on synaptic co-existence of vesicular transmitter transporters including changes in the excitatory/inhibitory balance under pathological conditions. Additionally, we discuss functional aspects of vesicular synergy of transmitter transporters.

  9. Co-Existence of Multicentric Castleman's Disease and Kaposi's Sarcoma

    PubMed Central

    Yaghoobi, Reza; Pazyar, Nader; Tavakoli, Sadigheh

    2015-01-01

    Castleman's disease (CD) or giant lymph node hyperplasia is a rare disorder that can be unicentric or multicentric. Multicentric Castleman's disease (MCD) is manifested by generalized lymphadenopathy, hepatosplenomegaly, polyclonal hypergammaglobulinemia, hematological abnormality, and constitutional symptoms. Human herpesvirus 8 (HHV-8) infection is present in nearly 100% MCD associated with HIV-1 infection, but in about 50% of cases of HIV negative. Herein, we report a 77-year-old man with systemic involvement and skin lesions on the anterior aspect of both legs in the previous site of saphenous vein angioplasty. Co-existence of MCD with Kaposi's sarcoma (KS) led us to present this rare case. PMID:26120185

  10. Electrical signaling and photosynthesis: can they co-exist together?

    PubMed

    Pavlovič, Andrej; Mancuso, Stefano

    2011-06-01

    Mechanical irritation of trigger hairs and subsequent generation of action potentials have significant impact on photosynthesis and respiration in carnivorous Venus flytrap (Dionaea muscipula). Action potential-mediated inhibition of photosynthesis and stimulation of respiration is confined only to the trap and was not recorded in adjacent photosynthetic lamina. We showed that the main primary target of electrical signals on assimilation is in the dark enzymatic reaction of photosynthesis. Without doubt, the electrical signaling is costly, and the possible co-existence of such type of signals and photosynthesis in plant cell is discussed.

  11. Coal and climate regulations can co-exist

    SciTech Connect

    Rogers, J.

    2006-07-15

    Jim Rogers, president and chief executive officer of Duke Energy Corporation, examines how coal and climate change regulations can co-exist. He addresses the need for economically sound choices for future energy needs, which is complicated by what he refers to as 'the elephant in the room'climate change. He observes that new CO{sub 2} regulations would increase the USA's cost of generating electricity over time and result in higher prices for customers, and he advocates that a gradual, economy-wide, market-based U.S. climate policy is the best option. 1 ref., 1 fig.

  12. Bacterial associations reveal spatial population dynamics in Anopheles gambiae mosquitoes

    PubMed Central

    Buck, Moritz; Nilsson, Louise K. J.; Brunius, Carl; Dabiré, Roch K.; Hopkins, Richard; Terenius, Olle

    2016-01-01

    The intolerable burden of malaria has for too long plagued humanity and the prospect of eradicating malaria is an optimistic, but reachable, target in the 21st century. However, extensive knowledge is needed about the spatial structure of mosquito populations in order to develop effective interventions against malaria transmission. We hypothesized that the microbiota associated with a mosquito reflects acquisition of bacteria in different environments. By analyzing the whole-body bacterial flora of An. gambiae mosquitoes from Burkina Faso by 16 S amplicon sequencing, we found that the different environments gave each mosquito a specific bacterial profile. In addition, the bacterial profiles provided precise and predicting information on the spatial dynamics of the mosquito population as a whole and showed that the mosquitoes formed clear local populations within a meta-population network. We believe that using microbiotas as proxies for population structures will greatly aid improving the performance of vector interventions around the world. PMID:26960555

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

    NASA Astrophysics Data System (ADS)

    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

  14. Measurement of Behavioral Evolution in Bacterial Populations

    NASA Astrophysics Data System (ADS)

    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

    Treesearch

    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. Which games are growing bacterial populations playing?

    PubMed Central

    Li, Xiang-Yi; Pietschke, Cleo; Fraune, Sebastian; Altrock, Philipp M.; Bosch, Thomas C. G.; Traulsen, Arne

    2015-01-01

    Microbial communities display complex population dynamics, both in frequency and absolute density. Evolutionary game theory provides a natural approach to analyse and model this complexity by studying the detailed interactions among players, including competition and conflict, cooperation and coexistence. Classic evolutionary game theory models typically assume constant population size, which often does not hold for microbial populations. Here, we explicitly take into account population growth with frequency-dependent growth parameters, as observed in our experimental system. We study the in vitro population dynamics of the two commensal bacteria (Curvibacter sp. (AEP1.3) and Duganella sp. (C1.2)) that synergistically protect the metazoan host Hydra vulgaris (AEP) from fungal infection. The frequency-dependent, nonlinear growth rates observed in our experiments indicate that the interactions among bacteria in co-culture are beyond the simple case of direct competition or, equivalently, pairwise games. This is in agreement with the synergistic effect of anti-fungal activity observed in vivo. Our analysis provides new insight into the minimal degree of complexity needed to appropriately understand and predict coexistence or extinction events in this kind of microbial community dynamics. Our approach extends the understanding of microbial communities and points to novel experiments. PMID:26236827

  17. Dynamics of Sequence -Discrete Bacterial Populations Inferred Using Metagenomes

    SciTech Connect

    Stevens, Sarah; Bendall, Matthew; Kang, Dongwan; Froula, Jeff; Egan, Rob; Chan, Leong-Keat; Tringe, Susannah; McMahon, Katherine; Malmstrom, Rex

    2014-03-14

    From a multi-year metagenomic time series of two dissimilar Wisconsin lakes we have assembled dozens of genomes using a novel approach that bins contigs into distinct genome based on sequence composition, e.g. kmer frequencies, and contig coverage patterns at various times points. Next, we investigated how these genomes, which represent sequence-discrete bacterial populations, evolved over time and used the time series to discover the population dynamics. For example, we explored changes in single nucleotide polymorphism (SNP) frequencies as well as patterns of gene gain and loss in multiple populations. Interestingly, SNP diversity was purged at nearly every genome position in some populations during the course of this study, suggesting these populations may have experienced genome-wide selective sweeps. This represents the first direct, time-resolved observations of periodic selection in natural populations, a key process predicted by the ecotype model of bacterial diversification.

  18. Genes and processed paralogs co-exist in plant mitochondria.

    PubMed

    Cuenca, Argelia; Petersen, Gitte; Seberg, Ole; Jahren, Anne Hoppe

    2012-04-01

    RNA-mediated gene duplication has been proposed to create processed paralogs in the plant mitochondrial genome. A processed paralog may retain signatures left by the maturation process of its RNA precursor, such as intron removal and no need of RNA editing. Whereas it is well documented that an RNA intermediary is involved in the transfer of mitochondrial genes to the nucleus, no direct evidence exists for insertion of processed paralogs in the mitochondria (i.e., processed and un-processed genes have never been found simultaneously in the mitochondrial genome). In this study, we sequenced a region of the mitochondrial gene nad1, and identified a number of taxa were two different copies of the region co-occur in the mitochondria. The two nad1 paralogs differed in their (a) presence or absence of a group II intron, and (b) number of edited sites. Thus, this work provides the first evidence of co-existence of processed paralogs and their precursors within the plant mitochondrial genome. In addition, mapping the presence/absence of the paralogs provides indirect evidence of RNA-mediated gene duplication as an essential process shaping the mitochondrial genome in plants.

  19. Sheehan's syndrome co-existing with Graves' disease.

    PubMed

    Arpaci, D; Cuhaci, N; Saglam, F; Ersoy, R; Cakir, B

    2014-01-01

    Sheehan's syndrome (SS), which is an important cause of hypopituitarism, is common in developing countries. The most common presentation is the absence of lactation and amenorrhea. Hypothyroidism rather than hyperthyroidism is the usual expected phenomenon in SS. Postpartum hyperthyroidism is also common and Graves' disease (GD) is an important cause of postpartum hyperthyroidism. Here we report a case of a 22-year-old female patient in our clinic presented symptoms of amenorrhea, lack of lactation, palpitations and sweating. Her physical examination revealed goiter, moist skin and proptosis. Her laboratory evaluation showed suppressed thyroid stimulating hormone, elevated levels of free thyroxine and free triiodothyronine. Thyroid antibodies were positive. Tec 99m thyroid scintigraphy results were gland hyperplasia and increased uptake consistent with GD. She gave birth 7 months ago; after delivery she had a history of prolonged bleeding, amenorrhea and inability to lactate. She had hypogonadotropic hypogonadism, hyperprolactinemia and growth hormone deficiency. Serum cortisol and adrenocorticotropic hormone levels were normal. Her magnetic resonance imaging was empty sella. Our diagnosis was GD co-existing with SS. GD with concomitant hypopituitarism is rare but has been described previously, but there are no reports of GD occurring with SS. In this case study, we report a patient with GD associated with SS.

  20. Dynamic control and quantification of bacterial population dynamics in droplets.

    PubMed

    Huang, Shuqiang; Srimani, Jaydeep K; Lee, Anna J; Zhang, Ying; Lopatkin, Allison J; Leong, Kam W; You, Lingchong

    2015-08-01

    Culturing and measuring bacterial population dynamics are critical to develop insights into gene regulation or bacterial physiology. Traditional methods, based on bulk culture to obtain such quantification, have the limitations of higher cost/volume of reagents, non-amendable to small size of population and more laborious manipulation. To this end, droplet-based microfluidics represents a promising alternative that is cost-effective and high-throughput. However, difficulties in manipulating the droplet environment and monitoring encapsulated bacterial population for long-term experiments limit its utilization. To overcome these limitations, we used an electrode-free injection technology to modulate the chemical environment in droplets. This ability is critical for precise control of bacterial dynamics in droplets. Moreover, we developed a trapping device for long-term monitoring of population dynamics in individual droplets for at least 240 h. We demonstrated the utility of this new microfluidic system by quantifying population dynamics of natural and engineered bacteria. Our approach can further improve the analysis for systems and synthetic biology in terms of manipulability and high temporal resolution.

  1. Dynamic control and quantification of bacterial population dynamics in droplets

    PubMed Central

    Huang, Shuqiang; Srimani, Jaydeep K.; Lee, Anna J.; Zhang, Ying; Lopatkin, Allison J.; Leong, Kam W.; You, Lingchong

    2015-01-01

    Culturing and measuring bacterial population dynamics are critical to develop insights into gene regulation or bacterial physiology. Traditional methods, based on bulk culture to obtain such quantification, have the limitations of higher cost/volume of reagents, non-amendable to small size of population and more laborious manipulation. To this end, droplet-based microfluidics represents a promising alternative that is cost-effective and high-throughput. However, difficulties in manipulating the droplet environment and monitoring encapsulated bacterial population for long-term experiments limit its utilization. To overcome these limitations, we used an electrode-free injection technology to modulate the chemical environment in droplets. This ability is critical for precise control of bacterial dynamics in droplets. Moreover, we developed a trapping device for long-term monitoring of population dynamics in individual droplets for at least 240 h. We demonstrated the utility of this new microfluidic system by quantifying population dynamics of natural and engineered bacteria. Our approach can further improve the analysis for systems and synthetic biology in terms of manipulability and high temporal resolution. PMID:26005763

  2. Spatiotemporal Co-existence of Female Thyroid and Breast Cancers in Hangzhou, China

    PubMed Central

    Fei, Xufeng; Christakos, George; Lou, Zhaohan; Ren, Yanjun; Liu, Qingmin; Wu, Jiaping

    2016-01-01

    Thyroid and breast cancers (TC, BC) are common female malignant tumors worldwide. Studies suggest that TC patients have a higher BC risk, and vice versa. However, it has not been investigated quantitatively if there is an association between the space-time TC and BC incidence distributions at the population level. This work aims to answer this question. 5358 TC and 8784 BC (female) cases were diagnosed in Hangzhou (China, 2008–2012). Pearson and Spearman rank correlation coefficients of the TC and BC incidences were high, and their patterns were geographically similar. The spatiotemporal co-existence of TC and BC distributions was investigated using the integrative disease predictability (IDP) criterion: if TC-BC association is part of the disease mapping knowledge bases, it should yield improved space-time incidence predictions. Improved TC (BC) incidence predictions were generated when integrating both TC and BC data than when using only TC (BC) data. IDP consistently demonstrated the spatiotemporal co-existence of TC and BC distributions throughout Hangzhou (2008–2012), which means that when the population experiences high incidences of one kind of cancer attention should be paid to the other kind of cancer too. The strength of TC-BC association was measured by the IDP coefficients and incidence prediction accuracy. PMID:27341638

  3. Spatiotemporal Co-existence of Female Thyroid and Breast Cancers in Hangzhou, China.

    PubMed

    Fei, Xufeng; Christakos, George; Lou, Zhaohan; Ren, Yanjun; Liu, Qingmin; Wu, Jiaping

    2016-06-24

    Thyroid and breast cancers (TC, BC) are common female malignant tumors worldwide. Studies suggest that TC patients have a higher BC risk, and vice versa. However, it has not been investigated quantitatively if there is an association between the space-time TC and BC incidence distributions at the population level. This work aims to answer this question. 5358 TC and 8784 BC (female) cases were diagnosed in Hangzhou (China, 2008-2012). Pearson and Spearman rank correlation coefficients of the TC and BC incidences were high, and their patterns were geographically similar. The spatiotemporal co-existence of TC and BC distributions was investigated using the integrative disease predictability (IDP) criterion: if TC-BC association is part of the disease mapping knowledge bases, it should yield improved space-time incidence predictions. Improved TC (BC) incidence predictions were generated when integrating both TC and BC data than when using only TC (BC) data. IDP consistently demonstrated the spatiotemporal co-existence of TC and BC distributions throughout Hangzhou (2008-2012), which means that when the population experiences high incidences of one kind of cancer attention should be paid to the other kind of cancer too. The strength of TC-BC association was measured by the IDP coefficients and incidence prediction accuracy.

  4. Spatiotemporal Co-existence of Female Thyroid and Breast Cancers in Hangzhou, China

    NASA Astrophysics Data System (ADS)

    Fei, Xufeng; Christakos, George; Lou, Zhaohan; Ren, Yanjun; Liu, Qingmin; Wu, Jiaping

    2016-06-01

    Thyroid and breast cancers (TC, BC) are common female malignant tumors worldwide. Studies suggest that TC patients have a higher BC risk, and vice versa. However, it has not been investigated quantitatively if there is an association between the space-time TC and BC incidence distributions at the population level. This work aims to answer this question. 5358 TC and 8784 BC (female) cases were diagnosed in Hangzhou (China, 2008-2012). Pearson and Spearman rank correlation coefficients of the TC and BC incidences were high, and their patterns were geographically similar. The spatiotemporal co-existence of TC and BC distributions was investigated using the integrative disease predictability (IDP) criterion: if TC-BC association is part of the disease mapping knowledge bases, it should yield improved space-time incidence predictions. Improved TC (BC) incidence predictions were generated when integrating both TC and BC data than when using only TC (BC) data. IDP consistently demonstrated the spatiotemporal co-existence of TC and BC distributions throughout Hangzhou (2008-2012), which means that when the population experiences high incidences of one kind of cancer attention should be paid to the other kind of cancer too. The strength of TC-BC association was measured by the IDP coefficients and incidence prediction accuracy.

  5. Phage selection for bacterial cheats leads to population decline.

    PubMed

    Vasse, Marie; Torres-Barceló, Clara; Hochberg, Michael E

    2015-11-07

    While predators and parasites are known for their effects on bacterial population biology, their impact on the dynamics of bacterial social evolution remains largely unclear. Siderophores are iron-chelating molecules that are key to the survival of certain bacterial species in iron-limited environments, but their production can be subject to cheating by non-producing genotypes. In a selection experiment conducted over approximately 20 bacterial generations and involving 140 populations of the pathogenic bacterium Pseudomonas aeruginosa PAO1, we assessed the impact of a lytic phage on competition between siderophore producers and non-producers. We show that the presence of lytic phages favours the non-producing genotype in competition, regardless of whether iron use relies on siderophores. Interestingly, phage pressure resulted in higher siderophore production, which constitutes a cost to the producers and may explain why they were outcompeted by non-producers. By the end of the experiment, however, cheating load reduced the fitness of mixed populations relative to producer monocultures, and only monocultures of producers managed to grow in the presence of phage in situations where siderophores were necessary to access iron. These results suggest that public goods production may be modulated in the presence of natural enemies with consequences for the evolution of social strategies. © 2015 The Author(s).

  6. Correlated Mutations and Homologous Recombination Within Bacterial Populations.

    PubMed

    Lin, Mingzhi; Kussell, Edo

    2017-02-01

    Inferring the rate of homologous recombination within a bacterial population remains a key challenge in quantifying the basic parameters of bacterial evolution. Due to the high sequence similarity within a clonal population, and unique aspects of bacterial DNA transfer processes, detecting recombination events based on phylogenetic reconstruction is often difficult, and estimating recombination rates using coalescent model-based methods is computationally expensive, and often infeasible for large sequencing data sets. Here, we present an efficient solution by introducing a set of mutational correlation functions computed using pairwise sequence comparison, which characterize various facets of bacterial recombination. We provide analytical expressions for these functions, which precisely recapitulate simulation results of neutral and adapting populations under different coalescent models. We used these to fit correlation functions measured at synonymous substitutions using whole-genome data on Escherichia coli and Streptococcus pneumoniae populations. We calculated and corrected for the effect of sample selection bias, i.e., the uneven sampling of individuals from natural microbial populations that exists in most datasets. Our method is fast and efficient, and does not employ phylogenetic inference or other computationally intensive numerics. By simply fitting analytical forms to measurements from sequence data, we show that recombination rates can be inferred, and the relative ages of different samples can be estimated. Our approach, which is based on population genetic modeling, is broadly applicable to a wide variety of data, and its computational efficiency makes it particularly attractive for use in the analysis of large sequencing datasets. Copyright © 2017 by the Genetics Society of America.

  7. Staphylococcus aureus SrrAB Affects Susceptibility to Hydrogen Peroxide and Co-Existence with Streptococcus sanguinis

    PubMed Central

    Oogai, Yuichi; Kawada-Matsuo, Miki; Komatsuzawa, Hitoshi

    2016-01-01

    Staphylococcus aureus is a pathogen and a commensal bacterial species that is found in humans. Bacterial two-component systems (TCSs) sense and respond to environmental stresses, which include antimicrobial agents produced by other bacteria. In this study, we analyzed the relation between the TCS SrrAB and susceptibility to the hydrogen peroxide (H2O2) that is produced by Streptococcus sanguinis, which is a commensal oral streptococcus. An srrA-inactivated S. aureus mutant demonstrated low susceptibility to the H2O2 produced by S. sanguinis. We investigated the expression of anti-oxidant factors in the mutant. The expression of katA in the mutant was significantly higher than in the wild-type (WT) in the presence or absence of 0.4 mM H2O2. The expression of dps in the mutant was significantly increased compared with the WT in the presence of H2O2 but not in the absence of H2O2. A katA or a dps-inactivated mutant had high susceptibility to H2O2 compared with WT. In addition, we found that the nitric oxide detoxification protein (flavohemoglobin: Hmp), which is regulated by SrrAB, was related to H2O2 susceptibility. The hmp-inactivated mutant had slightly lower susceptibility to the H2O2 produced by S. sanguinis than did WT. When a srrA-inactivated mutant or the WT were co-cultured with S. sanguinis, the population percentage of the mutant was significantly higher than the WT. In conclusion, SrrAB regulates katA, dps and hmp expression and affects H2O2 susceptibility. Our findings suggest that SrrAB is related in vivo to the co-existence of S. aureus with S. sanguinis. PMID:27441894

  8. In Situ Hydrocarbon Degradation by Indigenous Nearshore Bacterial Populations

    SciTech Connect

    Cherrier, J.

    2005-05-16

    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{sub 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{sub 2} was used as the indicator of hydrocarbon degradation and {delta}{sup 13}C analysis of the resultant CO{sub 2} was used to evaluate the source of the respired CO{sub 2} (i.e. petroleum hydrocarbons or the pinfish cometabolite

  9. Differential resistance of drinking water bacterial populations to monochloramine disinfection.

    PubMed

    Chiao, Tzu-Hsin; Clancy, Tara M; Pinto, Ameet; Xi, Chuanwu; Raskin, Lutgarde

    2014-04-01

    The impact of monochloramine disinfection on the complex bacterial community structure in drinking water systems was investigated using culture-dependent and culture-independent methods. Changes in viable bacterial diversity were monitored using culture-independent methods that distinguish between live and dead cells based on membrane integrity, providing a highly conservative measure of viability. Samples were collected from lab-scale and full-scale drinking water filters exposed to monochloramine for a range of contact times. Culture-independent detection of live cells was based on propidium monoazide (PMA) treatment to selectively remove DNA from membrane-compromised cells. Quantitative PCR (qPCR) and pyrosequencing of 16S rRNA genes was used to quantify the DNA of live bacteria and characterize the bacterial communities, respectively. The inactivation rate determined by the culture-independent PMA-qPCR method (1.5-log removal at 664 mg·min/L) was lower than the inactivation rate measured by the culture-based methods (4-log removal at 66 mg·min/L). Moreover, drastic changes in the live bacterial community structure were detected during monochloramine disinfection using PMA-pyrosequencing, while the community structure appeared to remain stable when pyrosequencing was performed on samples that were not subject to PMA treatment. Genera that increased in relative abundance during monochloramine treatment include Legionella, Escherichia, and Geobacter in the lab-scale system and Mycobacterium, Sphingomonas, and Coxiella in the full-scale system. These results demonstrate that bacterial populations in drinking water exhibit differential resistance to monochloramine, and that the disinfection process selects for resistant bacterial populations.

  10. Quantitation of major human cutaneous bacterial and fungal populations.

    PubMed

    Gao, Zhan; Perez-Perez, Guillermo I; Chen, Yu; Blaser, Martin J

    2010-10-01

    Because the human skin microbiota may play roles in the causation or modification of skin diseases, we sought to provide initial quantitative analysis from different cutaneous locations. We developed quantitative PCRs to enumerate the total bacterial and fungal populations, as well as the most common bacterial and fungal genera present in six locales, in eight healthy subjects. We used a set of primers and TaqMan MGB probes based on the bacterial 16S rRNA and fungal internally transcribed spacer region, as well as bacterial genus-specific probes for Propionibacterium, Corynebacterium, Streptococcus, and Staphylococcus and a fungal genus-specific probe for Malassezia. The extent of human DNA contamination of the specimen was determined by quantitating the human housekeeping GAPDH gene. The highest level of 16S rRNA copies of bacteria was present in the axilla (4.44 ± 0.18 log(10) copies/μl [mean ± standard error of the mean]), with normalization based on GAPDH levels, but the other five locations were similar to one another (range, 2.48 to 2.89 log(10) copies/μl). There was strong symmetry between the left and right sides. The four bacterial genera accounted for 31% to 59% of total bacteria, with the highest percent composition in the axilla and the lowest in the forearm. Streptococcus was the most common genus present on the forehead and behind the ear. Corynebacterium spp. were predominant in the axilla. Fungal levels were 1 to 2 log(10) lower than for bacteria, with Malassezia spp. accounting for the majority of fungal gene copies. These results provide the first quantitation of the site and host specificities of major bacterial and fungal populations in human skin and present simple methods for their assessment in studies of disease.

  11. Modeling Bacterial Population Growth from Stochastic Single-Cell Dynamics

    PubMed Central

    Molina, Ignacio; Theodoropoulos, Constantinos

    2014-01-01

    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

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

    PubMed

    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

  13. Cooperation and conflict in quorum-sensing bacterial populations.

    PubMed

    Diggle, Stephen P; Griffin, Ashleigh S; Campbell, Genevieve S; West, Stuart A

    2007-11-15

    It has been suggested that bacterial cells communicate by releasing and sensing small diffusible signal molecules in a process commonly known as quorum sensing (QS). It is generally assumed that QS is used to coordinate cooperative behaviours at the population level. However, evolutionary theory predicts that individuals who communicate and cooperate can be exploited. Here we examine the social evolution of QS experimentally in the opportunistic pathogen Pseudomonas aeruginosa, and show that although QS can provide a benefit at the group level, exploitative individuals can avoid the cost of producing the QS signal or of performing the cooperative behaviour that is coordinated by QS, and can therefore spread. We also show that a solution to the problem of exploitation is kin selection, if interacting bacterial cells tend to be close relatives. These results show that the problem of exploitation, which has been the focus of considerable attention in animal communication, also arises in bacteria.

  14. Bacteriocin-Mediated Competitive Interactions of Bacterial Populations and Communities

    NASA Astrophysics Data System (ADS)

    Riley, Margaret A.

    Explaining the coexistence of competing species is a major challenge in community ecology. In bacterial systems, competition is often driven by the production of bacteriocins; narrow spectrum proteinaceous toxins that serve to kill closely related species providing the producer better access to limited resources. Bacteriocin producers have been shown to competitively exclude sensitive, nonproducing strains. However, the interaction dynamics between bacteriocin producers, each lethal to its competitor, are largely unknown. Several recent studies have revealed some of the complexity of these interactions, employing a suite of in vitro, in vivo, and in silico bacterial model systems. This chapter describes the current state of knowledge regarding the population and community ecology of this potent family of toxins.

  15. Nonrandom assembly of bacterial populations in activated sludge flocs.

    PubMed

    Ayarza, Joaquín M; Guerrero, Leandro D; Erijman, Leonardo

    2010-04-01

    The aim of this work was to investigate the dynamics of assembly of bacterial populations in activated sludge flocs. We approached this question by following the development of active bacterial populations during floc development in four replicated lab-scale activated sludge reactors, in which solid retention time (SRT) was set at 4 days. The null hypothesis was that the similarities in community composition could be accounted for by the probability that the same organisms occur in more than one replicated reactor. Microscopic imaging showed that the size of flocs in reactors with biomass retention increased during the first few days until a steady-state size was reached. The diversity and community structure of the sludge in all reactors were analyzed during a period of up to ten SRT, using denaturing gradient gel electrophoresis (DGGE) of reverse-transcription polymerase chain reaction-amplified 16S rRNA. High rates of change in DGGE profiles from consecutive sampling points suggested a high level of dynamics in all reactors. This conclusion was confirmed by the application of the Raup and Crick probability-based similarity index (S(RC)) for the comparison of rRNA-based fingerprinting patterns, which indicated that bacterial communities within reactors were not significantly similar after three SRT (0.05 < S(RC) < 0.95) and became significantly dissimilar after five SRT (S(RC) < 0.05). More importantly, significant similarity between replicate reactors was observed at all times analyzed (S(RC) > 0.95). The fact that the patterns between replicates were more reproducible than expected by chance under highly dynamic conditions allowed us to reject the null hypothesis that activated sludge floc communities assemble randomly from the available source pool of bacteria. We suggest that communities progressively recruit from the available pool of bacterial species, each with particular ecological requirements that determine their time of emergence into the community.

  16. Spatio-temporal transitions in the dynamics of bacterial populations

    NASA Astrophysics Data System (ADS)

    Lin, Anna; Lincoln, Bryan; Mann, Bernward; Torres, Gelsy; Kas, Josef; Swinney, Harry

    2001-03-01

    We experimentally investigate the population dynamics of a strain of E. coli bacteria living under spatially inhomogeneous growth conditions. A localized perturbation that moves with a well-defined drift velocity is imposed on the system. A reaction-diffusion model of this situation^1 predicts that an abrupt transition between spatial localization and extinction of the colony occurs for a fixed average growth rate when the drift velocity exceeds a critical value. Also, a transition between localized and delocalized populations is predicted to occur at a fixed drift velocity when the spatially averaged growth rate is varied. We create a spatially localized perturbation with UV light and vary the strength and drift velocity of the perturbation to investigate the existence of the different bacterial population distributions and the transitions between them. Numerical simulations of a 250 mm by 20 mm system guide our experiments. ^1K. A. Dahmen, D. R. Nelson, N. M. Shnerb, Jour. Math. Bio., 41 1 (2000).

  17. Pecorino Crotonese cheese: study of bacterial population and flavour compounds.

    PubMed

    Randazzo, C L; Pitino, I; Ribbera, A; Caggia, C

    2010-05-01

    The diversity and dynamics of the dominant bacterial population during the manufacture and the ripening of two artisanal Pecorino Crotonese cheeses, provided by different farms, were investigated by the combination of culture-dependent and -independent approaches. Three hundred and thirty-three strains were isolated from selective culture media, clustered using Restriction Fragment Length Polymorphism and were identified by 16S rRNA gene sequencing. The results indicate a decrease in biodiversity during ripening, revealing the presence of Lactococcus lactis and Streptococcus thermophilus species in the curd and in aged cheese samples and the occurrence of several lactobacilli throughout cheese ripening, with the dominance of Lactobacillus rhamnosus species. Bacterial dynamics determined by Denaturant Gradient Gel Electrophoresis provided a more precise description of the distribution of bacteria, highlighting differences in the bacterial community among cheese samples, and allowed to detect Lactobacillus plantarum, Lactobacillus buchneri and Leuconostoc mesenteroides species, which were not isolated. Moreover, the concentration of flavour compounds produced throughout cheese ripening was investigated and related to lactic acid bacteria presence. Fifty-seven compounds were identified in the volatile fraction of Pecorino Crotonese cheeses by Gas Chromatography-Mass Spectrometry. Esters, alcohols and free fatty acids were the most abundant compounds, while aldehydes and hydrocarbons were present at low levels.

  18. Attached bacterial populations shared by four species of aquatic angiosperms.

    PubMed

    Crump, Byron C; Koch, Evamaria W

    2008-10-01

    Symbiotic relationships between microbes and plants are common and well studied in terrestrial ecosystems, but little is known about such relationships in aquatic environments. We compared the phylogenetic diversities of leaf- and root-attached bacteria from four species of aquatic angiosperms using denaturing gradient gel electrophoresis (DGGE) and DNA sequencing of PCR-amplified 16S rRNA genes. Plants were collected from three beds in Chesapeake Bay at sites characterized as freshwater (Vallisneria americana), brackish (Potomogeton perfoliatus and Stuckenia pectinata), and marine (Zostera marina). DGGE analyses showed that bacterial communities were very similar for replicate samples of leaves from canopy-forming plants S. pectinata and P. perfoliatus and less similar for replicate samples of leaves from meadow-forming plants Z. marina and V. americana and of roots of all species. In contrast, bacterial communities differed greatly among plant species and between leaves and roots. DNA sequencing identified 154 bacterial phylotypes, most of which were restricted to single plant species. However, 12 phylotypes were found on more than one plant species, and several of these phylotypes were abundant in clone libraries and represented the darkest bands in DGGE banding patterns. Root-attached phylotypes included relatives of sulfur-oxidizing Gammaproteobacteria and sulfate-reducing Deltaproteobacteria. Leaf-attached phylotypes included relatives of polymer-degrading Bacteroidetes and phototrophic Alphaproteobacteria. Also, leaves and roots of three plant species hosted relatives of methylotrophic Betaproteobacteria belonging to the family Methylophilaceae. These results suggest that aquatic angiosperms host specialized communities of bacteria on their surfaces, including several broadly distributed and potentially mutualistic bacterial populations.

  19. Comparative study of normal and sensitive skin aerobic bacterial populations

    PubMed Central

    Hillion, Mélanie; Mijouin, Lily; Jaouen, Thomas; Barreau, Magalie; Meunier, Pauline; Lefeuvre, Luc; Lati, Elian; Chevalier, Sylvie; Feuilloley, Marc G J

    2013-01-01

    The purpose of this study was to investigate if the sensitive skin syndrome, a frequent skin disorder characterized by abnormal painful reactions to environmental factors in the absence of visible inflammatory response, could be linked to a modification in the skin bacterial population. A total of 1706 bacterial isolates was collected at the levels of the forehead, cheekbone, inner elbow, and lower area of the scapula on the skin of normal and sensitive skin syndrome-suffering volunteers of both sexes and of different ages. Among these isolates, 21 strains were randomly selected to validate in a first step the Matrix-Assisted Laser Desorption/Ionization (MALDI)-Biotyper process as an efficient identification tool at the group and genus levels, by comparison to API® strips and 16S ribosomal RNA gene sequencing identification techniques. In a second step, identification of the skin microbiota isolates by the MALDI-Biotyper tool allowed to pinpoint some differences in terms of bacterial diversity with regard to the collection area, and the volunteer's age and gender. Finally, comparison of the skin microbiota from normal and sensitive skin syndrome-suffering volunteers pointed out gender-related variations but no detectable correlation between a phylum, a genus or a dominant bacterial species and the sensitive skin phenotype. This study reveals that there is no dysbiosis of aerobic cultivable bacteria associated with the sensitive skin syndrome and further demonstrates that the MALDI-Biotyper is a powerful technique that can be efficiently employed to the study of cultivable human skin bacteria. To our knowledge, this is the first study focusing on bacteria in the sensitive skin syndrome. These results are of potential importance for pharmaceutical and cosmetic industries, which are looking for new strategies to treat this multiparametric disorder. PMID:24151137

  20. Comparative study of normal and sensitive skin aerobic bacterial populations.

    PubMed

    Hillion, Mélanie; Mijouin, Lily; Jaouen, Thomas; Barreau, Magalie; Meunier, Pauline; Lefeuvre, Luc; Lati, Elian; Chevalier, Sylvie; Feuilloley, Marc G J

    2013-12-01

    The purpose of this study was to investigate if the sensitive skin syndrome, a frequent skin disorder characterized by abnormal painful reactions to environmental factors in the absence of visible inflammatory response, could be linked to a modification in the skin bacterial population. A total of 1706 bacterial isolates was collected at the levels of the forehead, cheekbone, inner elbow, and lower area of the scapula on the skin of normal and sensitive skin syndrome-suffering volunteers of both sexes and of different ages. Among these isolates, 21 strains were randomly selected to validate in a first step the Matrix-Assisted Laser Desorption/Ionization (MALDI)-Biotyper process as an efficient identification tool at the group and genus levels, by comparison to API(®) strips and 16S ribosomal RNA gene sequencing identification techniques. In a second step, identification of the skin microbiota isolates by the MALDI-Biotyper tool allowed to pinpoint some differences in terms of bacterial diversity with regard to the collection area, and the volunteer's age and gender. Finally, comparison of the skin microbiota from normal and sensitive skin syndrome-suffering volunteers pointed out gender-related variations but no detectable correlation between a phylum, a genus or a dominant bacterial species and the sensitive skin phenotype. This study reveals that there is no dysbiosis of aerobic cultivable bacteria associated with the sensitive skin syndrome and further demonstrates that the MALDI-Biotyper is a powerful technique that can be efficiently employed to the study of cultivable human skin bacteria. To our knowledge, this is the first study focusing on bacteria in the sensitive skin syndrome. These results are of potential importance for pharmaceutical and cosmetic industries, which are looking for new strategies to treat this multiparametric disorder. © 2013 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  1. Metagenomic reconstructions of bacterial CRISPR loci constrain population histories.

    PubMed

    Sun, Christine L; Thomas, Brian C; Barrangou, Rodolphe; Banfield, Jillian F

    2016-04-01

    Bacterial CRISPR-Cas systems provide insight into recent population history because they rapidly incorporate, in a unidirectional manner, short fragments (spacers) from coexisting infective virus populations into host chromosomes. Immunity is achieved by sequence identity between transcripts of spacers and their targets. Here, we used metagenomics to study the stability and dynamics of the type I-E CRISPR-Cas locus of Leptospirillum group II bacteria in biofilms sampled over 5 years from an acid mine drainage (AMD) system. Despite recovery of 452,686 spacers from CRISPR amplicons and metagenomic data, rarefaction curves of spacers show no saturation. The vast repertoire of spacers is attributed to phage/plasmid population diversity and retention of old spacers, despite rapid evolution of the targeted phage/plasmid genome regions (proto-spacers). The oldest spacers (spacers found at the trailer end) are conserved for at least 5 years, and 12% of these retain perfect or near-perfect matches to proto-spacer targets. The majority of proto-spacer regions contain an AAG proto-spacer adjacent motif (PAM). Spacers throughout the locus target the same phage population (AMDV1), but there are blocks of consecutive spacers without AMDV1 target sequences. Results suggest long-term coexistence of Leptospirillum with AMDV1 and periods when AMDV1 was less dominant. Metagenomics can be applied to millions of cells in a single sample to provide an extremely large spacer inventory, allow identification of phage/plasmids and enable analysis of previous phage/plasmid exposure. Thus, this approach can provide insights into prior bacterial environment and genetic interplay between hosts and their viruses.

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

    PubMed

    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.

  3. Bacterial finite-size effects for population expansion under flow

    NASA Astrophysics Data System (ADS)

    Toschi, Federico; Tesser, Francesca; Zeegers, Jos C. H.; Clercx, Herman J. H.; Brunsveld, Luc

    2016-11-01

    For organisms living in a liquid ecosystem, flow and flow gradients have a dual role as they transport nutrient while, at the same time, dispersing the individuals. In absence of flow and under homogeneous conditions, the growth of a population towards an empty region is usually described by a reaction-diffusion equation. The effect of fluid flow is not yet well understood and the interplay between transport of individuals and growth opens a wide scenario of possible behaviors. In this work, we study experimentally the dynamics of non-motile E. coli bacteria colonies spreading inside rectangular channels, in PDMS microfluidic devices. By use of a fluorescent microscope we analyze the dynamics of the population density subjected to different co- and counter-flow conditions and shear rates. A simple model incorporating growth, dispersion and drift of finite size beads is able to explain the experimental findings. This indicates that models based on the Fisher-Kolmogorov-Petrovsky-Piscounov equation (FKPP) may have to be supplemented with bacterial finite-size effects in order to be able to accurately reproduce experimental results for population spatial growth.

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

    PubMed Central

    Qu, Leilei; Pan, Qiuhui; Gao, Xubin; He, Mingfeng

    2016-01-01

    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. PMID:26904150

  5. Bacterial population solitary waves can defeat rings of funnels

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

    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.

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

    PubMed

    Qu, Leilei; Pan, Qiuhui; Gao, Xubin; He, Mingfeng

    2016-01-01

    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.

  7. The structure of bacterial cell cycle and age structure of bacterial populations.

    PubMed

    Ivanov, V N; Svechnikova, T A; Stabnikova, E V; Gregirchak, N N

    1995-01-01

    Study of synchronous and asynchronous cultures of Bacillus megaterium, Bacillus thuringiensis and Bacillus licheniformis has shown that the duration of chromosomal DNA replication (period C) is proportional to the generation time, and time between two cycles of the DNA replication (known as period I). The duration of period C is nearly constant and makes up from 0.5 to 1.0 hour at the variations of the generation time from 1.5 to 2.75 hours. The duration of period B (the time between the termination of the cell division and initiation of DNA replication), and period D (the time between the termination of DNA replication and initiation of cell division) were experimentally revealed as stochastic parameters. The theoretical model of the bacterial cell cycle and the age structure of bacterial population was suggested. The main points of this theory are that periods C and I may be stochastically disposed in the division cycle of individual cells and a sum of duration of C- and I-periods is equal to generation time. The data calculated from the theoretical model were confirmed by the experimental data of flow cytofluorometric analysis of the age structure of synchronous and asynchronous cultures of the bacilli.

  8. Patchiness and co-existence of indigenous and invasive mussels at small spatial scales: the interaction of facilitation and competition.

    PubMed

    Erlandsson, Johan; McQuaid, Christopher D; Sköld, Martin

    2011-01-01

    Ecological theory predicts that two species with similar requirements will fail to show long-term co-existence in situations where shared resources are limiting, especially at spatial scales that are small relative to the size of the organisms. Two species of intertidal mussels, the indigenous Perna perna and the invasive Mytilus galloprovincialis, form mixed beds on the south coast of South Africa in a situation that has been stable for several generations of these species, even though these populations are often limited by the availability of space. We examined the spatial structure of these species where they co-exist at small spatial scales in the absence of apparent environmental heterogeneity at two sites, testing: whether conspecific aggregation of mussels can occur (using spatial Monte-Carlo tests); the degree of patchiness (using Korcak B patchiness exponent), and whether there was a relationship between percent cover and patchiness. We found that under certain circumstances there is non-random conspecific aggregation, but that in other circumstances there may be random distribution (i.e. the two species are mixed), so that spatial patterns are context-dependent. The relative cover of the species differed between sites, and within each site, the species with higher cover showed low Korcak B values (indicating low patchiness, i.e. the existence of fewer, larger patches), while the less abundant species showed the reverse, i.e. high patchiness. This relationship did not hold for either species within sites. We conclude that co-existence between these mussels is possible, even at small spatial scales because each species is an ecological engineer and, while they have been shown to compete for space, this is preceded by initial facilitation. We suggest that a patchy pattern of co-existence is possible because of a balance between direct (competitive) and indirect (facilitative) interactions.

  9. Symptomatic Rathke's cleft cyst with a co-existing pituitary tumor; Brief review of the literature

    PubMed Central

    Babu, Ranjith; Back, Adam G.; Komisarow, Jordan M.; Owens, Timothy R.; Cummings, Thomas J.; Britz, Gavin W.

    2013-01-01

    Pituitary adenomas and Rathke's cleft cysts (RCCs) share a common embryological origin. Occasionally, these two lesions can present within the same patient. We present a case of a 39-year-old male who was found to have a large sellar lesion after complaints of persistent headaches and horizontal nystagmus. Surgical resection revealed components of a RCC co-existing with a pituitary adenoma. A brief review of the literature was performed revealing 38 cases of co-existing Rathke's cleft cysts and pituitary adenomas. Among the cases, the most common symptoms included headache and visual changes. Rathke's cleft cysts and pituitary adenomas are rarely found to co-exist, despite having common embryological origins. We review the existing literature, discuss the common embryology to these two lesions and describe a unique case from our institution of a co-existing Rathke's cleft cyst and pituitary adenoma. PMID:24551002

  10. MULTISCALE MODELS OF TAXIS-DRIVEN PATTERNING IN BACTERIAL POPULATIONS

    PubMed Central

    XUE, CHUAN; OTHMER, HANS G.

    2009-01-01

    Spatially-distributed populations of various types of bacteria often display intricate spatial patterns that are thought to result from the cellular response to gradients of nutrients or other attractants. In the past decade a great deal has been learned about signal transduction, metabolism and movement in E. coli and other bacteria, but translating the individual-level behavior into population-level dynamics is still a challenging problem. However, this is a necessary step because it is computationally impractical to use a strictly cell-based model to understand patterning in growing populations, since the total number of cells may reach 1012 - 1014 in some experiments. In the past phenomenological equations such as the Patlak-Keller-Segel equations have been used in modeling the cell movement that is involved in the formation of such patterns, but the question remains as to how the microscopic behavior can be correctly described by a macroscopic equation. Significant progress has been made for bacterial species that employ a “run-and-tumble” strategy of movement, in that macroscopic equations based on simplified schemes for signal transduction and turning behavior have been derived [14, 15]. Here we extend previous work in a number of directions: (i) we allow for time-dependent signals, which extends the applicability of the equations to natural environments, (ii) we use a more general turning rate function that better describes the biological behavior, and (iii) we incorporate the effect of hydrodynamic forces that arise when cells swim in close proximity to a surface. We also develop a new approach to solving the moment equations derived from the transport equation that does not involve closure assumptions. Numerical examples show that the solution of the lowest-order macroscopic equation agrees well with the solution obtained from a Monte Carlo simulation of cell movement under a variety of temporal protocols for the signal. We also apply the method to

  11. Population dynamics of zooxanthellae during a bacterial bleaching event

    NASA Astrophysics Data System (ADS)

    Shenkar, N.; Fine, M.; Kramarsky-Winter, E.; Loya, Y.

    2006-05-01

    Each summer 80-90% of the colonies of Oculina patagonica undergo bleaching off the Mediterranean coast of Israel. To investigate fluctuations through a yearly bleaching cycle, monthly measurements of zooxanthella density, mitotic index and chlorophyll- a concentration were conducted. Results showed (1) a significant negative correlation between sea surface temperature (SST) and zooxanthella density; (2) both significantly lower zooxanthella mitotic index and higher chlorophyll -a per zooxanthella content during the bleaching season compared with the non-bleaching period; (3) prior to bleaching, a lag between the peak of zooxanthella density and chlorophyll- a concentration followed by a similar lag during recovery. Zooxanthella density declined significantly between March and May while chlorophyll- a concentration peaked in April, and then declined. Zooxanthella density increased significantly in November while chlorophyll- a concentration increased significantly in January. We conclude that during bacterial bleaching events, zooxanthellae are severely damaged. However, by the time of the following bleaching event the coral tissues regain their “normal” (pre-bleaching) zooxanthella population density.

  12. Bacterial population structure and dynamics during the development of almond drupes

    USDA-ARS?s Scientific Manuscript database

    Aims: To describe the bacterial populations and their dynamics during the development of almond drupes. Methods and Results: We examined 16S rRNA gene libraries derived from the bacterial populations on almond drupes at three stages of development: 1) when the drupes were full sized, but before embr...

  13. GM crop co-existence: a question of choice, not prejudice.

    PubMed

    Pearsall, Daniel

    2013-01-01

    The rapid uptake of biotech crops around the world demonstrates not only strong producer and consumer demand for the technology and its products, but also that where regulatory regimes function effectively and markets are allowed to operate as normal, co-existence between genetically modified (GM) and non-GM supply chains is readily achievable. However, the polarized debate over GMOs within the European Union over the past 15 years has resulted in a highly politicized and progressively impractical approach to the issue of GM crop co-existence, which in itself has become a further barrier to the technology's development. This article argues that co-existence should not be treated as a pro- or anti-GM issue, and that the aim of co-existence measures should be to permit consumer choice and freedom to operate whatever the production method involved. It suggests that supply chain-based solutions to co-existence, rather than Government prescription, offer the most pragmatic and flexible response to the commercial realities of servicing differentiated market demands.

  14. MULTISCALE MODELS OF TAXIS-DRIVEN PATTERNING IN BACTERIAL POPULATIONS.

    PubMed

    Xue, Chuan; Othmer, Hans G

    2009-01-01

    Spatially-distributed populations of various types of bacteria often display intricate spatial patterns that are thought to result from the cellular response to gradients of nutrients or other attractants. In the past decade a great deal has been learned about signal transduction, metabolism and movement in E. coli and other bacteria, but translating the individual-level behavior into population-level dynamics is still a challenging problem. However, this is a necessary step because it is computationally impractical to use a strictly cell-based model to understand patterning in growing populations, since the total number of cells may reach 10(12) - 10(14) in some experiments. In the past phenomenological equations such as the Patlak-Keller-Segel equations have been used in modeling the cell movement that is involved in the formation of such patterns, but the question remains as to how the microscopic behavior can be correctly described by a macroscopic equation. Significant progress has been made for bacterial species that employ a "run-and-tumble" strategy of movement, in that macroscopic equations based on simplified schemes for signal transduction and turning behavior have been derived [14, 15]. Here we extend previous work in a number of directions: (i) we allow for time-dependent signals, which extends the applicability of the equations to natural environments, (ii) we use a more general turning rate function that better describes the biological behavior, and (iii) we incorporate the effect of hydrodynamic forces that arise when cells swim in close proximity to a surface. We also develop a new approach to solving the moment equations derived from the transport equation that does not involve closure assumptions. Numerical examples show that the solution of the lowest-order macroscopic equation agrees well with the solution obtained from a Monte Carlo simulation of cell movement under a variety of temporal protocols for the signal. We also apply the method to

  15. Bacterial Profile of Dentine Caries and the Impact of pH on Bacterial Population Diversity

    PubMed Central

    Kianoush, Nima; Adler, Christina J.; Nguyen, Ky-Anh T.; Browne, Gina V.; Simonian, Mary; Hunter, Neil

    2014-01-01

    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. PMID:24675997

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

    Treesearch

    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...

  17. Squamous cell carcinoma of kidney co-existing with renal calculi: a rare tumour

    PubMed Central

    Verma, Nidhi; Yadav, Gulabdhar; Dhawan, Nishi; Kumar, Awanish

    2011-01-01

    Squamous cell carcinoma (SCC) of urinary tract is a very rare tumour known to be associated with chronic renal calculi and infection. This tumour is highly aggressive and often detected at advanced stage with poor outcome. The authors describe a case report of a 62-year-old male patient who was diagnosed with right nephrolithiasis with non-functioning kidney. Histopathology revealed an unexpected co-existing SCC in renal pelvis. The present case highlights the careful search and use of newer imaging modalities in cases of long-standing renal calculi as they may have co-existing hidden malignancy which may change the treatment plan and prognosis. PMID:22707603

  18. Squamous cell carcinoma of kidney co-existing with renal calculi: a rare tumour.

    PubMed

    Verma, Nidhi; Yadav, Gulabdhar; Dhawan, Nishi; Kumar, Awanish

    2011-03-01

    Squamous cell carcinoma (SCC) of urinary tract is a very rare tumour known to be associated with chronic renal calculi and infection. This tumour is highly aggressive and often detected at advanced stage with poor outcome. The authors describe a case report of a 62-year-old male patient who was diagnosed with right nephrolithiasis with non-functioning kidney. Histopathology revealed an unexpected co-existing SCC in renal pelvis. The present case highlights the careful search and use of newer imaging modalities in cases of long-standing renal calculi as they may have co-existing hidden malignancy which may change the treatment plan and prognosis.

  19. Metatranscriptomic Analysis of Groundwater Reveals an Active Anammox Bacterial Population

    NASA Astrophysics Data System (ADS)

    Jewell, T. N. M.; Karaoz, U.; Thomas, B. C.; Banfield, J. F.; Brodie, E.; Williams, K. H.; Beller, H. R.

    2014-12-01

    Groundwater is a major natural resource, yet little is known about the contribution of microbial anaerobic ammonium oxidation (anammox) activity to subsurface nitrogen cycling. During anammox, energy is generated as ammonium is oxidized under anaerobic conditions to dinitrogen gas, using nitrite as the final electron acceptor. This process is a global sink for fixed nitrogen. Only a narrow range of monophyletic bacteria within the Planctomycetes carries out anammox, and the full extent of their metabolism, and subsequent impact on nitrogen cycling and microbial community structure, is still unknown. Here, we employ a metatranscriptomic analysis on enriched mRNA to identify the abundance and activity of a population of anammox bacteria within an aquifer at Rifle, CO. Planktonic biomass was collected over a two-month period after injection of up to 1.5 mM nitrate. Illumina-generated sequences were mapped to a phylogenetically binned Rifle metagenome database. We identified transcripts for genes with high protein sequence identities (81-98%) to those of anammox strain KSU-1 and to two of the five anammox bacteria genera, Brocadia and Kuenenia, suggesting an active, if not diverse, anammox population. Many of the most abundant anammox transcripts mapped to a single scaffold, indicative of a single dominant anammox species. Transcripts of the genes necessary for the anammox pathway were present, including an ammonium transporter (amtB), nitrite/formate transporter, nitrite reductase (nirK), and hydrazine oxidoreductase (hzoB). The form of nitrite reductase encoded by anammox is species-dependent, and we only identified nirK, with no evidence of anammox nirS. In addition to the anammox pathway we saw evidence of the anammox bacterial dissimilatory nitrate reduction to ammonium pathway (narH, putative nrfA, and nrfB), which provides an alternate means of generating substrates for anammox from nitrate, rather than relying on an external pool. Transcripts for hydroxylamine

  20. Compositional Stability of a Salivary Bacterial Population against Supragingival Microbiota Shift following Periodontal Therapy

    PubMed Central

    Yamanaka, Wataru; Takeshita, Toru; Shibata, Yukie; Matsuo, Kazuki; Eshima, Nobuoki; Yokoyama, Takeshi; Yamashita, Yoshihisa

    2012-01-01

    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. PMID:22916162

  1. Emergence and Spread of Antimicrobial Resistance: Recent Insights from Bacterial Population Genomics.

    PubMed

    Nübel, Ulrich

    Driven by progress of DNA sequencing technologies, recent population genomics studies have revealed that several bacterial pathogens constitute 'measurably evolving populations'. As a consequence, it was possible to reconstruct the emergence and spatial spread of drug-resistant bacteria on the basis of temporally structured samples of bacterial genome sequences. Based on currently available data, some general inferences can be drawn across different bacterial species as follows: (1) Resistance to various antibiotics evolved years to decades earlier than had been anticipated on the basis of epidemiological surveillance data alone. (2) Resistance traits are more rapidly acquired than lost and commonly persist in bacterial populations for decades. (3) Global populations of drug-resistant pathogens are dominated by very few clones, yet the features enabling such spreading success have not been revealed, aside from antibiotic resistance. (4) Whole-genome sequencing proved very effective at identifying bacterial isolates as parts of the same transmission networks.

  2. Mathematical Modelling of Bacterial Populations in Bio-remediation Processes

    NASA Astrophysics Data System (ADS)

    Vasiliadou, Ioanna A.; Vayenas, Dimitris V.; Chrysikopoulos, Constantinos V.

    2011-09-01

    An understanding of bacterial behaviour concerns many field applications, such as the enhancement of water, wastewater and subsurface bio-remediation, the prevention of environmental pollution and the protection of human health. Numerous microorganisms have been identified to be able to degrade chemical pollutants, thus, a variety of bacteria are known that can be used in bio-remediation processes. In this study the development of mathematical models capable of describing bacterial behaviour considered in bio-augmentation plans, such as bacterial growth, consumption of nutrients, removal of pollutants, bacterial transport and attachment in porous media, is presented. The mathematical models may be used as a guide in designing and assessing the conditions under which areas contaminated with pollutants can be better remediated.

  3. Evaluation of method bias for determining bacterial populations in bacterial community analyses.

    PubMed

    Takahashi, Masayuki; Kita, Yasuko; Mizuno, Akihiro; Goto-Yamamoto, Nami

    2017-10-01

    Various methods are used for analyzing a bacterial community. We recently developed a method for quantifying each bacterium constituting the microbiota by combining a next-generation sequencing (NGS) analysis with a quantitative polymerase chain reaction (NGS-qPCR) assay. Our NGS-qPCR method is useful for analyzing a comprehensive bacterial community because it is enables the easy calculation of the amounts of each bacterium constituting the microbiota. However, it has not been confirmed whether the estimated bacterial community obtained using this NGS-qPCR method corresponds to the results obtained using conventional methods. Accordingly, we prepared model bacterial community samples and analyzed them by several methods (NGS-qPCR, species-specific qPCR, flow cytometry, total direct counting by epifluorescent microscopy [TDC], and plate count). The total bacterial cell densities determined by the PCR-based methods were largely consistent with those determined by the TDC method. There was a difference between the amounts of each bacterium analyzed by NGS-qPCR and species-specific qPCR, although the same trend was shown by both species-specific qPCR and NGS-qPCR. Our findings also demonstrated that there is a strong positive correlation between the cell densities of a specific bacterial group in craft beer samples determined by group-specific qPCR and NGS-qPCR, and there were no significant differences among quantification methods (we tested two bacterial groups: lactic acid bacteria and acetic acid bacteria). Thus, the NGS-qPCR method is a practical method for analyzing a comprehensive bacterial community based on a bacterial cell density. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  4. Bewitchment, Biology, or Both: The Co-Existence of Natural and Supernatural Explanatory Frameworks across Development

    ERIC Educational Resources Information Center

    Legare, Cristine H.; Gelman, Susan A.

    2008-01-01

    Three studies examined the co-existence of natural and supernatural explanations for illness and disease transmission, from a developmental perspective. The participants (5-, 7-, 11-, and 15-year-olds and adults; N = 366) were drawn from 2 Sesotho-speaking South African communities, where Western biomedical and traditional healing frameworks were…

  5. Carbon and oxygen isotopes in apatite CO/sub 2/ and co-existing calcite

    SciTech Connect

    Kolodny, Y.; Kaplan, I. R.

    1981-04-01

    Carbon and oxygen isotopes were analyzed in carbonate apatite CO/sub 2/ and in co-existing calcite. Both C and O in apatite CO/sub 2/ are enriched in the respective light isotopes relative to calcite. These results confirm the proposition that carbonate is part of the apatite structure.

  6. Co-Existent Fruit Machine Addiction and Solvent Abuse in Adolescence: A Cause for Concern?

    ERIC Educational Resources Information Center

    Griffiths, Mark

    1994-01-01

    Data from study of gambling cross-addictions highlighted 16 agencies reporting that fruit machine gambling was specifically associated with some form of psychoactive substance abuse. Largest subgroup was cross-addictions involving solvent abuse and fruit machine gambling. Concluded that co-existence of fruit machine addiction and solvent abuse…

  7. Bewitchment, Biology, or Both: The Co-Existence of Natural and Supernatural Explanatory Frameworks across Development

    ERIC Educational Resources Information Center

    Legare, Cristine H.; Gelman, Susan A.

    2008-01-01

    Three studies examined the co-existence of natural and supernatural explanations for illness and disease transmission, from a developmental perspective. The participants (5-, 7-, 11-, and 15-year-olds and adults; N = 366) were drawn from 2 Sesotho-speaking South African communities, where Western biomedical and traditional healing frameworks were…

  8. Reductive genome evolution at both ends of the bacterial population size spectrum.

    PubMed

    Batut, Bérénice; Knibbe, Carole; Marais, Gabriel; Daubin, Vincent

    2014-12-01

    Bacterial genomes show substantial variations in size. The smallest bacterial genomes are those of endocellular symbionts of eukaryotic hosts, which have undergone massive genome reduction and show patterns that are consistent with the degenerative processes that are predicted to occur in species with small effective population sizes. However, similar genome reduction is found in some free-living marine cyanobacteria that are characterized by extremely large populations. In this Opinion article, we discuss the different hypotheses that have been proposed to account for this reductive genome evolution at both ends of the bacterial population size spectrum.

  9. Patterns of Genetic Diversity and Co-Existence in Open Ocean Diatoms: the Effects of Water Mass Structure, Selection and Sex

    NASA Astrophysics Data System (ADS)

    Rynearson, T. A.; Chen, G.

    2016-02-01

    The open ocean North Atlantic spring bloom influences regional ecology and global biogeochemistry. Diatoms dominate the peak of the bloom and significantly impact productivity and export of organic carbon from the bloom. Despite their key role in a yearly event with global impacts, the genetic diversity and population structure of diatoms that comprise this open ocean bloom are unknown. Here we investigated the population genetics of the diatom Thalassiosira gravida sampled during the 2008 North Atlantic Bloom Experiment using newly-developed microsatellite markers. Here, we show that the genetic diversity of open ocean diatoms is high and that their population structure differs dramatically from coastal diatoms. High levels of genetic diversity were observed across all water samples and did not change during the bloom. Four genetically distinct populations were identified but were not associated with different water masses, depths or time points during the bloom. Instead, all four populations co-existed within samples, spanning different water masses, stages of the bloom and depths of over >300 m. The pattern of genetically distinct, co-existing populations in the open ocean contrasts dramatically with coastal habitats, where distinct populations have not been observed to co-exist at the same time and place. It is likely that populations originate via transport from disparate locations combined with overwintering capacity in the water column or sediments. The pattern of co-existence suggests that the open ocean may serve as a gene pool that harbors different populations that are then available for selection to act upon, which may contribute to the ecological and biogeochemical success of diatoms and influence their long-term evolutionary survival.

  10. On a Mathematical Model with Noncompact Boundary Conditions Describing Bacterial Population

    NASA Astrophysics Data System (ADS)

    Boulanouar, Mohamed

    2013-04-01

    In this work, we are concerned with the well-posedness of a mathematical model describing a maturation-velocity structured bacterial population. Each bacterium is distinguished by its degree of maturity and its maturation velocity. The bacterial mitosis is mathematically described by noncompact boundary conditions. We show that the mathematical model is governed by a positive strongly continuous semigroup.

  11. Grazing activity and ruminal bacterial population associated with frothy bloat in steers grazing winter wheat

    USDA-ARS?s Scientific Manuscript database

    Two grazing experiments were designed to elucidate the shifts in rumen bacterial populations (Exp. 1) and grazing activities (Exp. 2) in wheat forage diets between bloated and non-bloated steers. In Exp. 1, the bacterial DNA density was greatest for Ruminococcus flavefaciens, Streptococcus bovis, a...

  12. Flow Cytometric Single-Cell Identification of Populations in Synthetic Bacterial Communities.

    PubMed

    Rubbens, Peter; Props, Ruben; Boon, Nico; Waegeman, Willem

    2017-01-01

    Bacterial cells can be characterized in terms of their cell properties using flow cytometry. Flow cytometry is able to deliver multiparametric measurements of up to 50,000 cells per second. However, there has not yet been a thorough survey concerning the identification of the population to which bacterial single cells belong based on flow cytometry data. This paper not only aims to assess the quality of flow cytometry data when measuring bacterial populations, but also suggests an alternative approach for analyzing synthetic microbial communities. We created so-called in silico communities, which allow us to explore the possibilities of bacterial flow cytometry data using supervised machine learning techniques. We can identify single cells with an accuracy >90% for more than half of the communities consisting out of two bacterial populations. In order to assess to what extent an in silico community is representative for its synthetic counterpart, we created so-called abundance gradients, a combination of synthetic (i.e., in vitro) communities containing two bacterial populations in varying abundances. By showing that we are able to retrieve an abundance gradient using a combination of in silico communities and supervised machine learning techniques, we argue that in silico communities form a viable representation for synthetic bacterial communities, opening up new opportunities for the analysis of synthetic communities and bacterial flow cytometry data in general.

  13. Flow Cytometric Single-Cell Identification of Populations in Synthetic Bacterial Communities

    PubMed Central

    Boon, Nico; Waegeman, Willem

    2017-01-01

    Bacterial cells can be characterized in terms of their cell properties using flow cytometry. Flow cytometry is able to deliver multiparametric measurements of up to 50,000 cells per second. However, there has not yet been a thorough survey concerning the identification of the population to which bacterial single cells belong based on flow cytometry data. This paper not only aims to assess the quality of flow cytometry data when measuring bacterial populations, but also suggests an alternative approach for analyzing synthetic microbial communities. We created so-called in silico communities, which allow us to explore the possibilities of bacterial flow cytometry data using supervised machine learning techniques. We can identify single cells with an accuracy >90% for more than half of the communities consisting out of two bacterial populations. In order to assess to what extent an in silico community is representative for its synthetic counterpart, we created so-called abundance gradients, a combination of synthetic (i.e., in vitro) communities containing two bacterial populations in varying abundances. By showing that we are able to retrieve an abundance gradient using a combination of in silico communities and supervised machine learning techniques, we argue that in silico communities form a viable representation for synthetic bacterial communities, opening up new opportunities for the analysis of synthetic communities and bacterial flow cytometry data in general. PMID:28122063

  14. Level of physical activity, well-being, stress and self-rated health in persons with migraine and co-existing tension-type headache and neck pain.

    PubMed

    Krøll, Lotte Skytte; Hammarlund, Catharina Sjödahl; Westergaard, Maria Lurenda; Nielsen, Trine; Sloth, Louise Bönsdorff; Jensen, Rigmor Højland; Gard, Gunvor

    2017-12-01

    The prevalence of migraine with co-existing tension-type headache and neck pain is high in the general population. However, there is very little literature on the characteristics of these combined conditions. The aim of this study was to investigate a) the prevalence of migraine with co-existing tension-type headache and neck pain in a clinic-based sample, b) the level of physical activity, psychological well-being, perceived stress and self-rated health in persons with migraine and co-existing tension-type headache and neck pain compared to healthy controls, c) the perceived ability of persons with migraine and co-existing tension-type headache and neck pain to perform physical activity, and d) which among the three conditions (migraine, tension-type headache or neck pain) is rated as the most burdensome condition. The study was conducted at a tertiary referral specialised headache centre where questionnaires on physical activity, psychological well-being, perceived stress and self-rated health were completed by 148 persons with migraine and 100 healthy controls matched by sex and average age. Semi-structured interviews were conducted to assess characteristics of migraine, tension-type headache and neck pain. Out of 148 persons with migraine, 100 (67%) suffered from co-existing tension-type headache and neck pain. Only 11% suffered from migraine only. Persons with migraine and co-existing tension-type headache and neck pain had lower level of physical activity and psychological well-being, higher level of perceived stress and poorer self-rated health compared to healthy controls. They reported reduced ability to perform physical activity owing to migraine (high degree), tension-type headache (moderate degree) and neck pain (low degree). The most burdensome condition was migraine, followed by tension-type headache and neck pain. Migraine with co-existing tension-type headache and neck pain was highly prevalent in a clinic-based sample. Persons with migraine and co-existing

  15. Magnesium aminoclay enhances lipid production of mixotrophic Chlorella sp. KR-1 while reducing bacterial populations.

    PubMed

    Kim, Bohwa; Praveenkumar, Ramasamy; Lee, Jiye; Nam, Bora; Kim, Dong-Myung; Lee, Kyubock; Lee, Young-Chul; Oh, You-Kwan

    2016-11-01

    Improving lipid productivity and preventing overgrowth of contaminating bacteria are critical issues relevant to the commercialization of the mixotrophic microalgae cultivation process. In this paper, we report the use of magnesium aminoclay (MgAC) nanoparticles for enhanced lipid production from oleaginous Chlorella sp. KR-1 with simultaneous control of KR-1-associated bacterial growth in mixotrophic cultures with glucose as the model substrate. Addition of 0.01-0.1g/L MgAC promoted microalgal biomass production better than the MgAC-less control, via differential biocidal effects on microalgal and bacterial cells (the latter being more sensitive to MgAC's bio-toxicity than the former). The inhibition effect of MgAC on co-existing bacteria was, as based on density-gradient-gel-electrophoresis (DGGE) analysis, largely dosage-dependent and species-specific. MgAC also, by inducing an oxidative stress environment, increased both the cell size and lipid content of KR-1, resulting in a considerable, ∼25% improvement of mixotrophic algal lipid productivity (to ∼410mgFAME/L/d) compared with the untreated control.

  16. Impact of Spontaneous Prophage Induction on the Fitness of Bacterial Populations and Host-Microbe Interactions

    PubMed Central

    Nanda, Arun M.; Thormann, Kai

    2014-01-01

    Bacteriophages and genetic elements, such as prophage-like elements, pathogenicity islands, and phage morons, make up a considerable amount of bacterial genomes. Their transfer and subsequent activity within the host's genetic circuitry have had a significant impact on bacterial evolution. In this review, we consider what underlying mechanisms might cause the spontaneous activity of lysogenic phages in single bacterial cells and how the spontaneous induction of prophages can lead to competitive advantages for and influence the lifestyle of bacterial populations or the virulence of pathogenic strains. PMID:25404701

  17. Characterization of N-acylhomoserine lactone-degrading bacteria associated with the Zingiber officinale (ginger) rhizosphere: Co-existence of quorum quenching and quorum sensing in Acinetobacter and Burkholderia

    PubMed Central

    2011-01-01

    Background Cell-to-cell communication (quorum sensing (QS)) co-ordinates bacterial behaviour at a population level. Consequently the behaviour of a natural multi-species community is likely to depend at least in part on co-existing QS and quorum quenching (QQ) activities. Here we sought to discover novel N-acylhomoserine lactone (AHL)-dependent QS and QQ strains by investigating a bacterial community associated with the rhizosphere of ginger (Zingiber officinale) growing in the Malaysian rainforest. Results By using a basal growth medium containing N-(3-oxohexanoyl)homoserine lactone (3-oxo-C6-HSL) as the sole source of carbon and nitrogen, the ginger rhizosphere associated bacteria were enriched for strains with AHL-degrading capabilities. Three isolates belonging to the genera Acinetobacter (GG2), Burkholderia (GG4) and Klebsiella (Se14) were identified and selected for further study. Strains GG2 and Se14 exhibited the broadest spectrum of AHL-degrading activities via lactonolysis while GG4 reduced 3-oxo-AHLs to the corresponding 3-hydroxy compounds. In GG2 and GG4, QQ was found to co-exist with AHL-dependent QS and GG2 was shown to inactivate both self-generated and exogenously supplied AHLs. GG2, GG4 and Se14 were each able to attenuate virulence factor production in both human and plant pathogens. Conclusions Collectively our data show that ginger rhizosphere bacteria which make and degrade a wide range of AHLs are likely to play a collective role in determining the QS-dependent phenotype of a polymicrobial community. PMID:21385437

  18. Aerobic Heterotrophic Bacterial Populations of Sewage and Activated Sludge

    PubMed Central

    Prakasam, T. B. S.; Dondero, N. C.

    1970-01-01

    Two procedures, the confidence interval method and Mountford's index, were tested in analyses of the microbial populations of 11 laboratory activated sludges acclimated to aromatic compounds. The two methods gave somewhat different results but indicated that the populations were quite dissimilar. The activity of seven of the sludges correlated well with the population structure. Some considerations in analysis of microbial population structure are discussed. PMID:5418947

  19. Bewitchment, biology, or both: the co-existence of natural and supernatural explanatory frameworks across development.

    PubMed

    Legare, Cristine H; Gelman, Susan A

    2008-06-01

    Three studies examined the co-existence of natural and supernatural explanations for illness and disease transmission, from a developmental perspective. The participants (5-, 7-, 11-, and 15-year-olds and adults; N = 366) were drawn from 2 Sesotho-speaking South African communities, where Western biomedical and traditional healing frameworks were both available. Results indicated that, although biological explanations for illness were endorsed at high levels, witchcraft was also often endorsed. More important, bewitchment explanations were neither the result of ignorance nor replaced by biological explanations. Instead, both natural and supernatural explanations were used to explain the same phenomena, and bewitchment explanations were highest among adults. Taken together, these data provide insight into how diverse, culturally constructed belief systems about illness co-exist across development.

  20. Co-existence of lichen sclerosus and localized scleroderma in female monozygotic twins.

    PubMed

    Lis-Święty, Anna; Mierzwińska, Katarzyna; Wodok-Wieczorek, Karolina; Widuchowska, Małgorzata; Brzezińska-Wcisło, Ligia

    2014-12-01

    Etiology of lichen sclerosus (LiS) and localized scleroderma (LoS) is uncertain and probably multifactorial. We describe a case of female monozygotic twins who presented co-existence of LiS and LoS. Skin lesions typical for LoS occurred in both patients, at the age of 10. One sister was diagnosed with linear LoS of the lower limb affecting deeper situated subcutaneous tissue and muscles. The other sister was diagnosed with guttate LoS of the trunk, with slow progression of the skin lesions. In both sisters vulvar LiS developed at the age of 19. Co-existence of LiS and LoS in monozygotic twins indicates the possible genetic contribution to the pathogenesis of these diseases and the close relationship between them. Copyright © 2014 North American Society for Pediatric and Adolescent Gynecology. Published by Elsevier Inc. All rights reserved.

  1. Co-existence of various clinical and histopathological features of mycosis fungoides in a young female.

    PubMed

    Naeini, Farahnaz Fatemi; Soghrati, Mehrnaz; Abtahi-Naeini, Bahareh; Najafian, Jamshid; Rajabi, Parvin

    2015-01-01

    Mycosis fungoides is the most common type of cutaneous T-cell lymphoma (CTCL) and a rare disorder that typically affects older adults with erythematous scaling patches and plaques. Hypopigmented patches are a rare clinical variant of the disease. Granulomatous mycosis fungoides (GMF) is also a rare type of CTCL. No particular clinical criteria are available for the diagnosis of GMF, because of its variable presentations, and so the detection of GMF is primarily considered as a histopathological diagnosis. Rarely, a co-existence of more than one clinical or histopathological feature of mycosis fungoides may be present. To the best of our knowledge this is the first report of MF that shows the simultaneous co-existence of more than one clinical and histopathological variant of MF. We present a 29-year-old female with clinical presentations of both classic and hypopigmented mycosis fungoides (MF), and also the histopathological features of the classic and granulomatous types of the disease.

  2. Sinobronchial allergic aspergillosis with allergic bronchopulmonary aspergillosis: a less common co-existence.

    PubMed

    Upadhyay, Rashmi; Kant, Surya; Prakash, Ved; Saheer, S

    2014-11-04

    Allergic bronchopulmonary aspergillosis (ABPA) is an immunological pulmonary disorder that is characterised by a hyper-responsiveness of the airways to Aspergillus fumigatus. Although several other fungi may also present with similar clinical conditions, Aspergillus remains the most common fungal pathogen causing airway infections. Co-existence of ABPA with allergic Aspergillus sinusitis (AAS) is an uncommon presentation. The concept of one airway/one disease justifies the co-existence of ABPA with AAS, but it does not always hold true. We report a case of a 35-year-old woman who presented with symptoms suggestive of bronchial asthma. On further investigation, the radiological pattern showed fleeting shadows and CT scan showed central cystic bronchiectatic changes characteristic of ABPA. The nasal secretions were investigated for the presence of Aspergillus and were found to be positive. Hence a diagnosis of ABPA with AAS was established. The patient was treated with oral steroids and antifungal drugs.

  3. Bacterial population structure of the jute-retting environment.

    PubMed

    Munshi, Tulika K; Chattoo, Bharat B

    2008-08-01

    Jute is one of the most versatile bast fibers obtained through the process of retting, which is a result of decomposition of stalks by the indigenous microflora. However, bacterial communities associated with the retting of jute are not well characterized. To investigate the presence of microorganisms during the process of jute retting, full-cycle rRNA approach was followed, and two 16S rRNA gene libraries, from jute-retting locations of Krishnanagar and Barrackpore, were constructed. Phylotypes affiliating to seven bacterial divisions were identified in both libraries. The bulk of clones came from Proteobacteria ( approximately 37, 41%) and a comparatively smaller proportion of clones from the divisions-Firmicutes ( approximately 11, 12%), Cytophaga-Flexibacter-Bacteroidetes group (CFB; approximately 9, 7%), Verrucomicrobia ( approximately 6, 5%), Acidobacteria ( approximately 4, 5%), Chlorobiales ( approximately 5, 5%), and Actinobacteria ( approximately 4, 2%) were identified. Percent coverage value and diversity estimations of phylotype richness, Shannon-Weiner index, and evenness confirmed the diverse nature of both the libraries. Evaluation of the retting waters by whole cell rRNA-targeted flourescent in situ hybridization, as detected by domain- and group-specific probes, we observed a considerable dominance of the beta-Proteobacteria (25.9%) along with the CFB group (24.4%). In addition, 32 bacterial species were isolated on culture media from the two retting environments and identified by 16S rDNA analysis, confirming the presence of phyla, Proteobacteria ( approximately 47%), Firmicutes ( approximately 22%), CFB group ( approximately 19%), and Actinobacteria ( approximately 13%) in the retting niche. Thus, our study presents the first quantification of the dominant and diverse bacterial phylotypes in the retting ponds, which will further help in improving the retting efficiency, and hence the fiber quality.

  4. Co-existence of GM, conventional and organic crops in developing countries: Main debates and concerns.

    PubMed

    Azadi, Hossein; Taube, Friedhelm; Taheri, Fatemeh

    2017-06-05

    The co-existence approach of GM crops with conventional agriculture and organic farming as a feasible agricultural farming system has recently been placed in the center of hot debates at the EU-level and become a source of anxiety in developing countries. The main promises of this approach is to ensure "food security" and "food safety" on the one hand, and to avoid the adventitious presence of GM crops in conventional and organic farming on the other, as well as to present concerns in many debates on implementing the approach in developing countries. Here, we discuss the main debates on ("what," "why," "who," "where," "which," and "how") applying this approach in developing countries and review the main considerations and tradeoffs in this regard. The paper concludes that a peaceful co-existence between GM, conventional, and organic farming is not easy but is still possible. The goal should be to implement rules that are well-established proportionately, efficiently and cost-effectively, using crop-case, farming system-based and should be biodiversity-focused ending up with "codes of good agricultural practice" for co-existence.

  5. [Influence of co-existing chloride on fluoride removal from drinking water by nanofiltration membrane].

    PubMed

    Ma, Wei-Fang; Liu, Wen-Jun

    2009-03-15

    The influence of co-existing chloride to defluoridation of groundwater using nanofiltration membrane and membrane fouling were studied. The results show that nanofiltration has retention effect to all co-existing anion. When influent fluoride concentration was less than 6 mg/L, the fluoride concentration in permeated water was less than 1.2 mg/L which could reach the drinking water standard in rural area. The fluoride retention rate decreases with the increase of influent fluoride concentration or co-existing chloride concentration. The decreasing percentage of fluoride retention rate is the same when Cl- concentration increased 1 mol or F- concentration increased 0.1 mol. The fluoride retention rate increased when influent chloride concentration exceeded 220 mg/L. But the variation had no significant change. Environmental scanning electron microscope (ESEM) and its energetic chart analysis apparatus, X-ray diffration (XRD) analysis showed that the main fouling component was CaCO3. The fouling membrane could be recovered flux using citric acid and ammonia cleaning method.

  6. Co-existence of Gel and Fluid Lipid Domains in Single-component Phospholipid Membranes

    SciTech Connect

    Armstrong, Clare L; Barrett, M; Toppozini, L; Yamani, Zahra; Kucerka, Norbert; Katsaras, John; Fragneto, Giovanna; Rheinstadter, Maikel C

    2012-01-01

    Lateral nanostructures in membranes, so-called rafts, are believed to strongly influence membrane properties and functions. The experimental observation of rafts has proven difficult as they are thought to be dynamic structures that likely fluctuate on nano- to microsecond time scales. Using neutron diffraction we present direct experimental evidence for the co-existence of gel and fluid lipid domains in a single-component phospholipid membrane made of DPPC as it undergoes its main phase transition. The coherence length of the neutron beam sets a lower limit for the size of structures that can be observed. Neutron coherence lengths between 30 and 242A used in this study were obtained by varying the incident neutron energy and the resolution of the neutron spectrometer. We observe Bragg peaks corresponding to co-existing nanometer sized structures, both in out-of-plane and in-plane scans, by tuning the neutron coherence length. During the main phase transition, instead of a continuous transition that shows a pseudo-critical behavior, we observe the co-existence of gel and fluid domains.

  7. Instability in bacterial populations and the curvature tensor

    NASA Astrophysics Data System (ADS)

    Melgarejo, Augusto; Langoni, Laura; Ruscitti, Claudia

    2016-09-01

    In the geometry associated with equilibrium thermodynamics the scalar curvature Rs is a measure of the volume of correlation, and therefore the singularities of Rs indicates the system instabilities. We explore the use of a similar approach to study instabilities in non-equilibrium systems and we choose as a test example, a colony of bacteria. In this regard we follow the proposal made by Obata et al. of using the curvature tensor for studying system instabilities. Bacterial colonies are often found in nature in concentrated biofilms, or other colony types, which can grow into spectacular patterns visible under the microscope. For instance, it is known that a decrease of bacterial motility with density can promote separation into bulk phases of two coexisting densities; this is opposed to the logistic law for birth and death that allows only a single uniform density to be stable. Although this homogeneous configuration is stable in the absence of bacterial interactions, without logistic growth, a density-dependent swim speed v(ρ) leads to phase separation via a spinodal instability. Thus we relate the singularities in the curvature tensor R to the spinodal instability, that is the appearance of regions of different densities of bacteria.

  8. Does Co-Existing Lumbar Spinal Canal Stenosis Impair Functional Outcomes and Activity Levels after Primary Total Hip Arthroplasty?

    PubMed

    Jauregui, Julio J; Banerjee, Samik; Issa, Kimona; Cherian, Jeffrey J; Mont, Michael A

    2015-09-01

    Degenerative lumbar spinal stenosis (LSS) is a cause for substantial morbidity in the elderly population: many often undergo total hip arthroplasty for associated hip arthritis. With a matched cohort we investigated the effect of co-existing LSS on aseptic survivorship, functional outcomes, activity levels, overall subjective physical and mental health status, and satisfaction rates in patients undergoing primary THA. The aseptic-implant survivorship was similar in LSS and non-stenosis cohort. Although both cohorts significantly improved, the LSS cohort achieved lower improvements in HHS, UCLA, SF-36 physical, and satisfaction rates than the matched non-stenotic cohort. Surgeons should consider cautioning patients with LSS that although they can expect relief of their arthritic symptoms following THA, they may continue to expect limitations in function, physical-status, activity-levels, and satisfaction rates. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Population expansions shared among coexisting bacterial lineages are revealed by genetic evidence

    PubMed Central

    Avitia, Morena; Escalante, Ana E.; Rebollar, Eria A.; Moreno-Letelier, Alejandra; Eguiarte, Luis E.

    2014-01-01

    Comparative population studies can help elucidate the influence of historical events upon current patterns of biodiversity among taxa that coexist in a given geographic area. In particular, comparative assessments derived from population genetics and coalescent theory have been used to investigate population dynamics of bacterial pathogens in order to understand disease epidemics. In contrast, and despite the ecological relevance of non-host associated and naturally occurring bacteria, there is little understanding of the processes determining their diversity. Here we analyzed the patterns of genetic diversity in coexisting populations of three genera of bacteria (Bacillus, Exiguobacterium, and Pseudomonas) that are abundant in the aquatic systems of the Cuatro Cienegas Basin, Mexico. We tested the hypothesis that a common habitat leaves a signature upon the genetic variation present in bacterial populations, independent of phylogenetic relationships. We used multilocus markers to assess genetic diversity and (1) performed comparative phylogenetic analyses, (2) described the genetic structure of bacterial populations, (3) calculated descriptive parameters of genetic diversity, (4) performed neutrality tests, and (5) conducted coalescent-based historical reconstructions. Our results show a trend of synchronic expansions across most populations independent of both lineage and sampling site. Thus, we provide empirical evidence supporting the analysis of coexisting bacterial lineages in natural environments to advance our understanding of bacterial evolution beyond medical or health-related microbes. PMID:25548732

  10. Population expansions shared among coexisting bacterial lineages are revealed by genetic evidence.

    PubMed

    Avitia, Morena; Escalante, Ana E; Rebollar, Eria A; Moreno-Letelier, Alejandra; Eguiarte, Luis E; Souza, Valeria

    2014-01-01

    Comparative population studies can help elucidate the influence of historical events upon current patterns of biodiversity among taxa that coexist in a given geographic area. In particular, comparative assessments derived from population genetics and coalescent theory have been used to investigate population dynamics of bacterial pathogens in order to understand disease epidemics. In contrast, and despite the ecological relevance of non-host associated and naturally occurring bacteria, there is little understanding of the processes determining their diversity. Here we analyzed the patterns of genetic diversity in coexisting populations of three genera of bacteria (Bacillus, Exiguobacterium, and Pseudomonas) that are abundant in the aquatic systems of the Cuatro Cienegas Basin, Mexico. We tested the hypothesis that a common habitat leaves a signature upon the genetic variation present in bacterial populations, independent of phylogenetic relationships. We used multilocus markers to assess genetic diversity and (1) performed comparative phylogenetic analyses, (2) described the genetic structure of bacterial populations, (3) calculated descriptive parameters of genetic diversity, (4) performed neutrality tests, and (5) conducted coalescent-based historical reconstructions. Our results show a trend of synchronic expansions across most populations independent of both lineage and sampling site. Thus, we provide empirical evidence supporting the analysis of coexisting bacterial lineages in natural environments to advance our understanding of bacterial evolution beyond medical or health-related microbes.

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

    PubMed

    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 < 0·05) in the bacterial populations at each time point. The 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.

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

    PubMed

    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.

  13. Aerobic Heterotrophic Bacterial Populations of Sewage and Activated Sludge1

    PubMed Central

    Prakasam, T. B. S.; Dondero, Norman C.

    1967-01-01

    The nature and behavior of the microbial population developed on a synthetic waste containing salts and sorbitol are compared to that of a treatment-plant activated sludge. The population of the adapted sludge developed on the synthetic waste consisted approximately of only six kinds of bacteria. Experiments with radioactive sorbitol indicate that the microbial population developed on the synthetic waste showed the effects of repression by glucose on the metabolism of sorbitol; in contrast, the activated sludge from a plant treating primarily domestic waste was able to attack both substrates immediately and simultaneously. PMID:16349727

  14. Populations of Stored Product Mite Tyrophagus putrescentiae Differ in Their Bacterial Communities

    PubMed Central

    Erban, Tomas; Klimov, Pavel B.; Smrz, Jaroslav; Phillips, Thomas W.; Nesvorna, Marta; Kopecky, Jan; Hubert, Jan

    2016-01-01

    Background: Tyrophagus putrescentiae colonizes different human-related habitats and feeds on various post-harvest foods. The microbiota acquired by these mites can influence the nutritional plasticity in different populations. We compared the bacterial communities of five populations of T. putrescentiae and one mixed population of T. putrescentiae and T. fanetzhangorum collected from different habitats. Material: The bacterial communities of the six mite populations from different habitats and diets were compared by Sanger sequencing of cloned 16S rRNA obtained from amplification with universal eubacterial primers and using bacterial taxon-specific primers on the samples of adults/juveniles or eggs. Microscopic techniques were used to localize bacteria in food boli and mite bodies. The morphological determination of the mite populations was confirmed by analyses of CO1 and ITS fragment genes. Results: The following symbiotic bacteria were found in compared mite populations: Wolbachia (two populations), Cardinium (five populations), Bartonella-like (five populations), Blattabacterium-like symbiont (three populations), and Solitalea-like (six populations). From 35 identified OTUs97, only Solitalea was identified in all populations. The next most frequent and abundant sequences were Bacillus, Moraxella, Staphylococcus, Kocuria, and Microbacterium. We suggest that some bacterial species may occasionally be ingested with food. The bacteriocytes were observed in some individuals in all mite populations. Bacteria were not visualized in food boli by staining, but bacteria were found by histological means in ovaria of Wolbachia-infested populations. Conclusion: The presence of Blattabacterium-like, Cardinium, Wolbachia, and Solitalea-like in the eggs of T. putrescentiae indicates mother to offspring (vertical) transmission. Results of this study indicate that diet and habitats influence not only the ingested bacteria but also the symbiotic bacteria of T. putrescentiae. PMID

  15. Effect of antibiotics on the bacterial population of the rabbit caecum.

    PubMed

    Abecia, Leticia; Fondevila, Manuel; Balcells, Joaquim; Edwards, Joan E; Newbold, C James; McEwan, Neil R

    2007-07-01

    The effect feeding antibiotics has on the bacterial population of the rabbit caecum was investigated. No changes in total volatile fatty acid production or total bacterial counts were observed compared with nonantibiotic treated controls. However, treatment with chlortetracycline resulted in an increase of propionate at the apparent cost of butyrate (P<0.05). Denaturing gradient gel electrophoresis analysis indicated that the two antibiotics that inhibit protein synthesis (chlortetracycline and tiamulin) exerted the most similar changes on the bacterial population structure, decreasing the diversity of the profiles. Sequence analysis of DNA from excised denaturing gradient gel electrophoresis bands was carried out. The majority of the sequences observed were most similar to bacterial sequences previously described in other gut environments, with 11% being most similar to those previously reported from the rabbit, and 95% of the sequences having 95% or greater identity to sequences already in GenBank.

  16. Anammox bacterial populations in deep marine hypersaline gradient systems.

    PubMed

    Borin, Sara; Mapelli, Francesca; Rolli, Eleonora; Song, Bongkeun; Tobias, Craig; Schmid, Markus C; De Lange, Gert J; Reichart, Gert J; Schouten, Stefan; Jetten, Mike; Daffonchio, Daniele

    2013-03-01

    To extend the knowledge of anaerobic ammonium oxidation (anammox) habitats, bacterial communities were examined in two hypersaline sulphidic basins in Eastern Mediterranean Sea. The 2 m thick seawater-brine haloclines of the deep anoxic hypersaline basins Bannock and L'Atalante were sampled in intervals of 10 cm with increasing salinity. (15)N isotope pairing incubation experiments showed the production of (29)N2 and (30)N2 gases in the chemoclines, ranging from 6.0 to 9.2 % salinity of the L'Atalante basin. Potential anammox rates ranged from 2.52 to 49.65 nmol N2 L(-1) day(-1) while denitrification was a major N2 production pathway, accounting for more than 85.5 % of total N2 production. Anammox-related 16S rRNA genes were detected along the L'Atalante and Bannock haloclines up to 24 % salinity, and the amplification of the hydrazine synthase genes (hzsA) further confirmed the presence of anammox bacteria in Bannock. Fluorescence in situ hybridisation and sequence analysis of 16S rRNA genes identified representatives of the marine anammox genus 'Candidatus Scalindua' and putatively new operational taxonomic units closely affiliated to sequences retrieved in marine environments that have documented anammox activity. 'Scalindua brodae' like sequences constituted up to 84.4 % of the sequences retrieved from Bannock. The anammox community in L'Atalante was different than in Bannock and was stratified according to salinity increase. This study putatively extends anammox bacterial habitats to extremely saline sulphidic ecosystems.

  17. Injury to Azygos Venous System: A Co-Existing Injury in High-Impact Lethal Trauma.

    PubMed

    Papadomanolakis, Antonios; Theodoridou, Eleni; Vogiatzis, Nikistratos; Pentheroudaki, Alexandra; Daskalaki, Despoina; Lolis, Evangelos D

    2016-06-01

    About 50 cases of azygos venous system injuries following civilian trauma have been published in current literature. The purpose of our study was to investigate the incidence of these injuries, the causative mechanism and type of trauma, the co-existing injuries, and the mortality rate in our institution. We performed a retrospective review of all trauma patients who were admitted to the surgical department of the General Hospital of Rethymno during an 11-year period. Our study included patients arriving at our institution dead or alive with an azygos venous system injury following blunt or penetrating civilian trauma. Seven patients-five men and two women-were identified with azygos venous system injuries. Five had an azygos vein laceration, one suffered from both azygos and hemiazygos vein lacerations, and the last one had sustained hemiazygos and accessory hemiazygos vein injuries. All of them suffered from a blunt trauma. Three arrived at our hospital in extremis, and all died within 24 h despite our resuscitation attempts. All of our patients were polytrauma patients. All of them had co-existing torso injuries which were severe in all but one case, three of them suffered also from serious head injuries, and all but one had at least serious extremity's injuries. Azygos venous system injuries are rare, although it seems that they are more frequent than current literature would indicate. Blunt trauma mechanism seems to be predominant in civilian trauma setting, and the patients have usually sustained a lot of serious and severe co-existing injuries with high resultant lethality.

  18. Possibility of Non Fermi Liquid Like States Co-exists With Superconductivity in Doubly Filled Skutterudites

    NASA Astrophysics Data System (ADS)

    Venkateshwarlu, D.; Shanmukhrao, S.; Pandya, Swati; Chandra, L. S. Sharath; Vishwakarma, P. N.; Jain, Deepti; Gangrade, Mohan; Ganesan, V.

    2011-07-01

    Skutterudites is known to have fascinating ground states depending upon the void filling. Heat capacity of partially filled Pr0.8Pt4Ge12 and doubly filled Pr0.8Nd0.2Pt4Ge12 skutterudites has been investigated. Superconducting gaps have been quantified through heat capacity in the presence of magnetic fields. C/T versus T2 plot of Pr0.8Nd0.2Pt4Ge12 shows an upturn at low temperatures and this tendency increases with magnetic field, suggesting the possibility of a field induced NFL like states due to magnetic correlations co-existing with superconductivity.

  19. The co-existence of life and death for the perioperative nurse.

    PubMed

    Perrin, Karen; Jones, Barbara; Winkelman, Cecelia

    2013-10-01

    Death and life co-exist in organ procurement surgery; untimely death for one provides hope for continued life for others. Drawing from interactionist theory, the impact of personal and environmental forces and functions specific to organ procurement surgery were examined. Seven nurses (6 women, 1 man aged 34-58 years) were provided with an opportunity to describe their experiences. Three core themes emerged from the qualitative analysis of the interviews: existential issues, coping strategies, and support for each other. Nurses spoke of ways in which they contribute to this challenging work and draw on inner resources.

  20. Bacterial populations growth under co- and counter-flow condition

    NASA Astrophysics Data System (ADS)

    Tesser, Francesca; Zeegers, Jos C. H.; Clercx, Herman J. H.; Toschi, Federico

    2014-11-01

    For organisms living in a liquid ecosystem, flow and flow gradients play a major role on the population level: the flow has a dual role as it transports the nutrient while dispersing the individuals. In absence of flow and under homogeneous conditions, the growth of a population towards an empty region is usually described by a reaction diffusion equation. The solution predicts the expansion as a wave front (Fisher wave) proceeding at constant speed, till the carrying capacity is reached everywhere. The effect of fluid flow, however, is not well understood and the interplay between transport of individuals and nutrient opens a wide scenario of possible behaviors. In this work, we experimentally observe non-motile E. coli bacteria spreading inside rectangular channels in a PDMS microfluidic device. By use of a fluorescent microscope we analyze the dynamics of the population density subjected to different co- and counter-flow conditions and shear rates.

  1. Bacterial populations and processes in sediments containing gas hydrates (ODP Leg 146: Cascadia Margin)

    NASA Astrophysics Data System (ADS)

    Cragg, B. A.; Parkes, R. J.; Fry, J. C.; Weightman, A. J.; Rochelle, P. A.; Maxwell, J. R.

    1996-04-01

    Bacterial populations and activity were quantified at three sites in the Cascadia Margin accretionary wedge, off the West Canadian/American coast (ODP Leg 146). At two sites sediments contained gas hydrates, Site 889/890 had a discrete zone of hydrate approximately 10 m above a bottom simulating reflector (BSR) at 225 m below sea floor (mbsf) and Site 892 had disseminated hydrate in the upper 20 mbsf and a BSR at 74 mbsf. Site 888 was a control site without gas hydrates. The control site (888) and top approximately 90 mbsf of Site 889/890 had bacterial distributions similar to previous Pacific Ocean sites. In the upper approximately 30 m of Site 892, however, bacterial populations were much lower, suggesting inhibition by the high concentrations of H 2S within the hydrate zone. Below this depth bacterial populations rose to concentrations consistent with other sites. The control site was dominated by SO 4 reduction and rates of CH 4 oxidation in the top 90 m were low (0.002-0.033 nmol cm -3 d -1). At Site 889/890 bacterial populations and activity were stimulated in the discrete hydrate zone. CH 4 oxidation rates increased in the middle of this zone to 134.5 nmol cm -3 d -1 (ca. 9 times the average rate at other depths), resulting in a significant (× 10) increase in the total bacterial population. The anaerobic process(es) responsible for this oxidation remain unclear, despite SO 4-reducing bacteria, previously associated with CH 4 oxidation, also being stimulated in this zone. Fluid flux into accretionary wedge sediments may be an important process in providing electron acceptors to maintain these relatively high rates of CH 4 oxidation. This first microbiological study of gas hydrates indicates that bacterial processes are influenced by gas and fluid venting, and they play a major role in geochemical changes within these deep (> 200 mbsf) sediments.

  2. Bacterial populations associated with rice seed in the tropical environment.

    PubMed

    Cottyn, B; Regalado, E; Lanoot, B; De Cleene, M; Mew, T W; Swings, J

    2001-03-01

    ABSTRACT During the 1995 wet season, harvested rice seed was collected from farmers' fields at different locations in Iloilo, Philippines. Bacterial isolations from crushed seed yielded 428 isolates. The isolates were characterized by BOX-polymerase chain reaction fingerprinting of total genomic DNA and represented 151 fingerprint types (FPT). Most FPTs were found on a single occasion, although matching fingerprints for isolates from different samples also were found. Identifications were made by cellular fatty acid methyl ester analysis and additional use of Biolog GN/GP MicroPlates and API 20E/50CHE systems. The predominant bacteria were Enterobacteriaceae (25%), Bacillus spp. (22%), and Pseu-domonas spp. (14%). Other bacteria regularly present were identified as Xanthomonas spp., Cellulomonas flavigena, and Clavibacter michiganense. Of the total number of isolated bacteria, 4% exhibited in vitro antifungal activity against Rhizoctonia solani or Pyricularia grisea. Two percent of isolates were pathogens identified as Burkholderia glumae and Burkholderia gladioli. Five percent of isolates induced sheath necrosis on only 50 to 90% of inoculated plants and were related to Bacillus pumilus, Paenibacillus spp., Pseudomonas spp., and Pantoea spp.

  3. A 46, XX SRY - negative man with infertility, and co-existing with chronic autoimmune thyroiditis.

    PubMed

    Mustafa, Ozbek; Mehmet, Erdogan

    2010-06-01

    46, XX male (de la Chapelle syndrome) is a rare syndrome with a frequency of 1 in 20,000-25,000 males. 46, XX males exist in different clinical categories with ambiguous genitalia or partially to fully mature male genitalia, in combination with complete or incomplete masculinisation. We herein report a case of SRY-negative XX male with complete masculinisation but with infertility, and co-existing with autoimmune thyroiditis. The patient had fully mature male genitalia with descended but small testes and no signs of undervirilisation. Peripheral blood culture for chromosome studies revealed 46 chromosomes with XX constitution. Repeat polymerase chain reaction analysis, using Y-specific sequence tagged sites analysing about 40 metaphases of genomic DNA, confirmed the absence of the Y chromosome, including any detectable SRY gene. We herein report a case of a man 46, XX male SRY with normal male phenotype and infertility. This case is the first reported case, co-existing with chronic autoimmune thyroiditis.

  4. Study of irritable bowel syndrome and co-existing psychological illness.

    PubMed

    Dainty, Andrew David; Allcock, Nick; Cooper, Joanne

    2014-03-01

    To assess the feasibility of using qualitative methods to explore psychological comorbidities associated with irritable bowel syndrome (IBS). IBS is a condition that often has a significant effect on quality of life. It has a high prevalence of co-existing psychological illness, which has been associated with more severe and persistent symptoms and an increased need for specialist referral. Only a small number of research studies have explored patients' perceptions and experiences of IBS, particularly when they are compounded by the presence of psychological comorbidity. Semi-structured interview methods were used to explore the patients' experiences and perceptions of IBS and co-existing psychological illness. All interview data were transcribed before conducting a thematic analysis. The paper reports the methods used to conduct a small feasibility study and discusses and justifies these methods. Methodological issues and the implications these may have on the conduct of the study are presented and critically discussed. Important issues were identified during the design and conduct of the feasibility study relating to the quality of participant information, participant recruitment and the suitability of the proposed methods. Semi-structured interviews are suitable methods for exploring complex issues such as the psychological comorbidities associated with IBS. Further research should explore the patient perception and experience of concomitant psychological illness, which would help researchers develop effective interventions for patients with IBS.

  5. Development of an Experimental Model of Diabetes Co-Existing with Metabolic Syndrome in Rats

    PubMed Central

    Suman, Rajesh Kumar; Ray Mohanty, Ipseeta; Borde, Manjusha K.; Maheshwari, Ujwala; Deshmukh, Y. A.

    2016-01-01

    Background. The incidence of metabolic syndrome co-existing with diabetes mellitus is on the rise globally. Objective. The present study was designed to develop a unique animal model that will mimic the pathological features seen in individuals with diabetes and metabolic syndrome, suitable for pharmacological screening of drugs. Materials and Methods. A combination of High-Fat Diet (HFD) and low dose of streptozotocin (STZ) at 30, 35, and 40 mg/kg was used to induce metabolic syndrome in the setting of diabetes mellitus in Wistar rats. Results. The 40 mg/kg STZ produced sustained hyperglycemia and the dose was thus selected for the study to induce diabetes mellitus. Various components of metabolic syndrome such as dyslipidemia {(increased triglyceride, total cholesterol, LDL cholesterol, and decreased HDL cholesterol)}, diabetes mellitus (blood glucose, HbA1c, serum insulin, and C-peptide), and hypertension {systolic blood pressure} were mimicked in the developed model of metabolic syndrome co-existing with diabetes mellitus. In addition to significant cardiac injury, atherogenic index, inflammation (hs-CRP), decline in hepatic and renal function were observed in the HF-DC group when compared to NC group rats. The histopathological assessment confirmed presence of edema, necrosis, and inflammation in heart, pancreas, liver, and kidney of HF-DC group as compared to NC. Conclusion. The present study has developed a unique rodent model of metabolic syndrome, with diabetes as an essential component. PMID:26880906

  6. Water-use strategies of six co-existing Mediterranean woody species during a summer drought.

    PubMed

    Quero, José L; Sterck, Frank J; Martínez-Vilalta, Jordi; Villar, Rafael

    2011-05-01

    Drought stress is known to limit plant performance in Mediterranean-type ecosystems. We have investigated the dynamics of the hydraulics, gas exchange and morphology of six co-existing Mediterranean woody species growing under natural field conditions during a drought that continued during the entire summer. Based on the observed minimum leaf water potentials, our results suggest that the six co-existing species cover a range of plant hydraulic strategies, from isohydric to anisohydric. These differences are remarkable since the selected individuals grow within several meters of each other, sharing the same environment. Surprisingly, whatever the leaf water potentials were at the end of the dry period, stomatal conductance, photosynthesis and transpiration rates were relatively similar and low across species. This result contradicts the classic view that anisohydric species are able to maintain gas exchange for longer periods of time during drought stress. None of the plants showed the expected structural acclimation response to the increasing drought (reduction of leaf-to-sapwood area ratio), thereby rejecting the functional equilibrium hypothesis for our study system. Instead, three of the six species increased photosynthetic area at the branch level. The observed dissimilar patterns of gas exchange, hydraulics and morphology across species seem to be equally successful given that photosynthesis at the leaf level was maintained at similar rates over the whole dry period.

  7. Bacterial Genetic Signatures of Human Social Phenomena among M. tuberculosis from an Aboriginal Canadian Population

    PubMed Central

    Pepperell, Caitlin; Hoeppner, Vernon H.; Lipatov, Mikhail; Wobeser, Wendy; Schoolnik, Gary K.; Feldman, Marcus W.

    2010-01-01

    Despite a widespread global distribution and highly variable disease phenotype, there is little DNA sequence diversity among isolates of Mycobacterium tuberculosis. In addition, many regional population genetic surveys have revealed a stereotypical structure in which a single clone, lineage, or clade makes up the majority of the population. It is often assumed that dominant clones are highly adapted, that is, the overall structure of M. tuberculosis populations is the result of positive selection. In order to test this assumption, we analyzed genetic data from extant populations of bacteria circulating in Aboriginal communities in Saskatchewan, Canada. Demographic parameters of the bacterial population were estimated from archival epidemiological data collected over ∼130 years since the onset of epidemic tuberculosis in the host communities. Bacterial genetic data were tested against neutral theory expectations and the local evolutionary history of M. tuberculosis investigated by phylogenetic analysis. Our findings are not consistent with positive selection on the bacterial population. Instead, we uncovered founder effects persisting over decades and barriers to gene flow within the bacterial population. Simulation experiments suggested that a combination of these neutral influences could result in the stereotypical structure of M. tuberculosis populations. Some aspects of population structure were suggestive of background selection, and data were on the whole consistent with combined effects of population bottlenecks, subdivision, and background selection. Neutral phenomena, namely, bottlenecks and partitions within populations, are prominent influences on the evolution of M. tuberculosis and likely contribute to restricted genetic diversity observed within this species. Given these influences, a complex evolutionary model will be required to define the relative fitness of different M. tuberculosis lineages and, ultimately, to uncover the genetic basis for its

  8. Bacterial Programmed Cell Death as a Population Phenomenon

    DTIC Science & Technology

    2013-06-11

    Moving in for the kil:Activation of an endoribonuclease toxin by quorum sensing peptide, Molecular Cell, (03 2011): . doi: 06/11/2013 11.00...shown that E. coli mazEF-mediated cell death is a population phenomenon requiring the E. coli quorum sensing factor EDF (Extracellular Death Factor... quorum - sensing factor required for mazEF-mediated cell death in Escherichia coli. Science 318: 652-655. 7) Kolodkin-Gal I, Engelberg-Kulka, H (2008

  9. Bacterial Diversity in a Nonsaline Alkaline Environment: Heterotrophic Aerobic Populations

    PubMed Central

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

    2004-01-01

    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 α-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. PMID:15574939

  10. Molecular Ecology of Bacterial Population in Environmental Hazardous Chemical Control

    DTIC Science & Technology

    1993-01-14

    Pseudomonas putida F1 to measure toluene driven co-metabolic oxidation of TCE. (2) Demonstration of a new pathway for aerobic biodegradation of DDT...mediated by Alcaligenes eutrophus strain A5 previously shown competent for biodegradation of chlorobiphenyl congeners. (3) Confirmation that...the dynamics in microbial population density and activity during environmental biodegradation processes. Metabolism of PAHs. Pseudomonas £luorescens 5RL

  11. Influence of sustainability and immigration in assembling bacterial populations of known size and function.

    PubMed

    Manefield, Mike; Whiteley, Andrew; Curtis, Tom; Watanabe, Kazuya

    2007-02-01

    The rational assembly of microbial communities to perform desired functions would be of great practical benefit to society. Broadly speaking, there are two major theoretical foundations for microbial community assembly: one based on island biogeography theory and another based on niche theory. In this study, we compared a parameter from each theory (immigration rate and sustainability, respectively) to ascertain which was more influential in establishing a functional bacterial population in phenol degrading activated sludge over a 30-day period. Two bacterial strains originally isolated from activated sludge, but differing in their ability to sustain a population in this environment, were repeatedly added to activated sludge reactors at different doses. The resulting size of each population was monitored by competitive polymerase chain reaction. Large, unexpected, yet reproducible fluctuations in population sizes were observed. Irrespective of this, difference in the ability to sustain a population in this environment, overshadowed the influence of 100-fold differences in immigration rate.

  12. Monitoring intraspecies competition in a bacterial cell population by cocultivation of fluorescently labelled strains.

    PubMed

    Stannek, Lorena; Egelkamp, Richard; Gunka, Katrin; Commichau, Fabian M

    2014-01-18

    Many microorganisms such as bacteria proliferate extremely fast and the populations may reach high cell densities. Small fractions of cells in a population always have accumulated mutations that are either detrimental or beneficial for the cell. If the fitness effect of a mutation provides the subpopulation with a strong selective growth advantage, the individuals of this subpopulation may rapidly outcompete and even completely eliminate their immediate fellows. Thus, small genetic changes and selection-driven accumulation of cells that have acquired beneficial mutations may lead to a complete shift of the genotype of a cell population. Here we present a procedure to monitor the rapid clonal expansion and elimination of beneficial and detrimental mutations, respectively, in a bacterial cell population over time by cocultivation of fluorescently labeled individuals of the Gram-positive model bacterium Bacillus subtilis. The method is easy to perform and very illustrative to display intraspecies competition among the individuals in a bacterial cell population.

  13. Socioeconomic Disparities in the Presentation of Acute Bacterial Sinusitis Complications in the Pediatric Population.

    PubMed

    Mehta, Viraj J; Ling, Jeanie D; Mawn, Louise A

    2016-01-01

    Acute bacterial sinusitis is a common disease in the pediatric population that typically resolves without significant complications. Children who do suffer from complications involving the orbit or the brain often experience significant morbidity and potential mortality, typically requiring hospitalization for management. Numerous studies have demonstrated that children from low-income families with public or no insurance are less likely to receive adequate preventative care, are more likely to present with later disease stages, and ultimately endure worse health outcomes. We review the literature to examine if there are socioeconomic disparities in the presentation of complications of acute bacterial sinusitis in the pediatric population.

  14. Interactions of bacterial and amoebal populations in soil microcosms with fluctuating moisture content.

    PubMed

    Bryant, R J; Woods, L E; Coleman, D C; Fairbanks, B C; McClellan, J F; Cole, C V

    1982-04-01

    Sterilized soil samples (20 g of soil per 50-ml flask), amended with 600 mug of glucose-carbon and 60 mug of NH(4)-N . g of dry soil, were inoculated with bacteria (Pseudomonas paucimobilis) alone or with bacteria and amoebae (Acanthamoeba polyphaga). We used wet-dry treatments, which involved air drying the samples to a moisture content of approximately 2% and remoistening the samples three times during the 83-day experiment. Control treatments were kept moist. In the absence of amoebae, bacterial populations were reduced by the first drying to about 60% of the moist control populations, but the third drying had no such effect. With amoebae present, bacterial numbers were not significantly affected by the dryings. Amoebal grazing reduced bacterial populations to 20 to 25% of the ungrazed bacterial populations in both moisture treatments. Encystment was an efficient survival mechanism for amoebae subjected to wet-dry cycles. The amoebal population was entirely encysted in dry soil, but the total number of amoebae was not affected by the three dryings. Growth efficiencies for amoebae feeding on bacteria were 0.33 and 0.39 for wet-dry and constantly moist treatments, respectively, results that compared well with those previously reported for Acanthamoeba spp.

  15. Interactions of Bacterial and Amoebal Populations in Soil Microcosms with Fluctuating Moisture Content

    PubMed Central

    Bryant, R. J.; Woods, L. E.; Coleman, D. C.; Fairbanks, B. C.; McClellan, J. F.; Cole, C. V.

    1982-01-01

    Sterilized soil samples (20 g of soil per 50-ml flask), amended with 600 μg of glucose-carbon and 60 μg of NH4-N · g of dry soil−1, were inoculated with bacteria (Pseudomonas paucimobilis) alone or with bacteria and amoebae (Acanthamoeba polyphaga). We used wet-dry treatments, which involved air drying the samples to a moisture content of approximately 2% and remoistening the samples three times during the 83-day experiment. Control treatments were kept moist. In the absence of amoebae, bacterial populations were reduced by the first drying to about 60% of the moist control populations, but the third drying had no such effect. With amoebae present, bacterial numbers were not significantly affected by the dryings. Amoebal grazing reduced bacterial populations to 20 to 25% of the ungrazed bacterial populations in both moisture treatments. Encystment was an efficient survival mechanism for amoebae subjected to wet-dry cycles. The amoebal population was entirely encysted in dry soil, but the total number of amoebae was not affected by the three dryings. Growth efficiencies for amoebae feeding on bacteria were 0.33 and 0.39 for wet-dry and constantly moist treatments, respectively, results that compared well with those previously reported for Acanthamoeba spp. PMID:16345984

  16. Analysis of bacterial populations in the environment using two-dimensional gel electrophoresis of genomic DNA and complementary DNA.

    PubMed

    Liu, Guo-Hua; Nakamura, Tatsuo; Amemiya, Takashi; Rajendran, Narasimmalu; Itoh, Kiminori

    2011-01-01

    Two-dimensional gel electrophoresis (2-DGE) mapping of genomic DNA and complementary DNA (cDNA) amplicons was attempted to analyze total and active bacterial populations within soil and activated sludge samples. Distinct differences in the number and species of bacterial populations and those that were metabolically active at the time of sampling were visually observed especially for the soil community. Statistical analyses and sequencing based on the 2-DGE data further revealed the relationships between total and active bacterial populations within each community. This high-resolution technique would be useful for obtaining a better understanding of bacterial population structures in the environment.

  17. Detection of Only Viable Bacterial Spores Using a Live/Dead Indicator in Mixed Populations

    NASA Technical Reports Server (NTRS)

    Behar, Alberto E.; Stam, Christina N.; Smiley, Ronald

    2013-01-01

    This method uses a photoaffinity label that recognizes DNA and can be used to distinguish populations of bacterial cells from bacterial spores without the use of heat shocking during conventional culture, and live from dead bacterial spores using molecular-based methods. Biological validation of commercial sterility using traditional and alternative technologies remains challenging. Recovery of viable spores is cumbersome, as the process requires substantial incubation time, and the extended time to results limits the ability to quickly evaluate the efficacy of existing technologies. Nucleic acid amplification approaches such as PCR (polymerase chain reaction) have shown promise for improving time to detection for a wide range of applications. Recent real-time PCR methods are particularly promising, as these methods can be made at least semi-quantitative by correspondence to a standard curve. Nonetheless, PCR-based methods are rarely used for process validation, largely because the DNA from dead bacterial cells is highly stable and hence, DNA-based amplification methods fail to discriminate between live and inactivated microorganisms. Currently, no published method has been shown to effectively distinguish between live and dead bacterial spores. This technology uses a DNA binding photoaffinity label that can be used to distinguish between live and dead bacterial spores with detection limits ranging from 109 to 102 spores/mL. An environmental sample suspected of containing a mixture of live and dead vegetative cells and bacterial endospores is treated with a photoaffinity label. This step will eliminate any vegetative cells (live or dead) and dead endospores present in the sample. To further determine the bacterial spore viability, DNA is extracted from the spores and total population is quantified by real-time PCR. The current NASA standard assay takes 72 hours for results. Part of this procedure requires a heat shock step at 80 degC for 15 minutes before the

  18. Papillary thyroid microcarcinoma co-exists with Hashimoto's thyroiditis: Is strain elastography still useful?

    PubMed

    Li, Yi; Wang, Yan; Wu, Qiong; Hu, Bing

    2016-05-01

    To study the performance of strain elastography in differentiating papillary thyroid microcarcinoma (PTMC) combined with Hashimoto's thyroiditis (HT), conventional ultrasound scan (US) and strain elastography (SE) were performed on 558 nodules smaller than 10 mm by one examiner before surgeries. Serum concentrations of thyroid peroxidase antibody (TPO-Ab) (normal range: 0-60 U/ml) were measured. Continuous variables were analyzed by independent t test. Receiver operating characteristics (ROC) curve analysis was applied to calculate the cut-off values of strain ratio (SR) and elastography score (ES). The comparison of AUCs is performed by Z test. 482 nodules were diagnosed as PTMC and there were 181 nodules co-existed with HT. SR measurements were lower in PTMC co-existed with HT when comparing to those without HT. (7.292±6.581 vs 11.319±13.155, p<0.000). Taking the data from all of the 558 nodules, the best cut-off of diagnosing PTMC was SR>2.58. When taking the data from 181 PTMC with HT, the best cut-off was SR>2.10. The diagnostic value of SR>2.1 were higher than ES>3, conventional US and combining US and SE (z=3.595, 4.876, 4.420, p<0.001), but cut-off of SR>2.1 did not show significant enhancement of diagnostic value compared to SR>2.58 (z=0.439, p=0.8903>0.001) in PTMC with HT. There is a negative relation between SR and titer of TPO-Ab (r=-0.650, p<0.0001). PTMC with high TPO-Ab (>1000) titer presented lower SR (5.972±4.118 vs 8.379±9.172, p=0.009). Although SR measurements were lower in nodules co-existed with HT when comparing those without HT, using a regular ES and cut-off of SR measurement would not influence the diagnosing performance. SE is still very useful for diagnosing PTMC with HT. PTMC with high TPO-Ab titer might require a lower cut-off of SR.

  19. Familiality of Co-existing ADHD and Tic Disorders: Evidence from a Large Sibling Study

    PubMed Central

    Roessner, Veit; Banaschewski, Tobias; Becker, Andreas; Buse, Judith; Wanderer, Sina; Buitelaar, Jan K.; Sergeant, Joseph A.; Sonuga-Barke, Edmund J.; Gill, Michael; Manor, Iris; Miranda, Ana; Mulas, Fernando; Oades, Robert D.; Roeyers, Herbert; Steinhausen, Hans-Christoph; Faraone, Steven V.; Asherson, Philip; Rothenberger, Aribert

    2016-01-01

    Background: The association of attention-deficit/hyperactivity disorder (ADHD) and tic disorder (TD) is frequent and clinically important. Very few and inconclusive attempts have been made to clarify if and how the combination of ADHD+TD runs in families. Aim: To determine the first time in a large-scale ADHD sample whether ADHD+TD increases the risk of ADHD+TD in siblings and, also the first time, if this is independent of their psychopathological vulnerability in general. Methods: The study is based on the International Multicenter ADHD Genetics (IMAGE) study. The present sub-sample of 2815 individuals included ADHD-index patients with co-existing TD (ADHD+TD, n = 262) and without TD (ADHD–TD, n = 947) as well as their 1606 full siblings (n = 358 of the ADHD+TD index patients and n = 1248 of the ADHD-TD index patients). We assessed psychopathological symptoms in index patients and siblings by using the Strength and Difficulties Questionnaire (SDQ) and the parent and teacher Conners' long version Rating Scales (CRS). For disorder classification the Parental Account of Childhood Symptoms (PACS-Interview) was applied in n = 271 children. Odds ratio with the GENMOD procedure (PROCGENMOD) was used to test if the risk for ADHD, TD, and ADHD+TD in siblings was associated with the related index patients' diagnoses. In order to get an estimate for specificity we compared the four groups for general psychopathological symptoms. Results: Co-existing ADHD+TD in index patients increased the risk of both comorbid ADHD+TD and TD in the siblings of these index patients. These effects did not extend to general psychopathology. Interpretation: Co-existence of ADHD+TD may segregate in families. The same holds true for TD (without ADHD). Hence, the segregation of TD (included in both groups) seems to be the determining factor, independent of further behavioral problems. This close relationship between ADHD and TD supports the clinical approach to carefully assess ADHD in any case

  20. Gender Dysphoria and Co-Existing Psychosis: Review and Four Case Examples of Successful Gender Affirmative Treatment.

    PubMed

    Meijer, Julia H; Eeckhout, Guus M; van Vlerken, Roy H T; de Vries, Annelou L C

    2017-04-01

    Controversy exists as to if, and when, gender affirmative (GA) treatment should be offered to individuals with gender dysphoria (GD) and co-existing psychosis. Concerns exist regarding a high risk of misdiagnosis, regret afterward due to impulsive decision making, and deterioration of psychotic symptoms. This case series aims at extending the sparse literature on GA treatment in this population by identifying challenges in diagnosis and treatment and offering recommendations to overcome them. The authors present case descriptions of two transgender men and two transgender women in the age range of 29-57 years with a diagnosis of GD and a schizophrenia-related diagnosis. All had undergone GA treatment with a minimum follow-up of 3 years. The gender diagnosis was complicated by the fact that feelings of GD were only shared after the onset of psychosis, and GA treatment was hampered by the persistence of mild psychotic symptoms despite antipsychotic treatment. Close communication with the psychosis treating clinicians proved useful to address these problems. GA treatment was paralleled by a stabilization of psychotic symptoms, and adherence to and satisfaction with the therapy was high. These case examples show that GA treatment is possible and safe in this vulnerable population.

  1. Surface growth of a motile bacterial population resembles growth in a chemostat.

    PubMed

    Koster, Daniel A; Mayo, Avraham; Bren, Anat; Alon, Uri

    2012-12-07

    The growth behavior in well-mixed bacterial cultures is relatively well understood. However, bacteria often grow in heterogeneous conditions on surfaces where their growth is dependent on spatial position, especially in the case of motile populations. For such populations, the relation between growth, motility and spatial position is unclear. We developed a microscope-based assay for quantifying in situ growth and gene expression in space and time, and we observe these parameters in populations of Escherichia coli swimming in galactose soft agar plates. We find that the bacterial density and the shape of the motile population, after an initial transient, are constant in time. By considering not only the advancing population but also the fraction that lags behind, we propose a growth model that relates spatial distribution, motility and growth rate. This model, that is similar to bacterial growth in a chemostat predicts that the fraction of the population lagging behind is inversely proportional to the velocity of the motile population. We test this prediction by modulating motility using inducible expression of the flagellar sigma factor FliA. Finally, we observe that bacteria in the chemotactic ring express higher relative levels of the chemotaxis and galactose metabolism genes fliC, fliL and galE than those that stay behind in the center of the plate. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

    PubMed

    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.

  3. Co-existence of cutaneous leishmaniasis with pleural effusion: a case report from Iran.

    PubMed

    Mortazavi, Hossein; Soori, Tahereh; Khamesipour, Ali; Khatami, Alireza; Vasheghani-Farahani, Amir

    2014-01-01

    Herein, a 12-year-old Afghan boy with chronic cutaneous leishmaniasis on the face and verrucous lesions on the body and pleural effusion suspected of having co-existent tuberculosis has been presented. The cutaneous lesions were appeared for five years before his admission. Leishman-Donovan bodies were seen in H&E (Hematoxylin and eosin) slide of skin lesion specimens. The pathogenic species was proved to be Leishmania tropica using Polymerase Chain Reaction (PCR) method. Purified Protein Derivative (PPD) and Leishmanin Skin Test (LST) were strongly positive. The patient was treated with systemic and intralesional meglumine antimoniate (Glucantime) for cutaneous leishmaniasis and then with anti-tuberculosis drugs for pleural effusion. Afterwards, pleural effusion was disappeared and cutaneous leishmaniasis cured.

  4. Population-based surveillance for bacterial meningitis in the Dominican Republic: implications for control by vaccination.

    PubMed Central

    Gomez, E.; Peguero, M.; Sanchez, J.; Castellanos, P. L.; Feris, J.; Peña, C.; Brudzinski-LaClaire, L.; Levine, O. S.

    2000-01-01

    Quantifying the local burden of disease is an important step towards the introduction of new vaccines, such as Haemophilus influenzae type b (Hib) conjugate vaccine. We adapted a generic protocol developed by the World Health Organization for population-based surveillance of bacterial meningitis. All hospitals that admit paediatric patients with meningitis in the National District, Dominican Republic were included in the system and standard laboratory methods were used. The system identified 111 cases of confirmed bacterial meningitis. Hib was the leading cause of bacterial meningitis, followed by group B streptococcus, S. pneumoniae, and N. meningitidis. Unlike hospital-based case series, this population-based system was able to calculate incidence rates. The incidence of Hib meningitis was 13 cases per 100,000 children < 5 years old. The data from this study were used by the Ministry of Health to support the introduction of routine Hib vaccination and will be used to monitor its effectiveness. PMID:11218205

  5. Population-based surveillance for bacterial meningitis in the Dominican Republic: implications for control by vaccination.

    PubMed

    Gomez, E; Peguero, M; Sanchez, J; Castellanos, P L; Feris, J; Peña, C; Brudzinski-LaClaire, L; Levine, O S

    2000-12-01

    Quantifying the local burden of disease is an important step towards the introduction of new vaccines, such as Haemophilus influenzae type b (Hib) conjugate vaccine. We adapted a generic protocol developed by the World Health Organization for population-based surveillance of bacterial meningitis. All hospitals that admit paediatric patients with meningitis in the National District, Dominican Republic were included in the system and standard laboratory methods were used. The system identified 111 cases of confirmed bacterial meningitis. Hib was the leading cause of bacterial meningitis, followed by group B streptococcus, S. pneumoniae, and N. meningitidis. Unlike hospital-based case series, this population-based system was able to calculate incidence rates. The incidence of Hib meningitis was 13 cases per 100,000 children < 5 years old. The data from this study were used by the Ministry of Health to support the introduction of routine Hib vaccination and will be used to monitor its effectiveness.

  6. Obligate bacterial mutualists evolving from environmental bacteria in natural insect populations.

    PubMed

    Hosokawa, Takahiro; Ishii, Yoshiko; Nikoh, Naruo; Fujie, Manabu; Satoh, Nori; Fukatsu, Takema

    2016-01-11

    Diverse organisms are associated with obligate microbial mutualists. How such essential symbionts have originated from free-living ancestors is of evolutionary interest. Here we report that, in natural populations of the stinkbug Plautia stali, obligate bacterial mutualists are evolving from environmental bacteria. Of six distinct bacterial lineages associated with insect populations, two are uncultivable with reduced genomes, four are cultivable with non-reduced genomes, one uncultivable symbiont is fixed in temperate populations, and the other uncultivable symbiont coexists with four cultivable symbionts in subtropical populations. Symbiont elimination resulted in host mortality for all symbionts, while re-infection with any of the symbionts restored normal host growth, indicating that all the symbionts are indispensable and almost equivalent functionally. Some aseptic newborns incubated with environmental soils acquired the cultivable symbionts and normal growth was restored, identifying them as environmental Pantoea spp. Our finding uncovers an evolutionary transition from a free-living lifestyle to obligate mutualism that is currently ongoing in nature.

  7. Bacterial quorum sensing and metabolic slowing in a cooperative population

    PubMed Central

    An, Jae Hyung; Goo, Eunhye; Kim, Hongsup; Seo, Young-Su; Hwang, Ingyu

    2014-01-01

    Acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) controls the production of numerous intra- and extracellular products across many species of Proteobacteria. Although these cooperative activities are often costly at an individual level, they provide significant benefits to the group. Other potential roles for QS include the restriction of nutrient acquisition and maintenance of metabolic homeostasis of individual cells in a crowded but cooperative population. Under crowded conditions, QS may function to modulate and coordinate nutrient utilization and the homeostatic primary metabolism of individual cells. Here, we show that QS down-regulates glucose uptake, substrate level and oxidative phosphorylation, and de novo nucleotide biosynthesis via the activity of the QS-dependent transcriptional regulator QsmR (quorum sensing master regulator R) in the rice pathogen Burkholderia glumae. Systematic analysis of glucose uptake and core primary metabolite levels showed that QS deficiency perturbed nutrient acquisition, and energy and nucleotide metabolism, of individuals within the group. The QS mutants grew more rapidly than the wild type at the early exponential stage and outcompeted wild-type cells in coculture. Metabolic slowing of individuals in a QS-dependent manner indicates that QS acts as a metabolic brake on individuals when cells begin to mass, implying a mechanism by which AHL-mediated QS might have evolved to ensure homeostasis of the primary metabolism of individuals under crowded conditions. PMID:25267613

  8. Bacterial quorum sensing and metabolic slowing in a cooperative population.

    PubMed

    An, Jae Hyung; Goo, Eunhye; Kim, Hongsup; Seo, Young-Su; Hwang, Ingyu

    2014-10-14

    Acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) controls the production of numerous intra- and extracellular products across many species of Proteobacteria. Although these cooperative activities are often costly at an individual level, they provide significant benefits to the group. Other potential roles for QS include the restriction of nutrient acquisition and maintenance of metabolic homeostasis of individual cells in a crowded but cooperative population. Under crowded conditions, QS may function to modulate and coordinate nutrient utilization and the homeostatic primary metabolism of individual cells. Here, we show that QS down-regulates glucose uptake, substrate level and oxidative phosphorylation, and de novo nucleotide biosynthesis via the activity of the QS-dependent transcriptional regulator QsmR (quorum sensing master regulator R) in the rice pathogen Burkholderia glumae. Systematic analysis of glucose uptake and core primary metabolite levels showed that QS deficiency perturbed nutrient acquisition, and energy and nucleotide metabolism, of individuals within the group. The QS mutants grew more rapidly than the wild type at the early exponential stage and outcompeted wild-type cells in coculture. Metabolic slowing of individuals in a QS-dependent manner indicates that QS acts as a metabolic brake on individuals when cells begin to mass, implying a mechanism by which AHL-mediated QS might have evolved to ensure homeostasis of the primary metabolism of individuals under crowded conditions.

  9. Humpback Whale Populations Share a Core Skin Bacterial Community: Towards a Health Index for Marine Mammals?

    PubMed Central

    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

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

    PubMed

    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

  11. Bacterial populations on the surfaces of organic and conventionally grown almond drupes

    USDA-ARS?s Scientific Manuscript database

    Aims: To compare the bacterial populations on organically and conventionally grown almond drupes before and after hull split. Methods and Results: We constructed 16S rRNA gene libraries containing approximately 3,000 sequences each from the bacteria from organically and conventionally grown drupes b...

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

    PubMed

    Gorochowski, Thomas E; Matyjaszkiewicz, Antoni; Todd, Thomas; Oak, Neeraj; Kowalska, Kira; Reid, Stephen; Tsaneva-Atanasova, Krasimira T; Savery, Nigel J; Grierson, Claire S; di Bernardo, Mario

    2012-01-01

    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.

  13. A network-based approach for resistance transmission in bacterial populations.

    PubMed

    Gehring, Ronette; Schumm, Phillip; Youssef, Mina; Scoglio, Caterina

    2010-01-07

    Horizontal transfer of mobile genetic elements (conjugation) is an important mechanism whereby resistance is spread through bacterial populations. The aim of our work is to develop a mathematical model that quantitatively describes this process, and to use this model to optimize antimicrobial dosage regimens to minimize resistance development. The bacterial population is conceptualized as a compartmental mathematical model to describe changes in susceptible, resistant, and transconjugant bacteria over time. This model is combined with a compartmental pharmacokinetic model to explore the effect of different plasma drug concentration profiles. An agent-based simulation tool is used to account for resistance transfer occurring when two bacteria are adjacent or in close proximity. In addition, a non-linear programming optimal control problem is introduced to minimize bacterial populations as well as the drug dose. Simulation and optimization results suggest that the rapid death of susceptible individuals in the population is pivotal in minimizing the number of transconjugants in a population. This supports the use of potent antimicrobials that rapidly kill susceptible individuals and development of dosage regimens that maintain effective antimicrobial drug concentrations for as long as needed to kill off the susceptible population. Suggestions are made for experiments to test the hypotheses generated by these simulations.

  14. The effects of warming on the ecophysiology of two co-existing kelp species with contrasting distributions.

    PubMed

    Hargrave, Matthew S; Foggo, Andrew; Pessarrodona, Albert; Smale, Dan A

    2017-02-01

    The northeast Atlantic has warmed significantly since the early 1980s, leading to shifts in species distributions and changes in the structure and functioning of communities and ecosystems. This study investigated the effects of increased temperature on two co-existing habitat-forming kelps: Laminaria digitata, a northern boreal species, and Laminaria ochroleuca, a southern Lusitanian species, to shed light on mechanisms underpinning responses of trailing and leading edge populations to warming. Kelp sporophytes collected from southwest United Kingdom were maintained under 3 treatments: ambient temperature (12 °C), +3 °C (15 °C) and +6 °C (18 °C) for 16 days. At higher temperatures, L. digitata showed a decline in growth rates and Fv/Fm, an increase in chemical defence production and a decrease in palatability. In contrast, L. ochroleuca demonstrated superior growth and photosynthesis at temperatures higher than current ambient levels, and was more heavily grazed. Whilst the observed decreased palatability of L. digitata held at higher temperatures could reduce top-down pressure on marginal populations, field observations of grazer densities suggest that this may be unimportant within the study system. Overall, our study suggests that shifts in trailing edge populations will be primarily driven by ecophysiological responses to high temperatures experienced during current and predicted thermal maxima, and although compensatory mechanisms may reduce top-down pressure on marginal populations, this is unlikely to be important within the current biogeographical context. Better understanding of the mechanisms underpinning climate-driven range shifts is important for habitat-forming species like kelps, which provide organic matter, create biogenic structure and alter environmental conditions for associated communities.

  15. Nutrient reduction induced stringent responses promote bacterial quorum-sensing divergence for population fitness

    PubMed Central

    Zhao, Kelei; Zhou, Xikun; Li, Wujiao; Zhang, Xiuyue; Yue, Bisong

    2016-01-01

    Bacteria use a cell-cell communication system termed quorum-sensing (QS) to adjust population size by coordinating the costly but beneficial cooperative behaviors. It has long been suggested that bacterial social conflict for expensive extracellular products may drive QS divergence and cause the “tragedy of the commons”. However, the underlying molecular mechanism of social divergence and its evolutionary consequences for the bacterial ecology still remain largely unknown. By using the model bacterium Pseudomonas aeruginosa PAO1, here we show that nutrient reduction can promote QS divergence for population fitness during evolution but requiring adequate cell density. Mechanically, decreased nutrient supplies can induce RpoS-directed stringent response and enhance the selection pressure on lasR gene, and lasR mutants are evolved in association with the DNA mismatch repair “switch-off”. The lasR mutants have higher relative fitness than QS-intact individuals due to their energy-saving characteristic under nutrient decreased condition. Furthermore an optimal incorporation of lasR mutants is capable of maximizing the fitness of entire population during in vitro culture and the colonization in mouse lung. Consequently, rather than worsen the population health, QS-coordinated social divergence is an elaborate evolutionary strategy that renders the entire bacterial population more fit in tough times. PMID:27713502

  16. Identification of Population Bottlenecks and Colonization Factors during Assembly of Bacterial Communities within the Zebrafish Intestine

    PubMed Central

    Wiles, Travis J.; Martinez, Emily S.; Jemielita, Matthew; Burns, Adam R.; Parthasarathy, Raghuveer; Bohannan, Brendan J. M.

    2015-01-01

    ABSTRACT The zebrafish, Danio rerio, is a powerful model for studying bacterial colonization of the vertebrate intestine, but the genes required by commensal bacteria to colonize the zebrafish gut have not yet been interrogated on a genome-wide level. Here we apply a high-throughput transposon mutagenesis screen to Aeromonas veronii Hm21 and Vibrio sp. strain ZWU0020 during their colonization of the zebrafish intestine alone and in competition with each other, as well as in different colonization orders. We use these transposon-tagged libraries to track bacterial population sizes in different colonization regimes and to identify gene functions required during these processes. We show that intraspecific, but not interspecific, competition with a previously established bacterial population greatly reduces the ability of these two bacterial species to colonize. Further, using a simple binomial sampling model, we show that under conditions of interspecific competition, genes required for colonization cannot be identified because of the population bottleneck experienced by the second colonizer. When bacteria colonize the intestine alone or at the same time as the other species, we find shared suites of functional requirements for colonization by the two species, including a prominent role for chemotaxis and motility, regardless of the presence of another species. PMID:26507229

  17. Bacterial populations on the surfaces of organic and conventionally grown almond drupes.

    PubMed

    McGarvey, J A; Han, R; Connell, J H; Stanker, L H; Hnasko, R

    2015-08-01

    To compare the bacterial populations on organically and conventionally grown almond drupes before and after hull split. We constructed 16S rRNA gene libraries, containing approx. 3000 sequences each, from the bacteria from organically and conventionally grown drupes before and after hull split. We observed that before hull split both conventionally and organically grown drupes were colonized by relatively few types of bacteria that were mostly common phyllosphere-associated Proteobacteria. However, the organically grown drupes contained significantly more Alphaproteobacteria and the conventionally grown drupes contained significantly more Gammaproteobacteria. The conventionally grown drupes also contained significantly more sequences associated with the phylum Actinobacteria. After hull split, we observed a significant increase in bacterial diversity, with many newly appearing sequences that were not normally associated with the phyllosphere. Organic and conventional growing methodologies influence the types of bacteria on almond drupes and hull split results in a burst of microbial diversification. Production of organic produce is increasing due to consumer preferences, but it was unknown how this methodology affects the bacterial populations on almond drupes. This is the first study to compare the bacterial populations of organically and conventionally grown almond drupes. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

  18. Bacterial recombination promotes the evolution of multi-drug-resistance in functionally diverse populations

    PubMed Central

    Perron, Gabriel G.; Lee, Alexander E. G.; Wang, Yun; Huang, Wei E.; Barraclough, Timothy G.

    2012-01-01

    Bacterial recombination is believed to be a major factor explaining the prevalence of multi-drug-resistance (MDR) among pathogenic bacteria. Despite extensive evidence for exchange of resistance genes from retrospective sequence analyses, experimental evidence for the evolutionary benefits of bacterial recombination is scarce. We compared the evolution of MDR between populations of Acinetobacter baylyi in which we manipulated both the recombination rate and the initial diversity of strains with resistance to single drugs. In populations lacking recombination, the initial presence of multiple strains resistant to different antibiotics inhibits the evolution of MDR. However, in populations with recombination, the inhibitory effect of standing diversity is alleviated and MDR evolves rapidly. Moreover, only the presence of DNA harbouring resistance genes promotes the evolution of resistance, ruling out other proposed benefits for recombination. Together, these results provide direct evidence for the fitness benefits of bacterial recombination and show that this occurs by mitigation of functional interference between genotypes resistant to single antibiotics. Although analogous to previously described mechanisms of clonal interference among alternative beneficial mutations, our results actually highlight a different mechanism by which interactions among co-occurring strains determine the benefits of recombination for bacterial evolution. PMID:22048956

  19. Novel, Deep-Branching Heterotrophic Bacterial Populations Recovered from Thermal Spring Metagenomes

    PubMed Central

    Colman, Daniel R.; Jay, Zackary J.; Inskeep, William P.; Jennings, Ryan deM.; Maas, Kendra R.; Rusch, Douglas B.; Takacs-Vesbach, Cristina D.

    2016-01-01

    Thermal spring ecosystems are a valuable resource for the discovery of novel hyperthermophilic Bacteria and Archaea, and harbor deeply-branching lineages that provide insight regarding the nature of early microbial life. We characterized bacterial populations in two circumneutral (pH ~8) Yellowstone National Park thermal (T ~80°C) spring filamentous “streamer” communities using random metagenomic DNA sequence to investigate the metabolic potential of these novel populations. Four de novo assemblies representing three abundant, deeply-branching bacterial phylotypes were recovered. Analysis of conserved phylogenetic marker genes indicated that two of the phylotypes represent separate groups of an uncharacterized phylum (for which we propose the candidate phylum name “Pyropristinus”). The third new phylotype falls within the proposed Calescamantes phylum. Metabolic reconstructions of the “Pyropristinus” and Calescamantes populations showed that these organisms appear to be chemoorganoheterotrophs and have the genomic potential for aerobic respiration and oxidative phosphorylation via archaeal-like V-type, and bacterial F-type ATPases, respectively. A survey of similar phylotypes (>97% nt identity) within 16S rRNA gene datasets suggest that the newly described organisms are restricted to terrestrial thermal springs ranging from 70 to 90°C and pH values of ~7–9. The characterization of these lineages is important for understanding the diversity of deeply-branching bacterial phyla, and their functional role in high-temperature circumneutral “streamer” communities. PMID:27014227

  20. Biological controls on bacterial populations in ballast water during ocean transit.

    PubMed

    Seiden, Jennica M; Rivkin, Richard B

    2014-01-15

    Bacteria (and viruses) numerically dominate ballast water communities, but what controls their population dynamics during transit is largely unexplored. Here, bacterial abundance, net and intrinsic growth rates, and grazing mortality were determined during a trans-Atlantic voyage. The effects of grazing pressure by microzooplankton on heterotrophic bacteria during transit were determined for source port, mid-ocean exchange (MOE), and six-day-old source port ballast water. When the grazer component was removed, bacterial abundances significantly increased. Additionally, we determined that the grazer-mediated mortality for ballast water originating from ports was greater than MOE water and that mortality decreased over time for the source port ballast water. This study shows that bacterial populations in transit are controlled by microzooplankton grazing. If these findings are representative of ballast water environments, they suggest that if the grazing component is selectively removed by various treatment methods, bacterial populations may increase; this could have environmental and human health consequences. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. Identification of Population Bottlenecks and Colonization Factors during Assembly of Bacterial Communities within the Zebrafish Intestine.

    PubMed

    Stephens, W Zac; Wiles, Travis J; Martinez, Emily S; Jemielita, Matthew; Burns, Adam R; Parthasarathy, Raghuveer; Bohannan, Brendan J M; Guillemin, Karen

    2015-10-27

    The zebrafish, Danio rerio, is a powerful model for studying bacterial colonization of the vertebrate intestine, but the genes required by commensal bacteria to colonize the zebrafish gut have not yet been interrogated on a genome-wide level. Here we apply a high-throughput transposon mutagenesis screen to Aeromonas veronii Hm21 and Vibrio sp. strain ZWU0020 during their colonization of the zebrafish intestine alone and in competition with each other, as well as in different colonization orders. We use these transposon-tagged libraries to track bacterial population sizes in different colonization regimes and to identify gene functions required during these processes. We show that intraspecific, but not interspecific, competition with a previously established bacterial population greatly reduces the ability of these two bacterial species to colonize. Further, using a simple binomial sampling model, we show that under conditions of interspecific competition, genes required for colonization cannot be identified because of the population bottleneck experienced by the second colonizer. When bacteria colonize the intestine alone or at the same time as the other species, we find shared suites of functional requirements for colonization by the two species, including a prominent role for chemotaxis and motility, regardless of the presence of another species. Zebrafish larvae, which are amenable to large-scale gnotobiotic studies, comprehensive sampling of their intestinal microbiota, and live imaging, are an excellent model for investigations of vertebrate intestinal colonization dynamics. We sought to develop a mutagenesis and tagging system in order to understand bacterial population dynamics and functional requirements during colonization of the larval zebrafish intestine. We explored changes in bacterial colonization dynamics and functional requirements when bacteria colonize a bacterium-free intestine, one previously colonized by their own species, or one colonized

  2. A mobile asset tracking system architecture under mobile-stationary co-existing WSNs.

    PubMed

    Kim, Tae Hyon; Jo, Hyeong Gon; Lee, Jae Shin; Kang, Soon Ju

    2012-12-14

    The tracking of multiple wireless mobile nodes is not easy with current legacy WSN technologies, due to their inherent technical complexity, especially when heavy traffic and frequent movement of mobile nodes are encountered. To enable mobile asset tracking under these legacy WSN systems, it is necessary to design a specific system architecture that can manage numerous mobile nodes attached to mobile assets. In this paper, we present a practical system architecture including a communication protocol, a three-tier network, and server-side middleware for mobile asset tracking in legacy WSNs consisting of mobile-stationary co-existing infrastructures, and we prove the functionality of this architecture through careful evaluation in a test bed. Evaluation was carried out in a microwave anechoic chamber as well as on a straight road near our office. We evaluated communication mobility performance between mobile and stationary nodes, location-awareness performance, system stability under numerous mobile node conditions, and the successful packet transfer rate according to the speed of the mobile nodes. The results indicate that the proposed architecture is sufficiently robust for application in realistic mobile asset tracking services that require a large number of mobile nodes.

  3. Hypothesis on two different functionalities co-existing in frontal lobe of human brains.

    PubMed

    Wang, Jue

    2013-09-01

    Human frontal lobe is a key area from where our cognition, memory and emotion display or function. In medical case study, there are patients with social dysfunctions, lack of passion or emotion as result of their frontal lobe damage caused by pathological changes, traumatic damage, and brain tumor remove operations. The syndrome of frontal lobe damage remains at large unanswered medically. From early stage of pregnancy, there exists lobe layers, nerve combine, and neurons synaptic, indicating a completion of growth of functionality inside frontal lobe. However, this completion of growth does not match the growth of human intelligence. Human infants only start and complete their cognition and memory functionality one full year after their birth which is marked by huge amount of neurons synaptic inside their frontal lobe, which is not part of a continual growth of originally developed functions. By reasoning on pathological changes of frontal lobe, a hypothesis was established that two individually functional mechanisms co-existed inside one frontal lobe. This neuron system is particularly for human beings. Copyright © 2013 Elsevier Ltd. All rights reserved.

  4. Nanoparticle interactions with co-existing contaminants: joint toxicity, bioaccumulation and risk.

    PubMed

    Deng, Rui; Lin, Daohui; Zhu, Lizhong; Majumdar, Sanghamitra; White, Jason C; Gardea-Torresdey, Jorge L; Xing, Baoshan

    2017-06-01

    With their growing production and application, engineered nanoparticles (NPs) are increasingly discharged into the environment. The released NPs can potentially interact with pre-existing contaminants, leading to biological effects (bioaccumulation and/or toxicity) that are poorly understood. Most studies on NPs focus on single analyte exposure; the existing literature on joint toxicity of NPs and co-existing contaminants is rather limited but beginning to develop rapidly. This is the first review paper evaluating the current state of knowledge regarding the joint effects of NPs and co-contaminants. Here, we review: (1) methods for investigating and evaluating joint effects of NPs and co-contaminants; (2) simultaneous toxicities from NPs co-exposed with organic contaminants, metal/metalloid ions, dissolved organic matter (DOM), inorganic ligands and additional NPs; and (3) the influence of NPs co-exposure on the bioaccumulation of organic contaminants and heavy metal ions, as well as the influence of contaminants on NPs bioaccumulation. In addition, future research needs are discussed so as to better understand risk associated with NPs-contaminant co-exposure.

  5. The clinicopathologic differences in papillary thyroid carcinoma with or without co-existing chronic lymphocytic thyroiditis.

    PubMed

    Yoon, Yeo-Hoon; Kim, Hak Joon; Lee, Jin Woo; Kim, Jin Man; Koo, Bon Seok

    2012-03-01

    The goal of this study is to determine the clinicopathologic differences in patients with papillary thyroid carcinoma (PTC) with or without chronic lymphocytic thyroiditis (CLT). We reviewed the medical records of 195 consecutive PTC patients who underwent total thyroidectomy and bilateral central lymph node dissection from April 2008 to March 2010. The differences in clinicopathologic factors, such as age, gender, size of primary tumor, perithyroidal invasion, lymphovascular invasion, capsular invasion, and central lymph node (CLN) metastasis, were analyzed in PTC patients with or without CLT. Among 195 patients, 56 (28.7%) had co-existing CLT. Patients with CLT had the following characteristics as compared to patients without CLT: significantly younger, female predominance, smaller tumor size, and lower incidence of capsular invasion (p = 0.038, 0.006, 0.037, and 0.026, respectively). Also, patients with CLT (12.5%) had a significantly lower incidence of CLN metastases than patients without CLT (28.1%; p = 0.025) based on univariate analysis. Moreover, multivariate analysis showed that younger age (p = 0.042, odds ratio = 1.033) and female gender (p = 0.012, odds ratio = 6.865) are independent clinical factors in patients with CLT compared to patients without CLT. CLT was shown to be commonly associated with PTC. Compared to patients with PTC without CLT, patients with CLT were younger with a female predominance, which are the most important and well-known prognostic variables for thyroid cancer mortality.

  6. Sickness absence among female employees with migraine and co-existing conditions.

    PubMed

    Mäki, K; Vahtera, J; Virtanen, M; Elovainio, M; Pentti, J; Keltikangas-Järvinen, L; Kivimäki, M

    2008-11-01

    This prospective cohort study examined the risk of sickness absence among 27,127 female public-sector employees by status of migraine and co-existing conditions. A baseline survey was used to assess chronic disorders and demographic factors. Information on sickness absence in the 3 years following the survey was obtained from employers' registers. Migraine was related to 5.4 extra sickness absence days per person-year, with the corresponding figures being 14.6 and 6.1 for depression and respiratory disorders, respectively. After adjusting for age, marital status, socioeconomic status and presence of depression or respiratory disorders, employees with migraine had a 1.21 (95% confidence interval 1.18, 1.24) times higher risk of self-certified sickness absence episodes (< or = 3 days) than did those without migraine. The corresponding excess risk for medically certified absence episodes (> 3 days) was 1.15 (1.12, 1.19). Among employees with depression or respiratory disorders, secondary migraine was associated with an increased risk of sickness absence episode of 1.15 to 1.23. These findings suggest that migraine is associated with increased risk of recorded sickness absence independent of depression and respiratory disorders.

  7. A Mobile Asset Tracking System Architecture under Mobile-Stationary Co-Existing WSNs

    PubMed Central

    Kim, Tae Hyon; Jo, Hyeong Gon; Lee, Jae Shin; Kang, Soon Ju

    2012-01-01

    The tracking of multiple wireless mobile nodes is not easy with current legacy WSN technologies, due to their inherent technical complexity, especially when heavy traffic and frequent movement of mobile nodes are encountered. To enable mobile asset tracking under these legacy WSN systems, it is necessary to design a specific system architecture that can manage numerous mobile nodes attached to mobile assets. In this paper, we present a practical system architecture including a communication protocol, a three-tier network, and server-side middleware for mobile asset tracking in legacy WSNs consisting of mobile-stationary co-existing infrastructures, and we prove the functionality of this architecture through careful evaluation in a test bed. Evaluation was carried out in a microwave anechoic chamber as well as on a straight road near our office. We evaluated communication mobility performance between mobile and stationary nodes, location-awareness performance, system stability under numerous mobile node conditions, and the successful packet transfer rate according to the speed of the mobile nodes. The results indicate that the proposed architecture is sufficiently robust for application in realistic mobile asset tracking services that require a large number of mobile nodes. PMID:23242277

  8. Comparative dynamics of adherent and nonadherent bacterial populations on maize leaves.

    PubMed

    Beattie, Gwyn A; Marcell, Lise M

    2002-09-01

    ABSTRACT The dynamics of the adherent and nonadherent populations of three bacterial species on maize leaves were examined to identify the extent to which bacteria adhere to leaves and the importance of this adhesion to leaf colonization. Pantoea agglomerans strain BRT98, Clavibacter michiganensis subsp. nebraskensis strain GH2390, and Pseudomonas syringae pv. syringae strain HS191R all rapidly adhered to maize leaves following inoculation, but differed in the percentage of cells that adhered to the leaves. Immediately following inoculation, the percentage of adherent cells was highest for the saprophyte P. agglomerans (8 to 10%) and was much lower for the pathogens C. michiganensis subsp. nebras-kensis and P. syringae pv. syringae (2 to 3 and <1%, respectively), although the results for P. syringae pv. syringae HS191R were based on only one experiment. In the 4 days following inoculation, the percentage of the P. agglomerans populations that adhered to the leaves increased to approximately 70%. Similarly, the percentage of C. michiganensis subsp. nebraskensis and P. syringae pv. syringae cells that resisted removal steadily increased in the days following inoculation, although these increases probably reflected both adherence and localization to endophytic sites. Based on differences in the percentage of cells adhering to several cuticular wax mutants of maize, the rapid adherence of C. michiganensis subsp. nebraskensis cells to maize leaves was influenced by the cuticular wax properties, while the rapid adherence of P. agglomerans was not. Finally, bacterial adherence to leaves was advantageous to P. agglomerans survival and growth on leaves based on the finding that the nonadherent populations of the P. agglomerans strain decreased significantly more than did the adherent populations in the 24 h following inoculation, and increased much less than did the adherent populations over the next 3 days. Similar results with the C. michiganensis subsp. nebraskensis and

  9. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

    SciTech Connect

    Bendall, Matthew L.; Stevens, Sarah L.R.; Chan, Leong-Keat; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Froula, Jeff; Kang, Dongwan; Tringe, Susannah G.; Bertilsson, Stefan; Moran, Mary A.; Shade, Ashley; Newton, Ryan J.; McMahon, Katherine D.; Malmstrom, Rex R.

    2016-01-08

    Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary models make different predictions regarding how adaptive alleles spread through populations and how genetic diversity is maintained. Processes predicted by competing evolutionary models, for example, genome-wide selective sweeps vs gene-specific sweeps, could be captured in natural populations using time-series metagenomics if the approach were applied over a sufficiently long time frame. Direct observations of either process would help resolve how distinct microbial groups evolve. Using a 9-year metagenomic study of a freshwater lake (2005–2013), we explore changes in single-nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in 30 bacterial populations. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied by >1000-fold among populations. SNP allele frequencies also changed dramatically over time within some populations. Interestingly, nearly all SNP variants were slowly purged over several years from one population of green sulfur bacteria, while at the same time multiple genes either swept through or were lost from this population. Furthermore, these patterns were consistent with a genome-wide selective sweep in progress, a process predicted by the ‘ecotype model’ of speciation but not previously observed in nature. In contrast, other populations contained large, SNP-free genomic regions that appear to have swept independently through the populations prior to the study without purging diversity elsewhere in the genome. Finally, evidence for both genome-wide and gene-specific sweeps suggests that different models of bacterial speciation may apply to different populations coexisting in the same environment.

  10. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

    PubMed Central

    Bendall, Matthew L; Stevens, Sarah LR; Chan, Leong-Keat; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Froula, Jeff; Kang, Dongwan; Tringe, Susannah G; Bertilsson, Stefan; Moran, Mary A; Shade, Ashley; Newton, Ryan J; McMahon, Katherine D; Malmstrom, Rex R

    2016-01-01

    Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary models make different predictions regarding how adaptive alleles spread through populations and how genetic diversity is maintained. Processes predicted by competing evolutionary models, for example, genome-wide selective sweeps vs gene-specific sweeps, could be captured in natural populations using time-series metagenomics if the approach were applied over a sufficiently long time frame. Direct observations of either process would help resolve how distinct microbial groups evolve. Here, from a 9-year metagenomic study of a freshwater lake (2005–2013), we explore changes in single-nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in 30 bacterial populations. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied by >1000-fold among populations. SNP allele frequencies also changed dramatically over time within some populations. Interestingly, nearly all SNP variants were slowly purged over several years from one population of green sulfur bacteria, while at the same time multiple genes either swept through or were lost from this population. These patterns were consistent with a genome-wide selective sweep in progress, a process predicted by the ‘ecotype model' of speciation but not previously observed in nature. In contrast, other populations contained large, SNP-free genomic regions that appear to have swept independently through the populations prior to the study without purging diversity elsewhere in the genome. Evidence for both genome-wide and gene-specific sweeps suggests that different models of bacterial speciation may apply to different populations coexisting in the same environment. PMID:26744812

  11. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

    DOE PAGES

    Bendall, Matthew L.; Stevens, Sarah L.R.; Chan, Leong-Keat; ...

    2016-01-08

    Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary models make different predictions regarding how adaptive alleles spread through populations and how genetic diversity is maintained. Processes predicted by competing evolutionary models, for example, genome-wide selective sweeps vs gene-specific sweeps, could be captured in natural populations using time-series metagenomics if the approach were applied over a sufficiently long time frame. Direct observations of either process would help resolve how distinct microbial groups evolve. Using a 9-year metagenomic study of a freshwater lake (2005–2013), we explore changes in single-nucleotide polymorphism (SNP) frequencies and patterns of genemore » gain and loss in 30 bacterial populations. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied by >1000-fold among populations. SNP allele frequencies also changed dramatically over time within some populations. Interestingly, nearly all SNP variants were slowly purged over several years from one population of green sulfur bacteria, while at the same time multiple genes either swept through or were lost from this population. Furthermore, these patterns were consistent with a genome-wide selective sweep in progress, a process predicted by the ‘ecotype model’ of speciation but not previously observed in nature. In contrast, other populations contained large, SNP-free genomic regions that appear to have swept independently through the populations prior to the study without purging diversity elsewhere in the genome. Finally, evidence for both genome-wide and gene-specific sweeps suggests that different models of bacterial speciation may apply to different populations coexisting in the same environment.« less

  12. Changes in bacterial population of gastrointestinal tract of weaned pigs fed with different additives.

    PubMed

    Roca, Mercè; Nofrarías, Miquel; Majó, Natàlia; Pérez de Rozas, Ana María; Segalés, Joaquim; Castillo, Marisol; Martín-Orúe, Susana María; Espinal, Anna; Pujols, Joan; Badiola, Ignacio

    2014-01-01

    This study aimed to provide novel insights into the gastrointestinal microbial diversity from different gastrointestinal locations in weaning piglets using PCR-restriction fragment length polymorphism (PCR-RFLP). Additionally, the effect of different feed additives was analyzed. Thirty-two piglets were fed with four different diets: a control group and three enriched diets, with avilamycin, sodium butyrate, and a plant extract mixture. Digesta samples were collected from eight different gastrointestinal segments of each animal and the bacterial population was analysed by a PCR-RFLP technique that uses 16S rDNA gene sequences. Bacterial diversity was assessed by calculating the number of bands and the Shannon-Weaver index. Dendrograms were constructed to estimate the similarity of bacterial populations. A higher bacterial diversity was detected in large intestine compared to small intestine. Among diets, the most relevant microbial diversity differences were found between sodium butyrate and plant extract mixture. Proximal jejunum, ileum, and proximal colon were identified as those segments that could be representative of microbial diversity in pig gut. Results indicate that PCR-RFLP technique allowed detecting modifications on the gastrointestinal microbial ecology in pigs fed with different additives, such as increased biodiversity by sodium butyrate in feed.

  13. Changes in Bacterial Population of Gastrointestinal Tract of Weaned Pigs Fed with Different Additives

    PubMed Central

    Roca, Mercè; Nofrarías, Miquel; Majó, Natàlia; Pérez de Rozas, Ana María; Castillo, Marisol; Martín-Orúe, Susana María; Espinal, Anna; Pujols, Joan; Badiola, Ignacio

    2014-01-01

    This study aimed to provide novel insights into the gastrointestinal microbial diversity from different gastrointestinal locations in weaning piglets using PCR-restriction fragment length polymorphism (PCR-RFLP). Additionally, the effect of different feed additives was analyzed. Thirty-two piglets were fed with four different diets: a control group and three enriched diets, with avilamycin, sodium butyrate, and a plant extract mixture. Digesta samples were collected from eight different gastrointestinal segments of each animal and the bacterial population was analysed by a PCR-RFLP technique that uses 16S rDNA gene sequences. Bacterial diversity was assessed by calculating the number of bands and the Shannon-Weaver index. Dendrograms were constructed to estimate the similarity of bacterial populations. A higher bacterial diversity was detected in large intestine compared to small intestine. Among diets, the most relevant microbial diversity differences were found between sodium butyrate and plant extract mixture. Proximal jejunum, ileum, and proximal colon were identified as those segments that could be representative of microbial diversity in pig gut. Results indicate that PCR-RFLP technique allowed detecting modifications on the gastrointestinal microbial ecology in pigs fed with different additives, such as increased biodiversity by sodium butyrate in feed. PMID:24575403

  14. Dietary format alters fecal bacterial populations in the domestic cat (Felis catus)

    PubMed Central

    Bermingham, Emma N; Young, Wayne; Kittelmann, Sandra; Kerr, Katherine R; Swanson, Kelly S; Roy, Nicole C; Thomas, David G

    2013-01-01

    The effects of short-term (5-week) exposure to wet or dry diets on fecal bacterial populations in the cat were investigated. Sixteen mixed-sex, neutered, domestic short-haired cats (mean age = 6 years; mean bodyweight = 3.4 kg) were randomly allocated to wet or dry diets in a crossover design. Fecal bacterial DNA was isolated and bacterial 16S rRNA gene amplicons generated and analyzed by 454 Titanium pyrosequencing. Cats fed dry diets had higher abundances (P < 0.05) of Actinobacteria (16.5% vs. 0.1%) and lower abundances of Fusobacteria (0.3% vs. 23.1%) and Proteobacteria (0.4% vs. 1.1%) compared with cats fed the wet diet. Of the 46 genera identified, 30 were affected (P < 0.05) by diet, with higher abundances of Lactobacillus (31.8% vs. 0.1%), Megasphaera (23.0% vs. 0.0%), and Olsenella (16.4% vs. 0.0%), and lower abundances of Bacteroides (0.6% vs. 5.7%) and Blautia (0.3% vs. 2.3%) in cats fed the dry diet compared with cats fed the wet diet. These results demonstrate that short-term dietary exposure to diet leads to large shifts in fecal bacterial populations that have the potential to affect the ability of the cat to process macronutrients in the diet. PMID:23297252

  15. Distribution and Life Strategies of Two Bacterial Populations in a Eutrophic Lake

    PubMed Central

    Weinbauer, Markus G.; Höfle, Manfred G.

    1998-01-01

    Monoclonal antibodies and epifluorescence microscopy were used to determine the depth distribution of two indigenous bacterial populations in the stratified Lake Plußsee and characterize their life strategies. Populations of Comamonas acidovorans PX54 showed a depth distribution with maximum abundances in the oxic epilimnion, whereas Aeromonas hydrophila PU7718 showed a depth distribution with maximum abundances in the anoxic thermocline layer (metalimnion), i.e., in the water layer with the highest microbial activity. Resistance of PX54 to protist grazing and high metabolic versatility and growth rate of PU7718 were the most important life strategy traits for explaining the depth distribution of the two bacterial populations. Maximum abundance of PX54 was 16,000 cells per ml, and maximum abundance of PU7718 was 20,000 cells per ml. Determination of bacterial productivity in dilution cultures with different-size fractions of dissolved organic matter (DOM) from lake water indicates that low-molecular-weight (LMW) DOM is less bioreactive than total DOM (TDOM). The abundance and growth rate of PU7718 were highest in the TDOM fractions, whereas those of PX54 were highest in the LMW DOM fraction, demonstrating that PX54 can grow well on the less bioreactive DOM fraction. We estimated that 13 to 24% of the entire bacterial community and 14% of PU7718 were removed by viral lysis, whereas no significant effect of viral lysis on PX54 could be detected. Growth rates of PX54 (0.11 to 0.13 h−1) were higher than those of the entire bacterial community (0.04 to 0.08 h−1) but lower than those of PU7718 (0.26 to 0.31 h−1). In undiluted cultures, the growth rates were significantly lower, pointing to density effects such as resource limitation or antibiosis, and the effects were stronger for PU7718 and the entire bacterial community than for PX54. Life strategy characterizations based on data from literature and this study revealed that the fast-growing and metabolically

  16. [Effects of grape-replanting on soil bacterial and fungal populations].

    PubMed

    Li, Kun; Guo, Xiu-wu; Sun, Ying-ni; Zhang, Li-heng; Hu, Xi-xi

    2009-12-01

    Rhizosphere and non-rhizosphere soil samples were collected from the vineyards having been planted for 3 and 30 years, and PCR-DGGE technique was adopted to study the effects of grape-replanting on the population structure and diversity of soil bacteria and fungi. The bacterial and fungal diversities were higher in 30-year-planted vineyard than in 3-year-planted vineyard, and higher in rhizosphere soil than in non-rhizosphere soil. After 30 years replanting, the population structure of bacteria and fungi approached the same in rhizosphere soil and non-rhizosphere soil but differed from that in fallow soil; while in the 3-year-planted vineyard, the population structure in rhizosphere soil was different from that in non-rhizosphere soil and fallow soil. Comparing with that in 3-year-planted vineyard, the rhizosphere soil microbial population in 30-year-planted vineyard had a greater change. In bacterial population, Flavobacterium sp. (DQ339585) and Bacillus sp. (AY039821) decreased while Pedobacter sp. (AJ871084) increased; in fungal population, Omphalina farinolens (EF413029) appeared, Pestalotiopsis sp. (DQ657877, DQ657875, DQ657871), Phacidium lacerum (DQ470976), and Lecythophora decumbens (AF353597) decreased, while Pilidium acerinum voucher (AY48709) increased. Bacillus sp., Flavobacterium sp. , and Pestalotiopsis sp. had antagonism to pathogen, and their decrease reduced the resistance of grape against pathogen. The increase of Pilidium acerinum voucher might relate to the severe disease after grape-replanting.

  17. Structural instability and phase co-existence driven non-Gaussian resistance fluctuations in metal nanowires at low temperatures

    NASA Astrophysics Data System (ADS)

    Bid, Aveek; Raychaudhuri, A. K.

    2016-11-01

    We report a detailed experimental study of the resistance fluctuations measured at low temperatures in high quality metal nanowires ranging in diameter from 15-200 nm. The wires exhibit co-existing face-centered-cubic and 4H hcp phases of varying degrees as determined from the x-ray diffraction data. We observe the appearance of a large non-Gaussian noise for nanowires of diameter smaller than 50 nm over a certain temperature range around ≈30 K. The diameter range ˜30 nm, where the noise has maxima coincides with the maximum volume fraction of the co-existing 4H hcp phase thus establishing a strong link between the fluctuation and the phase co-existence. The resistance fluctuation in the same temperature range also shows a deviation of 1/f behavior at low frequency with appearance of single frequency Lorentzian type contribution in the spectral power density. The fluctuations are thermally activated with an activation energy {E}{{a}}˜ 35 meV, which is of same order as the activation energy of creation of stacking fault in FCC metals that leads to the co-existing crystallographic phases. Combining the results of crystallographic studies of the nanowires and analysis of the resistance fluctuations we could establish the correlation between the appearance of the large resistance noise and the onset of phase co-existence in these nanowires.

  18. Co-existence of multiple strains of porcine circovirus type 2 in the same pig from China.

    PubMed

    Zhai, Shao-Lun; Chen, Sheng-Nan; Wei, Zu-Zhang; Zhang, Jian-Wu; Huang, Lv; Lin, Tao; Yue, Cheng; Ran, Duo-Liang; Yuan, Shi-Shan; Wei, Wen-Kang; Long, Jin-Xue

    2011-11-13

    Pigs are often co-infected by different viral strains from the same virus. Up to now, there are few reports about co-existence of different porcine circovirus type 2 (PCV2) strains in China. The aim of this study was to evaluate it in Chinese swine herds. 118 PCV2 positive DNAs isolated from diseased pigs identified by classic PCR were re-detected using a modified differential PCR assay. The results indicated that co-existence rates of PCV2 were 32.2% (38/118) in diseased pigs and 0% (0/41) in asymptomatic pigs. Four PCV2 complete genomes were cloned from two co-infected samples and their nucleotide (nt) identities were 95%-97.3%. The phylogenetic analysis showed that four PCV2 strains were divided into different genotypes, PCV2a, PCV2b, PCV2d and PCV2e, respectively. In addition, co-existence were not detected in 41 serum samples from healthy pigs but PCV2 single infection (31.7%, 13/41) existed. These data revealed that the co-existence of different strains of PCV2 might contribute to the development of more severe clinical symptoms for pigs. This is the first report confirming the co-existence of different PCV2 strains in Chinese swine herds. Meanwhile, this study could help us to understand new infection and prevalence forms of PCV2 clinically.

  19. Structural instability and phase co-existence driven non-Gaussian resistance fluctuations in metal nanowires at low temperatures.

    PubMed

    Bid, Aveek; Raychaudhuri, A K

    2016-11-11

    We report a detailed experimental study of the resistance fluctuations measured at low temperatures in high quality metal nanowires ranging in diameter from 15-200 nm. The wires exhibit co-existing face-centered-cubic and 4H hcp phases of varying degrees as determined from the x-ray diffraction data. We observe the appearance of a large non-Gaussian noise for nanowires of diameter smaller than 50 nm over a certain temperature range around ≈30 K. The diameter range ∼30 nm, where the noise has maxima coincides with the maximum volume fraction of the co-existing 4H hcp phase thus establishing a strong link between the fluctuation and the phase co-existence. The resistance fluctuation in the same temperature range also shows a deviation of [Formula: see text] behavior at low frequency with appearance of single frequency Lorentzian type contribution in the spectral power density. The fluctuations are thermally activated with an activation energy [Formula: see text] meV, which is of same order as the activation energy of creation of stacking fault in FCC metals that leads to the co-existing crystallographic phases. Combining the results of crystallographic studies of the nanowires and analysis of the resistance fluctuations we could establish the correlation between the appearance of the large resistance noise and the onset of phase co-existence in these nanowires.

  20. Children with burns referred for child abuse evaluation: Burn characteristics and co-existent injuries.

    PubMed

    Pawlik, Marie-Christin; Kemp, Alison; Maguire, Sabine; Nuttall, Diane; Feldman, Kenneth W; Lindberg, Daniel M

    2016-05-01

    Intentional burns represent a serious form of physical abuse that must be identified to protect children from further harm. This study is a retrospectively planned secondary analysis of the Examining Siblings To Recognize Abuse (ExSTRA) network data. Our objective was to describe the characteristics of burns injuries in children referred to Child Abuse Pediatricians (CAPs) in relation to the perceived likelihood of abuse. We furthermore compare the extent of diagnostic investigations undertaken in children referred to CAPs for burn injuries with those referred for other reasons. Within this dataset, 7% (215/2890) of children had burns. Children with burns were older than children with other injuries (median age 20 months vs. 10 months). Physical abuse was perceived as likely in 40.9% (88) and unlikely in 59.1% (127). Scalds accounted for 52.6% (113) and contact burns for 27.6% (60). Several characteristics of the history and burn injury were associated with a significantly higher perceived likelihood of abuse, including children with reported inflicted injury, absent or inadequate explanation, hot water as agent, immersion scald, a bilateral/symmetric burn pattern, total body surface area ≥10%, full thickness burns, and co-existent injuries. The rates of diagnostic testing were significantly lower in children with burns than other injuries, yet the yield of skeletal survey and hepatic transaminases testing were comparable between the two groups. This would imply that children referred to CAPs for burns warrant the same level of comprehensive investigations as those referred for other reasons.

  1. Co-existence of superconductivity and ferromagnetism in f-electron metals.

    NASA Astrophysics Data System (ADS)

    Huxley, Andrew

    2002-03-01

    In itinerant ferromagnets a strong spin polarisation might be expected to suppress any possibility of spin-singlet superconductivity. However spin triplet superconductivity may still occur if there is an appropriate pairing interaction and the material is sufficiently clean. The experimental evidence that a bulk superconducting state is indeed realised in two different f-electron ferromagnets will be reviewed, along with the special factors that might favour such a state. For UGe_2, samples that satisfy the clean limit condition are easily prepared. The superconducting transition temperature is however closely correlated with the proximity to a critical point for a magnetic transition within the ferromagnetic state, which is achieved only at high pressure. The same factors, perhaps related to Fermi surface nesting, which give rise to this complex magnetic behaviour, therefore appear to be implicated in the superconducting pairing. Superconductivity in ferromagnetic URhGe occurs at zero pressure, which has facilitated extensive magnetisation and heat-capacity studies. These confirm both the bulk nature of the two transitions and the co-existence of the two orders (ferromagnetism and superconductivity). Further, as expected for non s-wave pairing, it is found that only samples with a sufficiently low residual resistivity show superconductivity. In contrast to UGe_2, the magnetic state in URhGe behaves in accordance with the simplest version of the Moriya-Lonzarich theory. This, as well as the recent report that that the cubic itinerant ferromagnet ZrZn2 shows a low temperature transition, interpreted as an incomplete transition to superconductivity, suggest that superconductivity could occur more commonly in clean ferromagnets. The observed superconducting properties of UGe2 and URhGe appear to be consistent with a particular symmetry of the order parameter in these lower symmetry materials. Their lower symmetries also lead to several advantages relating to the

  2. ChAT and NOS in human myenteric neurons: co-existence and co-absence.

    PubMed

    Beck, Martin; Schlabrakowski, Anne; Schrödl, Falk; Neuhuber, Winfried; Brehmer, Axel

    2009-10-01

    Most myenteric neurons contain one of the two generating enzymes for major excitatory and inhibitory neurotransmitters: choline acetyltransferase (ChAT) or neuronal nitric oxide synthase (NOS). Two minor groups of myenteric neurons contain either both enzymes or neither. Our study had two aims: (1) to compare the proportions of neurons stained for ChAT and/or NOS in human small and large intestinal whole-mounts by co-staining with an antibody against the human neuronal protein Hu C/D (HU); (2) to characterize these neurons morphologically by co-staining with a neurofilament (NF) antibody. In small intestinal whole-mounts co-stained with HU, we counted more ChAT-positive (ChAT+) than NOS+ neurons (52% vs. 38%), whereas the large intestine exhibited fewer ChAT+ than NOS+ neurons (38% vs. 50%). Neurons co-reactive for both ChAT and NOS accounted for about 3% in both regions, whereas neurons negative for both enzymes accounted for 7% in the small intestine and 8% in the large intestine. Co-staining with NF revealed that, in both small and large intestine, ChAT+/NOS+ neurons were either spiny (type I) neurons or displayed smaller perikarya that were weakly or not NF-stained. Of all spiny neurons, almost one third was co-reactive for ChAT and NOS, whereas nearly two thirds were positive only for NOS. Neurons negative for both ChAT and NOS were heterogeneous in size and NF reactivity. Thus, neither the co-existence nor the co-absence of ChAT and NOS in human myenteric neurons is indicative for particular neuron types, with several qualitative and quantitative parameters showing a wide range of interindividual variability.

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

    PubMed Central

    Dini-Andreote, Francisco; Falcao Salles, Joana

    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

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

    PubMed

    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

  5. Flow cytometric determination of bacterial populations in bottled natural mineral waters

    NASA Astrophysics Data System (ADS)

    Beisker, Wolfgang; Meier, H.

    1998-04-01

    In order to enhance the quality and safety of bottled natural mineral waters, new methodologies besides classical bacteriology have been evaluated. Multi laser flow cytometry has been used to identify bacterial populations based on their DNA content, physiological activity and phylogeny from in situ hybridization with rRNA targeted DNA probes. Due to the low content of organic material in these waters, the bacterial population are under conditions (low ribosome content, low activity, etc.) which makes it hard to detect them flow cytometrically. The numbers of bacteria are in the range between 1000 and 100,000 per ml (for uncarbonated waters). Filtration techniques to enrich the bacterial population have been developed in combination with specific staining and hybridization protocols. First results on some selected brands show, that most bacteria belong to the beta subclass of proteobacteria. If the DNA containing cells (DAPI staining) are counted as 100%, 84% could be stained with a eubacteria probe. From these 84% 68% belong to the beta subclass, 8.2% to the alpha and 0.3% to the gamma subclass of roteobacteria. 8.5% could be identified as cytophaga flexibacter. By optimizing DNA staining with cyanine dyes and enhancing the sensitivity of light scatter detection, the detection limit could be considerably lowered.

  6. Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum

    PubMed Central

    Kumar, Nitin; Lad, Ganesh; Giuntini, Elisa; Kaye, Maria E.; Udomwong, Piyachat; Shamsani, N. Jannah; Young, J. Peter W.; Bailly, Xavier

    2015-01-01

    Biological species may remain distinct because of genetic isolation or ecological adaptation, but these two aspects do not always coincide. To establish the nature of the species boundary within a local bacterial population, we characterized a sympatric population of the bacterium Rhizobium leguminosarum by genomic sequencing of 72 isolates. Although all strains have 16S rRNA typical of R. leguminosarum, they fall into five genospecies by the criterion of average nucleotide identity (ANI). Many genes, on plasmids as well as the chromosome, support this division: recombination of core genes has been largely within genospecies. Nevertheless, variation in ecological properties, including symbiotic host range and carbon-source utilization, cuts across these genospecies, so that none of these phenotypes is diagnostic of genospecies. This phenotypic variation is conferred by mobile genes. The genospecies meet the Mayr criteria for biological species in respect of their core genes, but do not correspond to coherent ecological groups, so periodic selection may not be effective in purging variation within them. The population structure is incompatible with traditional ‘polyphasic taxonomy′ that requires bacterial species to have both phylogenetic coherence and distinctive phenotypes. More generally, genomics has revealed that many bacterial species share adaptive modules by horizontal gene transfer, and we envisage a more consistent taxonomic framework that explicitly recognizes this. Significant phenotypes should be recognized as ‘biovars' within species that are defined by core gene phylogeny. PMID:25589577

  7. Bacterial Population Dynamics in Dairy Waste during Aerobic and Anaerobic Treatment and Subsequent Storage▿

    PubMed Central

    McGarvey, Jeffery A.; Miller, William G.; Zhang, Ruihong; Ma, Yanguo; Mitloehner, Frank

    2007-01-01

    The objective of this study was to model a typical dairy waste stream, monitor the chemical and bacterial population dynamics that occur during aerobic or anaerobic treatment and subsequent storage in a simulated lagoon, and compare them to those of waste held without treatment in a simulated lagoon. Both aerobic and anaerobic treatment methods followed by storage effectively reduced the levels of total solids (59 to 68%), biological oxygen demand (85 to 90%), and sulfate (56 to 65%), as well as aerobic (83 to 95%), anaerobic (80 to 90%), and coliform (>99%) bacteria. However, only aerobic treatment reduced the levels of ammonia, and anaerobic treatment was more effective at reducing total sulfur and sulfate. The bacterial population structure of waste before and after treatment was monitored using 16S rRNA gene sequence libraries. Both treatments had unique effects on the bacterial population structure of waste. Aerobic treatment resulted in the greatest change in the type of bacteria present, with the levels of eight out of nine phyla being significantly altered. The most notable differences were the >16-fold increase in the phylum Proteobacteria and the approximately 8-fold decrease in the phylum Firmicutes. Anaerobic treatment resulted in fewer alterations, but significant decreases in the phyla Actinobacteria and Bacteroidetes, and increases in the phyla Planctomycetes, Spirochetes, and TM7 were observed. PMID:17085701

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

    PubMed Central

    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 < 0.05) the abundance of beneficial bifidobacteria and lactobacilli in the microbiota adherent to intestinal mucus of various gut segments of pigs. These changes were seen as proximal as in the jejunum with P95 but did not appear until the distal ileum or cecum with HP. Similar effects of 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

  9. Addition of arabinoxylan and mixed linkage glucans in porcine diets affects the large intestinal bacterial populations.

    PubMed

    Gorham, John B; Kang, Seungha; Williams, Barbara A; Grant, Lucas J; McSweeney, Christopher S; Gidley, Michael J; Mikkelsen, Deirdre

    2016-07-11

    To investigate the effects of two cereal soluble dietary fibres (SDF), wheat arabinoxylan (AX) and oat-mixed linkage glucans (MLG), on fermentative end-products and bacterial community profiles of the porcine caecum (Cae) and distal colon (DC). We hypothesised that feeding pigs these SDF would stimulate Cae and DC carbohydrate fermentation, resulting in a modification of the resident bacterial communities. Five groups of six pigs were each fed one diet based on wheat starch (WS) only, or treatment diets in which some WS was replaced by 10 % AX, or 10 % MLG, a combination of 5 % AX:5 % MLG (AXMLG), or completely replaced with ground whole wheat. Post-euthanasia, Cae and DC digesta were collected for analysis of fermentative end-products, and bacterial community profiles were determined by 16S rRNA gene amplicon 454 pyrosequencing. Across all the SDF-containing diets, predominantly in the proximal region of the large intestine, Prevotella, Lactobacillus, Mitsuokella and Streptococcus were most significantly influenced (P < 0.05), while notable changes were observed for the Ruminococcaceae and Lachnospiraceae families in the Cae and DC. The addition of MLG or AXMLG had the greatest effect of influencing bacterial profiles, reducing sequence proportions assigned to the genus Clostridium, considered detrimental to gut health, with associated increases in short-chain fatty acid and reduced ammonia concentrations. This study demonstrated how the cereal SDF AX and MLG altered the large intestinal bacterial community composition, particularly proximally, further giving insights into how diets rich in specific complex carbohydrates shift the bacterial population, by increasing abundance and promoting greater diversity of those bacteria considered beneficial to gut health.

  10. Changes in gut bacterial populations and their translocation into liver and ascites in alcoholic liver cirrhotics

    PubMed Central

    2014-01-01

    Background The liver is the first line of defence against continuously occurring influx of microbial-derived products and bacteria from the gut. Intestinal bacteria have been implicated in the pathogenesis of alcoholic liver cirrhosis. Escape of intestinal bacteria into the ascites is involved in the pathogenesis of spontaneous bacterial peritonitis, which is a common complication of liver cirrhosis. The association between faecal bacterial populations and alcoholic liver cirrhosis has not been resolved. Methods Relative ratios of major commensal bacterial communities (Bacteroides spp., Bifidobacterium spp., Clostridium leptum group, Enterobactericaea and Lactobacillus spp.) were determined in faecal samples from post mortem examinations performed on 42 males, including cirrhotic alcoholics (n = 13), non-cirrhotic alcoholics (n = 15), non-alcoholic controls (n = 14) and in 7 healthy male volunteers using real-time quantitative PCR (RT-qPCR). Translocation of bacteria into liver in the autopsy cases and into the ascites of 12 volunteers with liver cirrhosis was also studied with RT-qPCR. CD14 immunostaining was performed for the autopsy liver samples. Results Relative ratios of faecal bacteria in autopsy controls were comparable to those of healthy volunteers. Cirrhotics had in median 27 times more bacterial DNA of Enterobactericaea in faeces compared to the healthy volunteers (p = 0.011). Enterobactericaea were also the most common bacteria translocated into cirrhotic liver, although there were no statistically significant differences between the study groups. Of the ascites samples from the volunteers with liver cirrhosis, 50% contained bacterial DNA from Enterobactericaea, Clostridium leptum group or Lactobacillus spp.. The total bacterial DNA in autopsy liver was associated with the percentage of CD14 expression (p = 0.045). CD14 expression percentage in cirrhotics was significantly higher than in the autopsy controls (p = 0

  11. Chromosome painting in silico in a bacterial species reveals fine population structure.

    PubMed

    Yahara, Koji; Furuta, Yoshikazu; Oshima, Kenshiro; Yoshida, Masaru; Azuma, Takeshi; Hattori, Masahira; Uchiyama, Ikuo; Kobayashi, Ichizo

    2013-06-01

    Identifying population structure forms an important basis for genetic and evolutionary studies. Most current methods to identify population structure have limitations in analyzing haplotypes and recombination across the genome. Recently, a method of chromosome painting in silico has been developed to overcome these shortcomings and has been applied to multiple human genome sequences. This method detects the genome-wide transfer of DNA sequence chunks through homologous recombination. Here, we apply it to the frequently recombining bacterial species Helicobacter pylori that has infected Homo sapiens since their birth in Africa and shows wide phylogeographic divergence. Multiple complete genome sequences were analyzed including sequences from Okinawa, Japan, that we recently sequenced. The newer method revealed a finer population structure than revealed by a previous method that examines only MLST housekeeping genes or a phylogenetic network analysis of the core genome. Novel subgroups were found in Europe, Amerind, and East Asia groups. Examination of genetic flux showed some singleton strains to be hybrids of subgroups and revealed evident signs of population admixture in Africa, Europe, and parts of Asia. We expect this approach to further our understanding of intraspecific bacterial evolution by revealing population structure at a finer scale.

  12. Gene Expression Variability Underlies Adaptive Resistance in Phenotypically Heterogeneous Bacterial Populations.

    PubMed

    Erickson, Keesha E; Otoupal, Peter B; Chatterjee, Anushree

    2015-11-13

    The root cause of the antibiotic resistance crisis is the ability of bacteria to evolve resistance to a multitude of antibiotics and other environmental toxins. The regulation of adaptation is difficult to pinpoint due to extensive phenotypic heterogeneity arising during evolution. Here, we investigate the mechanisms underlying general bacterial adaptation by evolving wild-type Escherichia coli populations to dissimilar chemical toxins. We demonstrate the presence of extensive inter- and intrapopulation phenotypic heterogeneity across adapted populations in multiple traits, including minimum inhibitory concentration, growth rate, and lag time. To search for a common response across the heterogeneous adapted populations, we measured gene expression in three stress-response networks: the mar regulon, the general stress response, and the SOS response. While few genes were differentially expressed, clustering revealed that interpopulation gene expression variability in adapted populations was distinct from that of unadapted populations. Notably, we observed both increases and decreases in gene expression variability upon adaptation. Sequencing select genes revealed that the observed gene expression trends are not necessarily attributable to genetic changes. To further explore the connection between gene expression variability and adaptation, we propagated single-gene knockout and CRISPR (clustered regularly interspaced short palindromic repeats) interference strains and quantified impact on adaptation to antibiotics. We identified significant correlations that suggest genes with low expression variability have greater impact on adaptation. This study provides evidence that gene expression variability can be used as an indicator of bacterial adaptive resistance, even in the face of the pervasive phenotypic heterogeneity underlying adaptation.

  13. Co-existing autosomal dominant polycystic kidney disease and nephrotic syndrome in a Nigerian patient with lupus nephritis.

    PubMed

    Akinbodewa, A A; Adejumo, O A; Ogunsemoyin, A O; Osasan, S A; Adefolalu, O A

    2016-01-01

    A little over 30 cases on co-existing nephrotic syndrome and autosomal dominant polycystic kidney disease (ADPKD) have been reported from different regions of the world since 1957. We present a case report on co-existence of nephrotic syndrome (secondary to lupus nephritis) with ADPKD in a 24-year-old woman from Nigeria. She was positive for anti-double stranded DNA. Renal histology showed International Society of Nephrology/Renal Pathology Society Class II lupus nephritis. The co-existence of nephrotic syndrome and ADPKD may have been overlooked in Africa in the past. There is a need to screen for nephrotic syndrome in patients with ADPKD among clinicians in the African setting.

  14. One Year in the Lower St. Lawrence Estuary: Feeding Niche Separation of Two Co-existing Krill Species

    NASA Astrophysics Data System (ADS)

    Winkler, G.; Cabrol, J.; Sage, R.; Nozais, C.; Tremblay, R.; Starr, M.

    2016-02-01

    The lower St. Lawrence estuary (LSLE) is influenced by river discharge and saltwater inflow. Together with arctic water inflow and ice cover in winter a strong stratification occurs resulting in a cold intermediate layer (CIL) from spring to autumn. This stratification provides thermal habitats. Here, we focus on two krill species Thysanoessa raschii and Meganyctiphanes norvegica that aggregate in the CIL and the warmer deep water layer, respectively. Both species are known to migrate into the surface layer to feed and thus transfering energy through the food web by linking lower with higher trophic levels. However, their specific feeding biology and trophic interactions are poorly understood. We tested the following hypotheses: (1) the diets vary throughout the season depending on food availability, (2) similar to thermal habitat separation, trophic niche separation between T. raschii and M. norvegica occurs, characterized by herbivory in T. raschii and carnivory in M. norvegica. Trophic position and feeding behavior of theses krill populations were monitored throughout one year 2014-2015 using a stable isotope approach. The two species showed a seasonal shift in their trophic position being on a higher trophic level in summer than in spring and autumn, which did not correspond to phytoplankton or zooplankton availability. Within the trophic space of carbon and nitrogen stable isotopes M. norvegica showed a relatively stable position, whereas T. raschii covered a much larger space throughout the year. M. norvegica was always positioned at a higher trophic level than T. raschii. Results of a stable isotope mixing model (SIAR) revealed 50% phytoplankton and 50% copepods in the diet of M. norvegica, while T. raschii showed a higher proportion of ca. 70% phytoplankton in its diet. Both species exploited several trophic levels, but in different proportions, thereby minimizing diet overlap, suggesting a further mechanism to enhance stable co-existence of these krill

  15. Co-Existence of Acinic Cell Carcinoma - Papillary Cystic Variant and Extrapulmonary Tuberculosis - Report of A Case with Brief Review.

    PubMed

    Amita, Krishnappa; Vijayshankar, Shivshankar; Sanjay, Manchaiah

    2015-09-01

    Tuberculosis (TB) and cancer are two lethal diseases causing significant morbidity and mortality in developing countries like India. Co-existence of these two disease lead to diagnostic dielemma among the clinicians. Overlapping clinical manifestations lead to delay in diagnosis. We report a case of acinic cell carcinoma -papillary cystic variant of the salivary gland and extra pulmonary tuberculosis in a young female. We emphasize the importance of the awareness of the co-existence of these two diseases and the role of fine needle aspiration cytology in the initial diagnosis.

  16. Plant-associated bacterial populations on native and invasive plant species: comparisons between 2 freshwater environments.

    PubMed

    Olapade, Ola A; Pung, Kayleigh

    2012-06-01

    Plant-microbial interactions have been well studied because of the ecological importance of such relationships in aquatic systems. However, general knowledge regarding the composition of these biofilm communities is still evolving, partly as a result of several confounding factors that are attributable to plant host properties and to hydrodynamic conditions in aquatic environments. In this study, the occurrences of various bacterial phylogenetic taxa on 2 native plants, i.e., mayapple (Podophyllum peltatum L.) and cow parsnip (Heracleum maximum Bartram), and on an invasive species, i.e., garlic mustard (Alliaria petiolata (M. Bieb.) Cavara & Grande), were quantitatively examined using nucleic acid staining and fluorescence in situ hybridization. The plants were incubated in triplicates for about a week within the Kalamazoo River and Pierce Cedar Creek as well as in microcosms. The bacterial groups targeted for enumeration are known to globally occur in relatively high abundance and are also ubiquitously distributed in freshwater environments. Fluorescence in situ hybridization analyses of the bacterioplankton assemblages revealed that the majority of bacterial cells that hybridized with the different probes were similar between the 2 sites. In contrast, the plant-associated populations while similar on the 3 plants incubated in Kalamazoo River, their representations were highest on the 2 native plants relative to the invasive species in Pierce Cedar Creek. Overall, our results further suggested that epiphytic bacterial assemblages are probably under the influences of and probably subsequently respond to multiple variables and conditions in aquatic milieus.

  17. The population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens

    PubMed Central

    WILSON, BENJAMIN A.; GARUD, NANDITA R.; FEDER, ALISON F.; ASSAF, ZOE J.; PENNINGS, PLEUNI S.

    2016-01-01

    Drug resistance is a costly consequence of pathogen evolution and a major concern in public health. In this review, we show how population genetics can be used to study the evolution of drug resistance and also how drug resistance evolution is informative as an evolutionary model system. We highlight five examples from diverse organisms with particular focus on: (i) identifying drug resistance loci in the malaria parasite Plasmodium falciparum using the genomic signatures of selective sweeps, (ii) determining the role of epistasis in drug resistance evolution in influenza, (iii) quantifying the role of standing genetic variation in the evolution of drug resistance in HIV, (iv) using drug resistance mutations to study clonal interference dynamics in tuberculosis and (v) analysing the population structure of the core and accessory genome of Staphylococcus aureus to understand the spread of methicillin resistance. Throughout this review, we discuss the uses of sequence data and population genetic theory in studying the evolution of drug resistance. PMID:26578204

  18. Identifying currents in the gene pool for bacterial populations using an integrative approach.

    PubMed

    Tang, Jing; Hanage, William P; Fraser, Christophe; Corander, Jukka

    2009-08-01

    The evolution of bacterial populations has recently become considerably better understood due to large-scale sequencing of population samples. It has become clear that DNA sequences from a multitude of genes, as well as a broad sample coverage of a target population, are needed to obtain a relatively unbiased view of its genetic structure and the patterns of ancestry connected to the strains. However, the traditional statistical methods for evolutionary inference, such as phylogenetic analysis, are associated with several difficulties under such an extensive sampling scenario, in particular when a considerable amount of recombination is anticipated to have taken place. To meet the needs of large-scale analyses of population structure for bacteria, we introduce here several statistical tools for the detection and representation of recombination between populations. Also, we introduce a model-based description of the shape of a population in sequence space, in terms of its molecular variability and affinity towards other populations. Extensive real data from the genus Neisseria are utilized to demonstrate the potential of an approach where these population genetic tools are combined with an phylogenetic analysis. The statistical tools introduced here are freely available in BAPS 5.2 software, which can be downloaded from http://web.abo.fi/fak/mnf/mate/jc/software/baps.html.

  19. Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

    SciTech Connect

    Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Foster, Brian; Kang, Dongwan; Tringe, Susannah G.; Bertilsson, Stefan; Moran, Mary Ann; Shade, Ashley; Newton, Ryan J.; Stevens, Sarah; McMcahon, Katherine D.; Mamlstrom, Rex R.

    2014-05-12

    Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ecotype model? of diversification, but not previously observed in natural populations.

  20. Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

    SciTech Connect

    Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Foster, Brian; Kang, Dongwan; Tringe, Susannah G.; Bertilsson, Stefan; Moran, Mary Ann; Shade, Ashley; Newton, Ryan J.; Stevens, Sarah; McMahon, Katherine D.; Malmstrom, Rex R.

    2014-06-18

    Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ‘ecotype model’ of diversification, but not previously observed in natural populations.

  1. Elucidation of the tidal influence on bacterial populations in a monsoon influenced estuary through simultaneous observations.

    PubMed

    Khandeparker, Lidita; Eswaran, Ranjith; Gardade, Laxman; Kuchi, Nishanth; Mapari, Kaushal; Naik, Sneha D; Anil, Arga Chandrashekar

    2017-01-01

    The influence of tides on bacterial populations in a monsoon influenced tropical estuary was assessed through fine resolution sampling (1 to 3 h) during spring and neap tides from mouth to the freshwater end at four stations during pre-monsoon, monsoon and post-monsoon seasons. Higher abundance of total bacterial count (TBC) in surface water near the river mouth, compared to the upstream, during pre-monsoon was followed by an opposite scenario during the monsoon When seasonally compared, it was during the post-monsoon season when TBC in surface water was highest, with simultaneous decrease in their count in the river sediment. The total viable bacterial count (TVC) was influenced by the depth-wise stratification of salinity, which varied with tidal fluctuation, usually high and low during the neap and spring tides respectively. The abundance of both the autochthonous Vibrio spp. and allochthonous coliform bacteria was influenced by the concentrations of dissolved nutrients and suspended particulate matter (SPM). It is concluded that depending on the interplay of riverine discharge and tidal amplitude, sediment re-suspension mediated increase in SPM significantly regulates bacteria populations in the estuarine water, urging the need of systematic regular monitoring for better prediction of related hazards, including those associated with the rise in pathogenic Vibrio spp. in the changing climatic scenarios.

  2. Influence of Molecular Noise on the Growth of Single Cells and Bacterial Populations

    PubMed Central

    Schmidt, Mischa; Creutziger, Martin; Lenz, Peter

    2012-01-01

    During the last decades experimental studies have revealed that single cells of a growing bacterial population are significantly exposed to molecular noise. Important sources for noise are low levels of metabolites and enzymes that cause significant statistical variations in the outcome of biochemical reactions. In this way molecular noise affects biological processes such as nutrient uptake, chemotactic tumbling behavior, or gene expression of genetically identical cells. These processes give rise to significant cell-to-cell variations of many directly observable quantities such as protein levels, cell sizes or individual doubling times. In this study we theoretically explore if there are evolutionary benefits of noise for a growing population of bacteria. We analyze different situations where noise is either suppressed or where it affects single cell behavior. We consider two specific examples that have been experimentally observed in wild-type Escherichia coli cells: (i) the precision of division site placement (at which molecular noise is highly suppressed) and (ii) the occurrence of noise-induced phenotypic variations in fluctuating environments. Surprisingly, our analysis reveals that in these specific situations both regulatory schemes [i.e. suppression of noise in example (i) and allowance of noise in example (ii)] do not lead to an increased growth rate of the population. Assuming that the observed regulatory schemes are indeed caused by the presence of noise our findings indicate that the evolutionary benefits of noise are more subtle than a simple growth advantage for a bacterial population in nutrient rich conditions. PMID:22238678

  3. Changes in equine hindgut bacterial populations during oligofructose-induced laminitis.

    PubMed

    Milinovich, G J; Trott, D J; Burrell, P C; van Eps, A W; Thoefner, M B; Blackall, L L; Al Jassim, R A M; Morton, J M; Pollitt, C C

    2006-05-01

    In the horse, carbohydrate overload is thought to play an integral role in the onset of laminitis by drastically altering the profile of bacterial populations in the hindgut. The objectives of this study were to develop and validate microbial ecology methods to monitor changes in bacterial populations throughout the course of experimentally induced laminitis and to identify the predominant oligofructose-utilizing organisms. Laminitis was induced in five horses by administration of oligofructose. Faecal specimens were collected at 8 h intervals from 72 h before to 72 h after the administration of oligofructose. Hindgut microbiota able to utilize oligofructose were enumerated throughout the course of the experiment using habitat-simulating medium. Isolates were collected and representatives identified by 16S rRNA gene sequencing. The majority of these isolates collected belonged to the genus Streptococcus, 91% of which were identified as being most closely related to Streptococcus infantarius ssp. coli. Furthermore, S. infantarius ssp. coli was the predominant oligofructose-utilizing organism isolated before the onset of lameness. Fluorescence in situ hybridization probes developed to specifically target the isolated Streptococcus spp. demonstrated marked population increases between 8 and 16 h post oligofructose administration. This was followed by a rapid population decline which corresponded with a sharp decline in faecal pH and subsequently lameness at 24-32 h post oligofructose administration. This research suggests that streptococci within the Streptococcus bovis/equinus complex may be involved in the series of events which precede the onset of laminitis in the horse.

  4. Nonselective Bottlenecks Control the Divergence and Diversification of Phase-Variable Bacterial Populations

    PubMed Central

    Aidley, Jack; Rajopadhye, Shweta; Akinyemi, Nwanekka M.; Lango-Scholey, Lea

    2017-01-01

    ABSTRACT   Phase variation occurs in many pathogenic and commensal bacteria and is a major generator of genetic variability. A putative advantage of phase variation is to counter reductions in variability imposed by nonselective bottlenecks during transmission. Genomes of Campylobacter jejuni, a widespread food-borne pathogen, contain multiple phase-variable loci whose rapid, stochastic variation is generated by hypermutable simple sequence repeat tracts. These loci can occupy a vast number of combinatorial expression states (phasotypes) enabling populations to rapidly access phenotypic diversity. The imposition of nonselective bottlenecks can perturb the relative frequencies of phasotypes, changing both within-population diversity and divergence from the initial population. Using both in vitro testing of C. jejuni populations and a simple stochastic simulation of phasotype change, we observed that single-cell bottlenecks produce output populations of low diversity but with bimodal patterns of either high or low divergence. Conversely, large bottlenecks allow divergence only by accumulation of diversity, while interpolation between these extremes is observed in intermediary bottlenecks. These patterns are sensitive to the genetic diversity of initial populations but stable over a range of mutation rates and number of loci. The qualitative similarities of experimental and in silico modeling indicate that the observed patterns are robust and applicable to other systems where localized hypermutation is a defining feature. We conclude that while phase variation will maintain bacterial population diversity in the face of intermediate bottlenecks, narrow transmission-associated bottlenecks could produce host-to-host variation in bacterial phenotypes and hence stochastic variation in colonization and disease outcomes. PMID:28377533

  5. Spatial structure and nutrients promote invasion of IncP-1 plasmids in bacterial populations

    PubMed Central

    Fox, Randal E; Zhong, Xue; Krone, Stephen M; Top, Eva M

    2008-01-01

    In spite of the importance of plasmids in bacterial adaptation, we have a poor understanding of their dynamics. It is not known if or how plasmids persist in and spread through (invade) a bacterial population when there is no selection for plasmid-encoded traits. Moreover, the differences in dynamics between spatially structured and mixed populations are poorly understood. Through a joint experimental/theoretical approach, we tested the hypothesis that self-transmissible IncP-1 plasmids can invade a bacterial population in the absence of selection when initially very rare, but only in spatially structured habitats and when nutrients are regularly replenished. Using protocols that differed in the degree of spatial structure and nutrient levels, the invasiveness of plasmid pB10 in Escherichia coli was monitored during at least 15 days, with an initial fraction of plasmid-bearing (p+) cells as low as 10−7. To further explore the mechanisms underlying plasmid dynamics, we developed a spatially explicit mathematical model. When cells were grown on filters and transferred to fresh medium daily, the p+ fraction increased to 13%, whereas almost complete invasion occurred when the population structure was disturbed daily. The plasmid was unable to invade in liquid. When carbon source levels were lower or not replenished, plasmid invasion was hampered. Simulations of the mathematical model closely matched the experimental results and produced estimates of the effects of alternative experimental parameters. This allowed us to isolate the likely mechanisms most responsible for the observations. In conclusion, spatial structure and nutrient availability can be key determinants in the invasiveness of plasmids. PMID:18528415

  6. Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations.

    PubMed

    Fridman, Ofer; Goldberg, Amir; Ronin, Irine; Shoresh, Noam; Balaban, Nathalie Q

    2014-09-18

    The great therapeutic achievements of antibiotics have been dramatically undercut by the evolution of bacterial strategies that overcome antibiotic stress. These strategies fall into two classes. 'Resistance' makes it possible for a microorganism to grow in the constant presence of the antibiotic, provided that the concentration of the antibiotic is not too high. 'Tolerance' allows a microorganism to survive antibiotic treatment, even at high antibiotic concentrations, as long as the duration of the treatment is limited. Although both resistance and tolerance are important reasons for the failure of antibiotic treatments, the evolution of resistance is much better understood than that of tolerance. Here we followed the evolution of bacterial populations under intermittent exposure to the high concentrations of antibiotics used in the clinic and characterized the evolved strains in terms of both resistance and tolerance. We found that all strains adapted by specific genetic mutations, which became fixed in the evolved populations. By monitoring the phenotypic changes at the population and single-cell levels, we found that the first adaptive change to antibiotic stress was the development of tolerance through a major adjustment in the single-cell lag-time distribution, without a change in resistance. Strikingly, we found that the lag time of bacteria before regrowth was optimized to match the duration of the antibiotic-exposure interval. Whole genome sequencing of the evolved strains and restoration of the wild-type alleles allowed us to identify target genes involved in this antibiotic-driven phenotype: 'tolerance by lag' (tbl). Better understanding of lag-time evolution as a key determinant of the survival of bacterial populations under high antibiotic concentrations could lead to new approaches to impeding the evolution of antibiotic resistance.

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

    PubMed

    Khandeparker, Lidita; Anil, Arga Chandrashekar; Naik, Sneha D; Gaonkar, Chetan C

    2015-07-15

    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 by the intensity of rainfall. Vibrio spp. were abundant during the monsoon and so were faecal coliforms. Vibrio alginolyticus were negatively influenced by nitrate, whereas, silicate and rainfall positively influenced Vibrio parahaemolyticus numbers. It is also known that pathogenic bacteria are associated with the plankton. Changes in the abundance of plankton, which are governed mainly by environmental changes, could be responsible for variation in pathogenic bacterial abundance during monsoon, other than the land runoff due to precipitation and influx of fresh water.

  8. Bacterial Population in Intestines of the Black Tiger Shrimp (Penaeus monodon) under Different Growth Stages

    PubMed Central

    Rungrassamee, Wanilada; Klanchui, Amornpan; Chaiyapechara, Sage; Maibunkaew, Sawarot; Tangphatsornruang, Sithichoke; Jiravanichpaisal, Pikul; Karoonuthaisiri, Nitsara

    2013-01-01

    Intestinal bacterial communities in aquaculture have been drawn to attention due to potential benefit to their hosts. To identify core intestinal bacteria in the black tiger shrimp (Penaeus monodon), bacterial populations of disease-free shrimp were characterized from intestines of four developmental stages (15-day-old post larvae (PL15), 1- (J1), 2- (J2), and 3-month-old (J3) juveniles) using pyrosequencing, real-time PCR and denaturing gradient gel electrophoresis (DGGE) approaches. A total of 25,121 pyrosequencing reads (reading length = 442±24 bases) were obtained, which were categorized by barcode for PL15 (7,045 sequences), J1 (3,055 sequences), J2 (13,130 sequences) and J3 (1,890 sequences). Bacteria in the phyla Bacteroides, Firmicutes and Proteobacteria were found in intestines at all four growth stages. There were 88, 14, 27, and 20 bacterial genera associated with the intestinal tract of PL15, J1, J2 and J3, respectively. Pyrosequencing analysis revealed that Proteobacteria (class Gammaproteobacteria) was a dominant bacteria group with a relative abundance of 89% for PL15 and 99% for J1, J2 and J3. Real-time PCR assay also confirmed that Gammaproteobacteria had the highest relative abundance in intestines from all growth stages. Intestinal bacterial communities from the three juvenile stages were more similar to each other than that of the PL shrimp based on PCA analyses of pyrosequencing results and their DGGE profiles. This study provides descriptive bacterial communities associated to the black tiger shrimp intestines during these growth development stages in rearing facilities. PMID:23577162

  9. Bacterial population in intestines of the black tiger shrimp (Penaeus monodon) under different growth stages.

    PubMed

    Rungrassamee, Wanilada; Klanchui, Amornpan; Chaiyapechara, Sage; Maibunkaew, Sawarot; Tangphatsornruang, Sithichoke; Jiravanichpaisal, Pikul; Karoonuthaisiri, Nitsara

    2013-01-01

    Intestinal bacterial communities in aquaculture have been drawn to attention due to potential benefit to their hosts. To identify core intestinal bacteria in the black tiger shrimp (Penaeus monodon), bacterial populations of disease-free shrimp were characterized from intestines of four developmental stages (15-day-old post larvae (PL15), 1- (J1), 2- (J2), and 3-month-old (J3) juveniles) using pyrosequencing, real-time PCR and denaturing gradient gel electrophoresis (DGGE) approaches. A total of 25,121 pyrosequencing reads (reading length = 442±24 bases) were obtained, which were categorized by barcode for PL15 (7,045 sequences), J1 (3,055 sequences), J2 (13,130 sequences) and J3 (1,890 sequences). Bacteria in the phyla Bacteroides, Firmicutes and Proteobacteria were found in intestines at all four growth stages. There were 88, 14, 27, and 20 bacterial genera associated with the intestinal tract of PL15, J1, J2 and J3, respectively. Pyrosequencing analysis revealed that Proteobacteria (class Gammaproteobacteria) was a dominant bacteria group with a relative abundance of 89% for PL15 and 99% for J1, J2 and J3. Real-time PCR assay also confirmed that Gammaproteobacteria had the highest relative abundance in intestines from all growth stages. Intestinal bacterial communities from the three juvenile stages were more similar to each other than that of the PL shrimp based on PCA analyses of pyrosequencing results and their DGGE profiles. This study provides descriptive bacterial communities associated to the black tiger shrimp intestines during these growth development stages in rearing facilities.

  10. The population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens.

    PubMed

    Wilson, Benjamin A; Garud, Nandita R; Feder, Alison F; Assaf, Zoe J; Pennings, Pleuni S

    2016-01-01

    Drug resistance is a costly consequence of pathogen evolution and a major concern in public health. In this review, we show how population genetics can be used to study the evolution of drug resistance and also how drug resistance evolution is informative as an evolutionary model system. We highlight five examples from diverse organisms with particular focus on: (i) identifying drug resistance loci in the malaria parasite Plasmodium falciparum using the genomic signatures of selective sweeps, (ii) determining the role of epistasis in drug resistance evolution in influenza, (iii) quantifying the role of standing genetic variation in the evolution of drug resistance in HIV, (iv) using drug resistance mutations to study clonal interference dynamics in tuberculosis and (v) analysing the population structure of the core and accessory genome of Staphylococcus aureus to understand the spread of methicillin resistance. Throughout this review, we discuss the uses of sequence data and population genetic theory in studying the evolution of drug resistance. © 2015 John Wiley & Sons Ltd.

  11. Horizontal Gene Transfer and the Evolution of Bacterial and Archaeal Population Structure

    PubMed Central

    Alm, Eric J.; Hanage, William P.

    2013-01-01

    Many bacterial and archaeal lineages have a history of extensive and ongoing horizontal gene transfer and loss, as evidenced by the large differences in genome content even among otherwise closely related isolates. How ecologically cohesive populations might evolve and be maintained under such conditions of rapid gene turnover has remained controversial. Here we synthesize recent literature demonstrating the importance of habitat and niche in structuring horizontal gene transfer. This leads to a model of ecological speciation via gradual genetic isolation triggered by differential habitat association of nascent populations. Further, we hypothesize that subpopulations can evolve through local gene exchange networks by tapping into a gene pool that is adaptive towards local, continuously changing organismic interactions and is, to a large degree, responsible for the observed rapid gene turnover. Overall, these insights help explain how bacteria and archaea form populations that display both ecological cohesion and high genomic diversity. PMID:23332119

  12. Alterations in the major heterotrophic bacterial populations isolated from a still bottled mineral water.

    PubMed

    Morais, P V; da Costa, M S

    1990-11-01

    The heterotrophic bacterial population of a bottled mineral water stored in returnable glass bottles and in polyvinyl chloride (PVC) bottles at room temperature was studied over 9-12 months. The plate counts in R2A medium incubated at 22 degrees and 37 degrees C were low initially, increasing to 10(4)-10(5) cfu/ml within a few days of bottling. The number of bacteria recovered at 22 degrees C from PVC bottles was fairly constant during the storage period, but the population isolated at 37 degrees C decreased markedly after storage for 1 year. The major components of the population were Pseudomonas strains, one of which was identified as Pseudomonas vesicularis. Major changes took place during storage; two groups of bacteria (B and C) were dominant initially, but during the latter period of storage other groups (F, G and H) increased in number.

  13. A comparative study on the co-existing attractors in the Gaussian map and its q-deformed version

    NASA Astrophysics Data System (ADS)

    Patidar, Vinod; Sud, K. K.

    2009-03-01

    In a recent study Jaganathan and Sinha [Jaganathan R, Sinha S. A q-deformed nonlinear map. Phys Lett A 2005;338:277-87] have introduced a scheme for the q-deformation of nonlinear maps using the logistic map as an example and shown that the q-logistic map exhibits a wide spectrum of dynamical behaviours including the co-existence of attractors (which is a rare phenomenon in one-dimensional maps). In this paper, we aim to analyze another famous one-dimensional map - the Gaussian map (a known one-dimensional map exhibiting co-existing attractors) subject to the same q-deformation scheme. We compare the dynamical behaviour of the Gaussian map and q-deformed Gaussian map with a special attention on the regions of the parameter space, where these maps exhibit co-existing attractors. An important conclusion of the present study is that the appearance of co-existing attractors for a particular choice of system parameters can be understood as a consequence of the presence of multiple fixed points in one-dimensional nonlinear maps; however the converse is not always true.

  14. Negotiating Co-Existence in Divided Societies: Teachers, Students and Parents' Perspectives at a Shared School in Cyprus

    ERIC Educational Resources Information Center

    Zembylas, Michalinos

    2010-01-01

    This article describes a study conducted at a shared secondary school in Cyprus - that is, a school which co-educates children coming from two conflicting ethnic communities on the island. The study focuses on teachers', students' and parents' perspectives about the struggles to negotiate co-existence in this school. Drawing on a three-month…

  15. Amplification with hearing aids for patients with tinnitus and co-existing hearing loss.

    PubMed

    Hoare, Derek J; Edmondson-Jones, Mark; Sereda, Magdalena; Akeroyd, Michael A; Hall, Deborah

    2014-01-31

    Tinnitus is described as the perception of sound or noise in the absence of real acoustic stimulation. In the current absence of a cure for tinnitus, clinical management typically focuses on reducing the effects of co-morbid symptoms such as distress or hearing loss. Hearing loss is commonly co-morbid with tinnitus and so logic implies that amplification of external sounds by hearing aids will reduce perception of the tinnitus sound and the distress associated with it. To assess the effects of hearing aids specifically in terms of tinnitus benefit in patients with tinnitus and co-existing hearing loss. We searched the Cochrane Ear, Nose and Throat Disorders Group Trials Register; the Cochrane Central Register of Controlled Trials (CENTRAL); PubMed; EMBASE; CINAHL; Web of Science; Cambridge Scientific Abstracts; ICTRP and additional sources for published and unpublished trials. The date of the search was 19 August 2013. Randomised controlled trials and non-randomised controlled trials recruiting adults with subjective tinnitus and some degree of hearing loss, where the intervention involves amplification with hearing aids and this is compared to interventions involving other medical devices, other forms of standard or complementary therapy, or combinations of therapies, no intervention or placebo interventions. Three authors independently screened all selected abstracts. Two authors independently extracted data and assessed those potentially suitable studies for risk of bias. For studies meeting the inclusion criteria, we used the mean difference (MD) to compare hearing aids with other interventions and controls. One randomised controlled trial (91 participants) was included in this review. We judged the trial to have a low risk of bias for method of randomisation and outcome reporting, and an unclear risk of bias for other criteria. No non-randomised controlled trials meeting our inclusion criteria were identified. The included study measured change in tinnitus

  16. Molecular analysis of bacterial population structure and dynamics during cold storage of untreated and treated milk.

    PubMed

    Rasolofo, Eric Andriamahery; St-Gelais, Daniel; LaPointe, Gisele; Roy, Denis

    2010-03-31

    Spoilage bacteria in milk are controlled by treatments such as thermization, microfiltration and addition of carbon dioxide. However, little information is known about the changes in microbial communities during subsequent cold storage of treated milk. Culture-dependent methods and a direct molecular approach combining 16S rRNA gene clone libraries and quantitative PCR (Q-PCR) were applied to obtain a better overview of the structure and the dynamics of milk microbiota. Raw milk samples were treated by the addition of carbon dioxide (CO(2)), thermization (TH) or microfiltration (MF) and stored at 4 degrees C or 8 degrees C up to 7d. Untreated milk (UT) was used as a control. Psychrotrophic and staphylococci bacteria were enumerated in the milk samples by culture methods. For the molecular approach, DNA was extracted from milk samples and 16S rRNA gene was amplified by PCR with universal primers prior to cloning. The Q-PCR method was used to evaluate the dynamics of dominant bacterial species revealed by clone library analysis of 16S rRNA gene. Comparison of the 16S rRNA gene sequence indicated that the two most abundant operational taxonomic units (OTU), determined at 97% identity, belonged to the class Gammaproteobacteria (40.3% of the 1415 sequences) and Bacilli (40%). Dominant bacterial species in UT, CO(2) and TH milk samples at day 3 were affiliated with Staphylococcus, Streptococcus, Clostridia, Aerococcus, Facklamia, Corynebacterium, Acinetobacter and Trichococcus. Dominant bacterial species detected in MF milk were Stenotrophomonas, Pseudomonas and Delftia, while Pseudomonas species dominated the bacterial population of UT, CO(2) and MF milk samples at day 7. Staphylococcus and Delftia were the dominant bacterial species in thermized milk. Q-PCR results showed that populations of S. aureus, A. viridans, A. calcoaceticus, C. variabile and S. uberis were stable during 7d of storage at 4 degrees C. Populations of P. fluorescens, S. uberis and total bacteria

  17. Bacterial microbiota in small brown planthopper populations with different rice viruses.

    PubMed

    Li, Shuo; Zhou, Changwei; Chen, Guangyi; Zhou, Yijun

    2017-07-01

    The small brown planthopper (SBPH) is an important virus vector, transmitting Rice stripe virus (RSV), and Rice black-streaked dwarf virus (RBSDV). Insect symbionts play an essential role in the insect fitness, however, it is still unclear about their contributions to viral transmission by SBPH. Here, we investigated endosymbiont communities in non-viruliferous, RSV-infected, and RBSDV-infected SBPH populations using Illumina 16S rRNA gene MiSeq sequencing. In total, 281,803 effective sequences of the 16S rRNA gene were generated from different samples. Sequence analysis revealed the percentages of these bacterial groups in different SBPH populations on several taxonomic levels ranging from phyla to genera. The extremely consistent bacterial diversity and abundance indicated that RSV or RBSDV infection did not affect the composition and abundance of symbionts in SBPH. It was notable that Wolbachia was dominant in all populations. The symbiosis between Wolbachia and SBPH might be potentially studied and utilized to control pest SBPH in the future. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Characterisation of the bacterial populations in a saline heat storage aquifer in the North German Basin

    NASA Astrophysics Data System (ADS)

    Alawi, M.; Lerm, S.; Vetter, A.; Vieth, A.; Mangelsdorf, K.; Seibt, A.; Wolfgramm, M.; Würdemann, H.

    2009-04-01

    The colonization and the ecology of microorganisms in the deep biosphere arouse increasing interest of scientists because of utilizing the subsurface for e.g. energy storage and recovery. The research project AquiScreen investigates the operational reliability of eight geothermally used groundwater systems in Germany under microbial, geochemical, mineralogical, and petrological aspects. This study shows the results of the heat storage in Neubrandenburg (depth: 1250 m), a typical site for saline fluids in the North German Basin. The seasonal alternation in charge and discharge mode enabled sampling the warm (75˚ C) and the cold (45˚ C) side of the geothermal doublet. The analyses focus on microbially induced corrosion on plant components and scaling resulting in filter and/or formation clogging. Microbiological analyses were carried out with fluid and solid phase samples by 16S rDNA based Single Strand Conformation Polymorphism (SSCP) fingerprinting. The analyses are utilized to evaluate the impact of microbial populations on such systems. The genetic fingerprinting revealed significant differences in the bacterial community structure between the warm and cold side of the heat storage. Since the geochemical analyses revealed no remarkable differences, the temperature might be crucial for the different community structures. At the warm side of the aquifer the identified bacteria are closely related to Variovorax and Sphingomonas. At the cold side of the heat storage sulphate reducing and fermentative bacteria were detected. These results correspond with locally observed iron sulphide precipitation and corrosion processes on plant components. Particularly the bacterial population of the cold side was studied over a period of two years. Thereby seasonal changes in the abundance of the identified bacteria, depending on the operational mode of the geothermal plant, were observed. After a malfunction in the pump system of the cold side of the heat storage changes in

  19. Association of Co-Existing Impairments in Cognition and Self-Rated Vision and Hearing With Health Outcomes in Older Adults

    PubMed Central

    Liu, Phillip L.; Cohen, Harvey Jay; Fillenbaum, Gerda G.; Burchett, Bruce M.; Whitson, Heather E.

    2016-01-01

    Objective: The objective of this study was to assess the relationship of disability (activities of daily living [ADL] and instrumental ADL [IADL]), self-rated health (SRH), and 6-year mortality with co-existing impairments in vision (self-rated), hearing (self-rated), and/or cognition (Short Portable Mental Status Questionnaire) in older adults. Method: The study sample comprised of 3,871 participants from the North Carolina Established Populations for Epidemiologic Studies of the Elderly study (NC EPESE). Results: Persons with all three impairments had increased odds of ADL/IADL disability and low SRH. Participants with combined visual and cognitive impairments had increased odds of mortality. Whereas sensory impairments were associated with poor SRH, cognitive impairment was not unless both sensory impairments were present. Conclusion: Co-existent sensory and cognitive impairments were associated with higher risk of impaired functional status. Self-rated auditory impairment alone was not associated with higher odds of death, but mortality was linked to visual and, particularly, cognitive impairment, alone or combined. PMID:27054148

  20. Multiplicity of Quorum Quenching Enzymes: A Potential Mechanism to Limit Quorum Sensing Bacterial Population.

    PubMed

    Koul, Shikha; Kalia, Vipin Chandra

    2017-03-01

    Bacteria express certain of their characteristics especially, pathogenicity factors at high cell densities. The process is termed as quorum sensing (QS). QS operates via signal molecules such as acylhomoserine lactones (AHLs). Other bacteria inhibit QS through the inactivation of AHL signals by producing enzymes like AHL-lactonases and -acylases. Comparative genomic analysis has revealed the multiplicity of genes for AHL lactonases (up to 12 copies per genome) among Bacillus spp. and that of AHL-acylases (up to 5 copies per genome) among Pseudomonas spp. This genetic evolution can be envisaged to enable host to withstand the attacks from bacterial population, which regulates its functioning through QS.

  1. Optimization of conditions for profiling bacterial populations in food by culture-independent methods.

    PubMed

    Cocolin, Luca; Diez, Ana; Urso, Rosalinda; Rantsiou, Kalliopi; Comi, Giuseppe; Bergmaier, Ingrid; Beimfohr, Claudia

    2007-11-30

    In this study we used culture-independent methods to profile bacterial populations in food products. Denaturing gradient gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH) were employed in order to identify bacterial species without the need of isolation and biochemical identification. The protocols used to extract the DNA, subsequently subjected to PCR amplification for DGGE, as well as the hybridization procedure for FISH, were optimised. Moreover, an extensive study on the primers and probes to be used for the direct detection and identification of microorganisms commonly found in food, was carried out. Meat and cheese samples, fresh or processed, were subjected to DGGE and FISH analysis and the results obtained highlighted how the processing in food industry is decreasing the bacterial biodiversity. Not only processed cheese or meat but also fermented products were dominated by only one or few species. Lactobacillus sakei, Lactobacillus curvatus and Brochothrix thermosphacta were the main species found in meat products, while in cheese(s) Lactococcus lactis, Streptococcus thermophilus and Leuconostoc spp. were repeatedly detected. The results obtained by the two culture-independent methods used always correlated well.

  2. The structure of resting bacterial populations in soil and subsoil permafrost.

    PubMed

    Soina, Vera S; Mulyukin, Andrei L; Demkina, Elena V; Vorobyova, Elena A; El-Registan, Galina I

    2004-01-01

    The structure of individual cells in microbial populations in situ of the Arctic and Antarctic permafrost was studied by scanning and transmission electron microscopy methods and compared with that of cyst-like resting forms generated under special conditions by the non-spore-forming bacteria Arthrobacter and Micrococcus isolated from the permafrost. Electron microscopy examination of microorganisms in situ revealed several types of bacterial cells having no signs of damage, including "dwarf" curved forms similar to nanoforms. Intact bacterial cells in situ and frozen cultures of the permafrost isolates differed from vegetative cells by thickened cell walls, the altered structure of cytoplasm, and the compact nucleoid, and were similar in these features to cyst-like resting forms of non-spore-forming "permafrost" bacterial strains of Arthrobacter and Micrococcus spp. Cyst-like cells, being resistant to adverse external factors, are regarded as being responsible for survival of the non-spore-formers under prolonged exposure to subzero temperatures and can be a target to search for living microorganisms in natural environments both on the Earth and on extraterrestrial bodies.

  3. The Structure of Resting Bacterial Populations in Soil and Subsoil Permafrost

    NASA Astrophysics Data System (ADS)

    Soina, Vera S.; Mulyukin, Andrei L.; Demkina, Elena V.; Vorobyova, Elena A.; El-Registan, Galina I.

    2004-09-01

    The structure of individual cells in microbial populations in situ of the Arctic and Antarctic permafrost was studied by scanning and transmission electron microscopy methods and compared with that of cyst-like resting forms generated under special conditions by the non-sporeforming bacteria Arthrobacter and Micrococcus isolated from the permafrost. Electron microscopy examination of microorganisms in situ revealed several types of bacterial cells having no signs of damage, including "dwarf" curved forms similar to nanoforms. Intact bacterial cells in situ and frozen cultures of the permafrost isolates differed from vegetative cells by thickened cell walls, the altered structure of cytoplasm, and the compact nucleoid, and were similar in these features to cyst-like resting forms of non-spore-forming "permafrost" bacterial strains of Arthrobacter and Micrococcus spp. Cyst-like cells, being resistant to adverse external factors, are regarded as being responsible for survival of the non-spore-formers under prolonged exposure to subzero temperatures and can be a target to search for living microorganisms in natural environments both on the Earth and on extraterrestrial bodies.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

    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.

  6. Mechanisms Leading to Co-Existence of Gas Hydrate in Ocean Sediments [Part 1 of 2

    SciTech Connect

    Bryant, Steven; Juanes, Ruben

    2011-12-31

    In this project we have sought to explain the co-existence of gas and hydrate phases in sediments within the gas hydrate stability zone. We have focused on the gas/brine interface at the scale of individual grains in the sediment. The capillary forces associated with a gas/brine interface play a dominant role in many processes that occur in the pores of sediments and sedimentary rocks. The mechanical forces associated with the same interface can lead to fracture initiation and propagation in hydrate-bearing sediments. Thus the unifying theme of the research reported here is that pore scale phenomena are key to understanding large scale phenomena in hydrate-bearing sediments whenever a free gas phase is present. Our analysis of pore-scale phenomena in this project has delineated three regimes that govern processes in which the gas phase pressure is increasing: fracturing, capillary fingering and viscous fingering. These regimes are characterized by different morphology of the region invaded by the gas. On the other hand when the gas phase pressure is decreasing, the corresponding regimes are capillary fingering and compaction. In this project, we studied all these regimes except compaction. Many processes of interest in hydrate-bearing sediments can be better understood when placed in the context of the appropriate regime. For example, hydrate formation in sub-permafrost sediments falls in the capillary fingering regime, whereas gas invasion into ocean sediments is likely to fall into the fracturing regime. Our research provides insight into the mechanisms by which gas reservoirs are converted to hydrate as the base of the gas hydrate stability zone descends through the reservoir. If the reservoir was no longer being charged, then variation in grain size distribution within the reservoir explain hydrate saturation profiles such as that at Mt. Elbert, where sand-rich intervals containing little hydrate are interspersed between intervals containing large hydrate

  7. Mechanisms Leading to Co-Existence of Gas Hydrate in Ocean Sediments [Part 2 of 2

    SciTech Connect

    Bryant, Steven; Juanes, Ruben

    2011-12-31

    In this project we have sought to explain the co-existence of gas and hydrate phases in sediments within the gas hydrate stability zone. We have focused on the gas/brine interface at the scale of individual grains in the sediment. The capillary forces associated with a gas/brine interface play a dominant role in many processes that occur in the pores of sediments and sedimentary rocks. The mechanical forces associated with the same interface can lead to fracture initiation and propagation in hydrate-bearing sediments. Thus the unifying theme of the research reported here is that pore scale phenomena are key to understanding large scale phenomena in hydrate-bearing sediments whenever a free gas phase is present. Our analysis of pore-scale phenomena in this project has delineated three regimes that govern processes in which the gas phase pressure is increasing: fracturing, capillary fingering and viscous fingering. These regimes are characterized by different morphology of the region invaded by the gas. On the other hand when the gas phase pressure is decreasing, the corresponding regimes are capillary fingering and compaction. In this project, we studied all these regimes except compaction. Many processes of interest in hydrate-bearing sediments can be better understood when placed in the context of the appropriate regime. For example, hydrate formation in sub-permafrost sediments falls in the capillary fingering regime, whereas gas invasion into ocean sediments is likely to fall into the fracturing regime. Our research provides insight into the mechanisms by which gas reservoirs are converted to hydrate as the base of the gas hydrate stability zone descends through the reservoir. If the reservoir was no longer being charged, then variation in grain size distribution within the reservoir explain hydrate saturation profiles such as that at Mt. Elbert, where sand-rich intervals containing little hydrate are interspersed between intervals containing large hydrate

  8. Effect of Hydrogenase and Mixed Sulfate-Reducing Bacterial Populations on the Corrosion of Steel

    PubMed Central

    Bryant, Richard D.; Jansen, Wayne; Boivin, Joe; Laishley, Edward J.; Costerton, J. William

    1991-01-01

    The importance of hydrogenase activity to corrosion of steel was assessed by using mixed populations of sulfate-reducing bacteria isolated from corroded and noncorroded oil pipelines. Biofilms which developed on the steel studs contained detectable numbers of sulfate-reducing bacteria (104 increasing to 107/0.5 cm2). However, the biofilm with active hydrogenase activity (i.e., corrosion pipeline organisms), as measured by a semiquantitative commercial kit, was associated with a significantly higher corrosion rate (7.79 mm/year) relative to noncorrosive biofilm (0.48 mm/year) with 105 sulfate-reducing bacteria per 0.5 cm2 but no measurable hydrogenase activity. The importance of hydrogenase and the microbial sulfate-reducing bacterial population making up the biofilm are discussed relative to biocorrosion. Images PMID:16348560

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

    NASA Astrophysics Data System (ADS)

    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.

  10. Active Marine Subsurface Bacterial Population Composition in Low Organic Carbon Environments from IODP Expedition 320

    NASA Astrophysics Data System (ADS)

    Shepard, A.; Reese, B. K.; Mills, H. J.; IODP Expedition 320 Shipboard Science Party

    2011-12-01

    The marine subsurface environment contains abundant and active microorganisms. These microbial populations are considered integral players in the marine subsurface biogeochemical system with significance in global geochemical cycles and reservoirs. However, variations in microbial community structure, activity and function associated with the wide-ranging sedimentary and geochemical environments found globally have not been fully resolved. Integrated Ocean Drilling Program Expedition 320 recovered sediments from site U1332. Two sampling depths were selected for analysis that spanned differing lithological units in the sediment core. Sediments were composed of mostly clay with zeolite minerals at 8 meters below sea floor (mbsf). At 27 mbsf, sediments were composed of alternating clayey radiolarian ooze and nannofossil ooze. The concentration of SO42- had little variability throughout the core and the concentration of Fe2+ remained close to, or below, detection limits (0.4 μM). Total organic carbon content ranged from a low of 0.03 wt% to a high of 0.07 wt% between 6 and 30 mbsf providing an opportunity to evaluate marine subsurface microbial communities under extreme electron donor limiting conditions. The metabolically active fraction of the bacterial population was isolated by the extraction and amplification of 16S ribosomal RNA. Pyrosequencing of 16S rRNA transcripts and subsequent bioinformatic analyses provided a robust data set (15,931 total classified sequences) to characterize the community at a high resolution. As observed in other subsurface environments, the overall diversity of active bacterial populations decreased with depth. The population shifted from a diverse but evenly distributed community at approximately 8 mbsf to a Firmicutes dominated population at 27 mbsf (80% of sequences). A total of 95% of the sequences at 27 mbsf were grouped into three genera: Lactobacillus (phylum Firmicutes) at 80% of the total sequences, Marinobacter (phylum

  11. EFFECT OF SITE ON BACTERIAL POPULATIONS IN THE SAPWOOD OF COARSE WOODY DEBRIS.

    SciTech Connect

    Porter, Emma, G.,; Waldrop, Thomas, A.; McElreath, Susan, D.; Tainter, Frank, H.

    1998-01-01

    Porter, Emma G., T.A. Waldrop, Susan D. McElreath, and Frank H. Tainter. 1998. Effect of site on bacterial populations in the sapwood of coarse woody debris. Pp. 480-484. In: Proc. 9th Bienn. South. Silv. Res. Conf. T.A. Waldrop (ed). USDA Forest Service, Southern Research Station. Gen. Tech. Rep. SRS-20. Abstract: Coarse woody debris (CWD) is an important structural component of southeastern forest ecosystems, yet little is known about its dynamics in these systems. This project identified bacterial populations associated with CWD and their dynamics across landscape ecosystem classification (LEC) units. Bolts of red oak and loblolly pine were placed on plots at each of three hydric, mesic, and xeric sites at the Savannah River Station. After the controls were processed, samples were taken at four intervals over a 16-week period. Samples were ground within an anaerobe chamber using nonselective media. Aerobic and facultative anaerobic bacteria were identified using the Biolog system and the anaerobes were identified using the API 20A system. Major genera isolated were: Bacillus, Buttiauxella, Cedecea, Enterobacter, Erwinia, Escherichia, Klebsiella, Pantoea, Pseudomonas, Serratia, and Xanthomonas. The mean total isolates were determined by LEC units and sample intervals. Differences occurred between the sample intervals with total isolates of 6.67, 13.33, 10.17, and 9.50 at 3, 6, 10, and 16 weeks, respectively. No significant differences in the numbers of bacteria isolated were found between LEC units.

  12. Optimal Control Strategies for Disinfection of Bacterial Populations with Persister and Susceptible Dynamics

    PubMed Central

    Brown, Jason; Darres, Kyle; Petty, Katherine

    2012-01-01

    It is increasingly clear that bacteria manage to evade killing by antibiotics and antimicrobials in a variety of ways, including mutation, phenotypic variations, and formation of biofilms. With recent advances in understanding the dynamics of the tolerance mechanisms, there have been subsequent advances in understanding how to manipulate the bacterial environments to eradicate the bacteria. This study focuses on using mathematical techniques to find the optimal disinfection strategy to eliminate the bacteria while managing the load of antibiotic that is applied. In this model, the bacterial population is separated into those that are tolerant to the antibiotic and those that are susceptible to disinfection. There are transitions between the two populations whose rates depend on the chemical environment. Our results extend previous mathematical studies to include more realistic methods of applying the disinfectant. The goal is to provide experimentally testable predictions that have been lacking in previous mathematical studies. In particular, we provide the optimal disinfection protocol under a variety of assumptions within the model that can be used to validate or invalidate our simplifying assumptions and the experimental hypotheses that we used to develop the model. We find that constant dosing is not the optimal method for disinfection. Rather, cycling between application and withdrawal of the antibiotic yields the fastest killing of the bacteria. PMID:22751538

  13. Composition of bacterial communities associated with natural and laboratory populations of Asobara tabida infected with Wolbachia.

    PubMed

    Zouache, Karima; Voronin, Denis; Tran-Van, Van; Mavingui, Patrick

    2009-06-01

    Asobara tabida wasps are fly endoparasitoids that naturally harbor three Wolbachia strains, which induce cytoplasmic incompatibility and control oogenesis. To investigate whether other bacteria play a role in wasp biology, we surveyed the bacterial communities of wild A. tabida populations originating from different regions of France and of laboratory colonies using PCR-denaturing gradient gel electrophoresis and culture methods. Proteobacteria and Firmicutes were found to be the main phyla represented in these populations. Among these were several cultured and uncultured representatives of the genera Acetobacter, Acidomonas, Bacillus, Brevibacillus, Duganella, Herbaspirillum, Pseudomonas, Staphylococcus, and Streptococcus. In addition to Wolbachia, wild individuals harbored Rickettsia, which tended to be lost when insects were reared in the laboratory. The antibiotic treatment used to generate wasp sublines singly infected with Wolbachia also affected the overall bacterial composition, with most fingerprint sequences being characteristic of the family Enterobacteriaceae. We also screened for potentially heritable endosymbionts by PCR and fluorescence in situ hybridization in stable laboratory lines, with only Wolbachia being consistently found in wasp ovaries.

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

    PubMed

    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.

  15. Diversity of bacterial population of table olives assessed by PCR-DGGE analysis.

    PubMed

    Randazzo, Cinzia L; Ribbera, Angela; Pitino, Iole; Romeo, Flora V; Caggia, Cinzia

    2012-10-01

    Nocellara Etnea and Geracese table olives are produced according to traditional process, in which lactic acid bacteria (LAB) and yeasts are the dominant microorganisms. With the aim to evaluate the effect of selected starter cultures on dynamics of bacterial population during fermentation and on growth/survival of Listeria spp. artificially inoculated into the olive brine, a polyphasic approach based on the combination of culturing and PCR-DGGE analysis was applied. Plating results showed a different concentration of the major bacterial groups considered among cultivars and the beneficial effect of LAB starters, which clearly inhibited Enterobacteriaceae. Moreover, results indicated that the brine conditions applied did not support the growth/survival of Listeria monocytogenes strain, artificially inoculated, highlighting the importance of selecting right fermentation parameters for assuring microbiological safety of the final products. Comparison of DGGE profile of Nocellara Etnea and Geracese table olives, displayed a great difference among cultivars, revealing a wide biodiversity within Lactobacillus population during Geracese olives fermentation. Based on cloning and sequencing of the most dominant amplicons, the presence, among others, of Lactobacillus paracollinoides and Lactobacillus coryniformis in Geracese table olives was revealed in table olives for the first time.

  16. Foolish Dreams in a Fabled Land: Living Co-Existence in an Israeli Arab School

    ERIC Educational Resources Information Center

    Court, Deborah

    2006-01-01

    This article presents the results of an ethnographic case study of an Israeli Arab middle school whose staff and students are Arab Israelis from the Moslem, Druze, and Christian population sectors. Against the Israeli backdrop of multiculturalism, political tensions, and terrorism, this school has created a multi-faceted curriculum for teaching…

  17. Foolish Dreams in a Fabled Land: Living Co-Existence in an Israeli Arab School

    ERIC Educational Resources Information Center

    Court, Deborah

    2006-01-01

    This article presents the results of an ethnographic case study of an Israeli Arab middle school whose staff and students are Arab Israelis from the Moslem, Druze, and Christian population sectors. Against the Israeli backdrop of multiculturalism, political tensions, and terrorism, this school has created a multi-faceted curriculum for teaching…

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

    PubMed Central

    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. Systemic increased immune response to Nocardia brasiliensis co-exists with local immunosuppressive microenvironment.

    PubMed

    Salinas-Carmona, Mario Cesar; Rosas-Taraco, Adrian Geovanni; Welsh, Oliverio

    2012-10-01

    Human diseases produced by pathogenic actinomycetes are increasing because they may be present as opportunistic infections. Some of these microbes cause systemic infections associated with immunosuppressive conditions, such as chemotherapy for cancer, immunosuppressive therapy for transplant, autoimmune conditions, and AIDS; while others usually cause localized infection in immunocompetent individuals. Other factors related to this increase in incidence are: antibiotic resistance, not well defined taxonomy, and a delay in isolation and identification of the offending microbe. Examples of these infections are systemic disease and brain abscesses produced by Nocardia asteroides or the located disease by Nocardia brasiliensis, named actinomycetoma. During the Pathogenic Actinomycetes Symposium of the 16th International Symposium on Biology of Actinomycetes (ISBA), held in Puerto Vallarta, Mexico, several authors presented recent research on the mechanisms by which N. brasiliensis modulates the immune system to survive in the host and advances in medical treatment of human actinomycetoma. Antibiotics and antimicrobials that are effective against severe actinomycetoma infections with an excellent therapeutic outcome and experimental studies of drugs that show promising bacterial inhibition in vivo and in vitro were presented. Here we demonstrate a systemic strong acquired immune response in humans and experimental mice at the same time of a local dominance of anti inflammatory cytokines environment. The pathogenic mechanisms of some actinomycetes include generation of an immunosuppressive micro environment to evade the protective immune response. This information will be helpful in understanding pathogenesis and to design new drugs for treatment of actinomycetoma.

  20. GAPO syndrome associated with pyoderma vegetans: an unreported co-existence.

    PubMed

    Karadag, A S; Calka, O; Bilgili, S G; Karadag, R; Bulut, G

    2013-01-01

    GAPO syndrome is a rare autosomal recessive disease and an acronym composed of growth retardation, alopecia, pseudoanodontia, optic atrophy. Approximately 38 cases have been reported in literature until now. Pyoderma vegetans is a chronic inflammatory disease characterized with vesicopustular, exudative and vegetative lesions usually localized on face, scalp, axilla and genitalia. Pyoderma vegetans is attributed to a bacterial infection frequently occurring in individuals with an underlying immunosuppressive condition. A 30-year-old female patient was admitted to our clinic with complaint of a hemorrhagic, crusted, exudative vegetative two plaques on the scalp. On her physical examination, she had a prematurely aged face, predominant lower lips, total tooth loss, frontal bossing, enlarged anterior fontanelle, marked scalp veins, micrognatia, depressed nasal bridge, short stature, growth retardation. She was diagnosed as GAPO syndrome as the result of her physical examination. Result of the biopsy taken from scalp was evaluated as pyoderma vegetans. And the diagnosis of pyoderma vegetans was established based on the correlate of both clinical and histopathologic findings. Pyoderma vegetans coexisting with GAPO syndrome has not been reported previously. Thus we wished to report it.

  1. Effect of co-existing biologically relevant molecules and ions on DNA photocleavage caused by pyrene and its derivatives.

    PubMed

    Wang, Shuguang; Yu, Hongtao

    2005-04-01

    Inorganic ions, coenzymes, amino acids, and saccharides could co-exist with toxic environmental chemicals, such as polycyclic aromatic hydrocarbons (PAHs), in the cell. The presence of these co-existing chemicals can modulate the toxicity of the PAHs. One of the genotoxic effects by PAHs is light-induced cleavage, or photocleavage, of DNA. The effect of inorganic ions I-, Na+, Ca2+, Mg2+, Fe3+, Mn2+, Cu2+, and Zn2+ and biological molecules riboflavin, histidine, mannitol, nicotinamide adenine dinucleotide (NAD), glutathione, and glutamic acid on the DNA photocleavage by pyrene, 1-hydroxypyrene (1-HP), and 1-aminopyrene (1-AP), is studied. The non-transition metal ions Na+, Ca2+, and Mg2+, usually have very little inhibitory effects, while the transition metal ions Fe3+, Cu2+, and Zn2+ enhance, Mn2+ inhibits the DNA photocleavage. The effect by biological molecules is complex, depending on the photochemical reaction mechanisms of the compounds tested (1-AP, 1-HP and pyrene) and on the chemical nature of the added biological molecules. Riboflavin, histidine, and mannitol enhance DNA photocleavage by all three compounds, except that mannitol has no effect on the photocleavage of DNA by pyrene. Glutathione inhibits the DNA photocleavage by 1-AP and 1-HP, but has no effect on that by pyrene. NAD enhances the DNA photocleavage by 1-AP, but has no effect on that by 1-HP and pyrene. Glutamic acid enhances the DNA photocleavage by 1-AP and pyrene, but inhibits that by 1-HP. These results show that the co-existing chemicals may have a profound effect on the toxicity of PAHs, or possibly on the toxicity of many other chemicals. Therefore, if one studies the toxic effects of PAHs or other toxic chemicals, the effect of the co-existing chemicals or ions needs to be considered.

  2. Co-Existence of Modified Chaplygin Gas and Other Dark Energies in the Framework of Fractal Universe

    NASA Astrophysics Data System (ADS)

    Maity, Sayani; Debnath, Ujjal

    2016-05-01

    In this work, we consider a non-flat universe in the framework of fractal cosmology. We have investigated the co-existence of different kinds of dark energy models such as tachyonic field, DBI-essence, hessence, k-essence, dilaton, quintessence with the modified Chaplygin gas (MCG) in fractal universe and obtained the statefinder parameters. The natures of the scalar fields and the concerned potentials have been analyzed by the correspondence scenario in the fractal universe.

  3. Co-existence of non-alcoholic fatty liver disease and inflammatory bowel disease: A review article

    PubMed Central

    Chao, Che-Yung; Battat, Robert; Al Khoury, Alex; Restellini, Sophie; Sebastiani, Giada; Bessissow, Talat

    2016-01-01

    Emerging data have highlighted the co-existence of non-alcoholic fatty liver disease (NAFLD) and inflammatory bowel disease; both of which are increasingly prevalent disorders with significant complications and impact on future health burden. Cross-section observational studies have shown widely variable prevalence rates of co-existing disease, largely due to differences in disease definition and diagnostic tools utilised in the studies. Age, obesity, insulin resistance and other metabolic conditions are common risks factors in observational studies. However, other studies have also suggested a more dominant role of inflammatory bowel disease related factors such as disease activity, duration, steroid use and prior surgical intervention, in the development of NAFLD. This suggests a potentially more complex pathogenesis and relationship between the two diseases which may be contributed by factors including altered intestinal permeability, gut dysbiosis and chronic inflammatory response. Commonly used immunomodulation agents pose potential hepatic toxicity, however no definitive evidence exist linking them to the development of hepatic steatosis, nor are there any data on the impact of therapy and prognosis in patient with co-existent diseases. Further studies are required to assess the impact and establish appropriate screening and management strategies in order to allow early identification, intervention and improve patient outcomes. PMID:27678354

  4. Co-existence of non-alcoholic fatty liver disease and inflammatory bowel disease: A review article.

    PubMed

    Chao, Che-Yung; Battat, Robert; Al Khoury, Alex; Restellini, Sophie; Sebastiani, Giada; Bessissow, Talat

    2016-09-14

    Emerging data have highlighted the co-existence of non-alcoholic fatty liver disease (NAFLD) and inflammatory bowel disease; both of which are increasingly prevalent disorders with significant complications and impact on future health burden. Cross-section observational studies have shown widely variable prevalence rates of co-existing disease, largely due to differences in disease definition and diagnostic tools utilised in the studies. Age, obesity, insulin resistance and other metabolic conditions are common risks factors in observational studies. However, other studies have also suggested a more dominant role of inflammatory bowel disease related factors such as disease activity, duration, steroid use and prior surgical intervention, in the development of NAFLD. This suggests a potentially more complex pathogenesis and relationship between the two diseases which may be contributed by factors including altered intestinal permeability, gut dysbiosis and chronic inflammatory response. Commonly used immunomodulation agents pose potential hepatic toxicity, however no definitive evidence exist linking them to the development of hepatic steatosis, nor are there any data on the impact of therapy and prognosis in patient with co-existent diseases. Further studies are required to assess the impact and establish appropriate screening and management strategies in order to allow early identification, intervention and improve patient outcomes.

  5. Group acceptance and commitment therapy (ACT) for bipolar disorder and co-existing anxiety - an open pilot study.

    PubMed

    Pankowski, Sara; Adler, Mats; Andersson, Gerhard; Lindefors, Nils; Svanborg, Cecilia

    2017-03-01

    Previous studies have supported acceptance and commitment therapy (ACT) for reducing impairment related to various chronic conditions. ACT may possibly be beneficial for bipolar disorder (BD) with co-existing anxiety, which is associated with a poorer treatment outcome. Efforts are needed to identify suitable psychological interventions for BD and co-existing anxiety. In this open clinical trial, we included 26 patients with BD type 1 or 2 at an outpatient psychiatric unit specializing in affective disorders. The intervention consisted of a 12-session manualized group treatment that included psychoeducation, mindfulness, engaging in values-based behaviour, cognitive defusion, acceptance and relapse prevention modules. Participants completed four self-report questionnaires covering anxiety symptoms (Beck Anxiety Inventory - BAI), depressive symptoms (Beck Depression Inventory - BDI-II), quality of life (Quality of Life Inventory - QOLI) and psychological flexibility (Acceptance and Action Questionnaire - AAQ-2) before, during and after the treatment. At post-treatment, the participants reported significant improvements in all outcome measures, with large effects (Cohen's d between 0.73 and 1.98). The mean reduction in anxiety symptoms was 45%. At post-treatment, 96% of the patients were classified as responders on at least one of the outcome measures. A limitation is that the trial is uncontrolled. The results suggest that ACT has the potential to be an effective treatment for BD patients with co-existing anxiety. Further randomized studies are warranted.

  6. Morphological peculiarities of Calanus finmarchicus and Calanus glacialis in the areas of the co-existence of their populations

    NASA Astrophysics Data System (ADS)

    Berchenko, I. V.; Stupnikova, A. N.

    2014-07-01

    Morphological studies of the females of Calanus finmarchicus, C. glacialis, and C. hyperboreus were performed for specimens sampled in different areas of the Greenland, Barents, Kara, and Laptev seas. Intraspecific variability was found for the ratio of the specimens characterized by different types of setae patterns on the endopodites of C. glacialis and C. finmarchicus. The variability of this parameter did not relate to the environmental peculiarities of the sampling sites and did not depend on the temperature regime. We assume that such differences may be the result of the hybridization of C. glacialis and C. finmarchicus due to the similarity of their reproduction systems and the overlapping of the body size ranges.

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

    PubMed

    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.

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

    PubMed

    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

  9. Co-existence of clonal expanded autologous and transplacental-acquired maternal T cells in recombination activating gene-deficient severe combined immunodeficiency

    PubMed Central

    Lev, A; Simon, A J; Ben-Ari, J; Takagi, D; Stauber, T; Trakhtenbrot, L; Rosenthal, E; Rechavi, G; Amariglio, N; Somech, R

    2014-01-01

    It is commonly accepted that the presence of high amounts of maternal T cells excludes Omenn syndrome (OS) in severe combined immunodeficiency (SCID). We report a SCID patient with a novel mutation in the recombination activating gene (RAG)1 gene (4-BP DEL.1406 TTGC) who presented with immunodeficiency and OS. Several assays, including representatives of specific T cell receptors (TCR), Vβ families and TCR-γ rearrangements, were performed in order to understand more clearly the nature and origin of the patient's T cells. The patient had oligoclonal T cells which, based on the patient–mother human leucocyte antigen (HLA)-B50 mismatch, were either autologous or of maternal origin. These cell populations were different in their numbers of regulatory T cells (Treg) and the diversity of TCR repertoires. This is the first description of the co-existence of large amounts of clonal expanded autologous and transplacental-acquired maternal T cells in RAG1-deficient SCID. PMID:24666246

  10. Co-existence of clonal expanded autologous and transplacental-acquired maternal T cells in recombination activating gene-deficient severe combined immunodeficiency.

    PubMed

    Lev, A; Simon, A J; Ben-Ari, J; Takagi, D; Stauber, T; Trakhtenbrot, L; Rosenthal, E; Rechavi, G; Amariglio, N; Somech, R

    2014-06-01

    It is commonly accepted that the presence of high amounts of maternal T cells excludes Omenn syndrome (OS) in severe combined immunodeficiency (SCID). We report a SCID patient with a novel mutation in the recombination activating gene (RAG)1 gene (4-BP DEL.1406 TTGC) who presented with immunodeficiency and OS. Several assays, including representatives of specific T cell receptors (TCR), Vβ families and TCR-γ rearrangements, were performed in order to understand more clearly the nature and origin of the patient's T cells. The patient had oligoclonal T cells which, based on the patient-mother human leucocyte antigen (HLA)-B50 mismatch, were either autologous or of maternal origin. These cell populations were different in their numbers of regulatory T cells (T(reg)) and the diversity of TCR repertoires. This is the first description of the co-existence of large amounts of clonal expanded autologous and transplacental-acquired maternal T cells in RAG1-deficient SCID.

  11. Bacterial community associated with Pfiesteria-like dinoflagellate cultures.

    PubMed

    Alavi, M; Miller, T; Erlandson, K; Schneider, R; Belas, R

    2001-06-01

    Dinoflagellates (Eukaryota; Alveolata; Dinophyceae) are single-cell eukaryotic microorganisms implicated in many toxic outbreaks in the marine and estuarine environment. Co-existing with dinoflagellate communities are bacterial assemblages that undergo changes in species composition, compete for nutrients and produce bioactive compounds, including toxins. As part of an investigation to understand the role of the bacteria in dinoflagellate physiology and toxigenesis, we have characterized the bacterial community associated with laboratory cultures of four 'Pfiesteria-like' dinoflagellates isolated from 1997 fish killing events in Chesapeake Bay. A polymerase chain reaction with oligonucleotide primers specific to prokaryotic 16S rDNA gene sequences was used to characterize the total bacterial population, including culturable and non-culturable species, as well as possible endosymbiotic bacteria. The results indicate a diverse group of over 30 bacteria species co-existing in the dinoflagellate cultures. The broad phylogenetic types of dinoflagellate-associated bacteria were generally similar, although not identical, to those bacterial types found in association with other harmful algal species. Dinoflagellates were made axenic, and the culturable bacteria were added back to determine the contribution of the bacteria to dinoflagellate growth. Confocal scanning laser fluorescence microscopy with 16S rDNA probes was used to demonstrate a physical association of a subset of the bacteria and the dinoflagellate cells. These data point to a key component in the bacterial community being species in the marine alpha-proteobacteria group, most closely associated with the alpha-3 or SAR83 cluster.

  12. Adherence, accumulation, and cell division of a natural adherent bacterial population.

    PubMed Central

    Bloomquist, C G; Reilly, B E; Liljemark, W F

    1996-01-01

    Developing dental bacterial plaques formed in vivo on enamel surfaces were examined in specimens from 18 adult volunteers during the first day of plaque formation. An intraoral model placing enamel pieces onto teeth was used to study bacterial plaque populations developing naturally to various cell densities per square millimeter of surface area of the enamel (W. F. Liljemark, C. G. Bloomquist, C. L. Bandt, B. L. Philstrom, J. E. Hinrichs, and L. F. Wolff, Oral Microbiol. Immunol. 8:5-15, 1993). Radiolabeled nucleoside incorporation was used to measure DNA synthesis concurrent with the taking of standard viable cell counts of the plaque samples. Results showed that in vivo plaque formation began with the rapid adherence of bacteria until ca. 12 to 32% of the enamel's salivary pellicle was saturated (ca. 2.5 x 10(5) to 6.3 x 10(5) cells per mm2). The pioneer adherent species were predominantly those of the "sanguis streptococci." At the above-noted density, the bacteria present on the salivary pellicle incorporated low levels of radiolabeled nucleoside per viable cell. As bacterial numbers reached densities between 8.0 x 10(5) and 2.0 x 10(6) cells per mm2, there was a small increase in the incorporation of radiolabeled nucleosides per cell. At 2.5 x 10(6) to 4.0 x 10(6) cells per mm2 of enamel surface, there was a marked increase in the incorporation of radiolabeled nucleosides per cell which appeared to be cell-density dependent. The predominant species group in developing dental plaque films during density-dependent growth was the sanguis streptococci; however, most other species present showed similar patterns of increased DNA synthesis as the density noted above approached 2.5 x 10(6) to 4.0 x 10(6) cells per mm2. PMID:8576054

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

    PubMed Central

    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

  14. Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms

    PubMed Central

    Santegoeds, Cecilia M.; Ferdelman, Timothy G.; Muyzer, Gerard; de Beer, Dirk

    1998-01-01

    We describe the combined application of microsensors and molecular techniques to investigate the development of sulfate reduction and of sulfate-reducing bacterial populations in an aerobic bacterial biofilm. Microsensor measurements for oxygen showed that anaerobic zones developed in the biofilm within 1 week and that oxygen was depleted in the top 200 to 400 μm during all stages of biofilm development. Sulfate reduction was first detected after 6 weeks of growth, although favorable conditions for growth of sulfate-reducing bacteria (SRB) were present from the first week. In situ hybridization with a 16S rRNA probe for SRB revealed that sulfate reducers were present in high numbers (approximately 108 SRB/ml) in all stages of development, both in the oxic and anoxic zones of the biofilm. Denaturing gradient gel electrophoresis (DGGE) showed that the genetic diversity of the microbial community increased during the development of the biofilm. Hybridization analysis of the DGGE profiles with taxon-specific oligonucleotide probes showed that Desulfobulbus and Desulfovibrio were the main sulfate-reducing bacteria in all biofilm samples as well as in the bulk activated sludge. However, different Desulfobulbus and Desulfovibrio species were found in the 6th and 8th weeks of incubation, respectively, coinciding with the development of sulfate reduction. Our data indicate that not all SRB detected by molecular analysis were sulfidogenically active in the biofilm. PMID:9758792

  15. p-Cresol mineralization and bacterial population dynamics in a nitrifying sequential batch reactor.

    PubMed

    Silva, Carlos David; Beristain-Montiel, Lizeth; de Maria Cuervo-López, Flor; Texier, Anne-Claire

    2014-09-01

    The ability of a nitrifying sludge to oxidize p-cresol was evaluated in a sequential batch reactor (SBR). p-Cresol was first transformed to p-hydroxybenzaldehyde and p-hydroxybenzoate, which were later mineralized. The specific rates of p-cresol consumption increased throughout the cycles. The bacterial population dynamics were monitored by using denaturing gradient gel electrophoresis (DGGE) and sequencing of DGGE fragments. The ability of the sludge to consume p-cresol and intermediates might be related to the presence of species such as Variovorax paradoxus and Thauera mechernichensis. p-Cresol (25 to 200mgC/L) did not affect the nitrifying SBR performance (ammonium consumption efficiency and nitrate production yield were close to 100% and 1, respectively). This may be related to the high stability observed in the nitrifying communities. It was shown that a nitrifying SBR may be a good alternative to eliminate simultaneously ammonium and p-cresol, maintaining stable the respiratory process as the bacterial community.

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

    PubMed

    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

    2016-02-19

    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.

  17. Detection of bacterial-reactive natural IgM antibodies in desert bighorn sheep populations

    PubMed Central

    Palmer, Amy L.; Zielke, Ryszard A.; Sikora, Aleksandra E.; Beechler, Brianna R.; Jolles, Anna E.; Epps, Clinton W.

    2017-01-01

    Ecoimmunology is a burgeoning field of ecology which studies immune responses in wildlife by utilizing general immune assays such as the detection of natural antibody. Unlike adaptive antibodies, natural antibodies are important in innate immune responses and often recognized conserved epitopes present in pathogens. Here, we describe a procedure for measuring natural antibodies reactive to bacterial antigens that may be applicable to a variety of organisms. IgM from desert bighorn sheep plasma samples was tested for reactivity to outer membrane proteins from Vibrio coralliilyticus, a marine bacterium to which sheep would have not been exposed. Immunoblotting demonstrated bighorn sheep IgM could bind to a variety of bacterial cell envelope proteins while ELISA analysis allowed for rapid determination of natural antibody levels in hundreds of individual animals. Natural antibody levels were correlated with the ability of plasma to kill laboratory strains of E. coli bacteria. Finally, we demonstrate that natural antibody levels varied in two distinct populations of desert bighorn sheep. These data demonstrate a novel and specific measure of natural antibody function and show that this varies in ecologically relevant ways. PMID:28662203

  18. Effect of antibiotics on bacterial populations: a multi-hierachical selection process

    PubMed Central

    Martínez, José Luis

    2017-01-01

    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. PMID:28163908

  19. Effect of antibiotics on bacterial populations: a multi-hierachical selection process.

    PubMed

    Martínez, José Luis

    2017-01-01

    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.

  20. Nonlinearity in bacterial population dynamics: proposal for experiments for the observation of abrupt transitions in patches.

    PubMed

    Kenkre, V M; Kumar, Niraj

    2008-12-02

    An explicit proposal for experiments leading to abrupt transitions in spatially extended bacterial populations in a Petri dish is presented on the basis of an exact formula obtained through an analytic theory. The theory provides accurately the transition expressions despite the fact that the actual solutions, which involve strong nonlinearity, are inaccessible to it. The analytic expressions are verified through numerical solutions of the relevant nonlinear equation. The experimental setup suggested uses opaque masks in a Petri dish bathed in ultraviolet radiation [Lin A-L, et al. (2004) Biophys J 87:75-80 and Perry N (2005) J R Soc Interface 2:379-387], but is based on the interplay of two distances the bacteria must traverse, one of them favorable and the other adverse. As a result of this interplay feature, the experiments proposed introduce highly enhanced reliability in interpretation of observations and in the potential for extraction of system parameters.

  1. Critical dynamics of self-gravitating Langevin particles and bacterial populations.

    PubMed

    Sire, Clément; Chavanis, Pierre-Henri

    2008-12-01

    We study the critical dynamics of the generalized Smoluchowski-Poisson system (for self-gravitating Langevin particles) or generalized Keller-Segel model (for the chemotaxis of bacterial populations). These models [P. H. Chavanis and C. Sire, Phys. Rev. E 69, 016116 (2004)] are based on generalized stochastic processes leading to the Tsallis statistics. The equilibrium states correspond to polytropic configurations with index n similar to polytropic stars in astrophysics. At the critical index n_{3}=d(d-2) (where d>or=2 is the dimension of space), there exists a critical temperature Theta_{c} (for a given mass) or a critical mass M_{c} (for a given temperature). For Theta>Theta_{c} or MM_{c} the system collapses and forms, in a finite time, a Dirac peak containing a finite fraction M_{c} of the total mass surrounded by a halo. We study these regimes numerically and, when possible, analytically by looking for self-similar or pseudo-self-similar solutions. This study extends the critical dynamics of the ordinary Smoluchowski-Poisson system and Keller-Segel model in d=2 corresponding to isothermal configurations with n_{3}-->+infinity . We also stress the analogy between the limiting mass of white dwarf stars (Chandrasekhar's limit) and the critical mass of bacterial populations in the generalized Keller-Segel model of chemotaxis.

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

    PubMed Central

    Minard, G.; Tran, F. H.; Van, Van Tran; Goubert, C.; Bellet, C.; Lambert, G.; Kim, Khanh Ly Huynh; Thuy, Trang Huynh Thi; Mavingui, P.; Valiente Moro, C.

    2015-01-01

    The Asian tiger mosquito Aedes albopictus is one of the most significant pathogen vectors of the twenty-first 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. PMID:26441903

  3. Co-existence of Benign Paroxysmal Positional Vertigo and Meniere's Syndrome.

    PubMed

    Yetişer, Sertaç

    2017-04-01

    Recent studies indicate interrelation of benign paroxysmal positional vertigo (BPPV) and Meniere's disease (MD). These two entities may have different clinical characteristics. Five hundred thirty patients with BPPV evaluated between 2009-2015 were enrolled in the study. 351 patients who had no clear problem associated with BPPV (idiopathic) and 17 patients with MD were analyzed in detail. The age, sex, site of involvement, type of BPPV, symptom duration, and treatment outcome were compared. Meniere's disease + BPPV was more common in the female population (2/15; 7.5 v 127/224; 1.8, p<0.05). Comparative analysis of average age was not statistically significant (42.82±9.94 v. 40.29±1.65, p=0.601). There was no difference in right and left ear involvement between groups. Lateral canal involvement was more common in the BPPV + MD group (9/17; 53% v. 100/351; 28%, p<0.05). BPPV was ipsilateral to the ear with MD in 75% of patients and it was present before the diagnosis of BPPV in 82.3% of patients. Comparative analysis of cure rate between idiopathic BPPV and BPPV + MD after one session was significant (64.7% v 78%, p<0.05). Benign paroxysmal positional vertigo associated with MD presented a divergent picture. It was more frequent in females. Lateral canal involvement was higher. Patients had MD before the development of BPPV and they had prolonged symptoms, which raised a question of diagnostic delay since these two problems were in the same ear in majority of patients. Finally, relief of symptoms required more attempts of repositioning maneuvers.

  4. Sebaceous neoplasms with mismatch repair protein expressions and the frequency of co-existing visceral tumors.

    PubMed

    Lee, Bonnie A; Yu, Limin; Ma, Linglei; Lind, Anne C; Lu, Dongsi

    2012-12-01

    Visceral malignancy has been associated with sebaceous neoplasms in patients with Muir-Torre syndrome. However, no large studies have been done to evaluate the frequency of visceral tumors in patients with sebaceous neoplasms and mismatch repair (MMR) protein expression of the sebaceous tumors. We sought to determine the frequency of visceral tumors in patients with sebaceous neoplasms, MMR protein expression of the sebaceous tumors, and the related surveillance practices of physicians. We identified 85 patients with sebaceous neoplasms. Relevant clinical information was obtained via chart review and database searches. MMR protein expression was examined by immunohistochemistry. Nineteen of the 85 patients had a total of 22 visceral malignancies, of which 41% were genitourinary in origin. Ten of the 17 patients (59%) with visceral malignancy had loss of MMR expression in their sebaceous neoplasms or somatic MMR mutation. Thirty patients had other findings such as colonic adenomas and polyps. Of the 23 patients who had a family history of visceral malignancy, 9 had a personal history of visceral malignancy. Only one sebaceous tumor from each patient (except one) was tested for MMR, which might reduce the sensitivity. Our findings demonstrate an increased frequency of internal malignancy in patients with sebaceous neoplasms compared with the general population, and highlight the heterogeneous nature of the visceral tumors. A majority of the sebaceous tumors show loss of MMR expression. The study reminds us to strive toward a consistent and comprehensive approach to screening for internal malignancy when a patient is given a diagnosis of a sebaceous neoplasm. Copyright © 2012 American Academy of Dermatology, Inc. Published by Mosby, Inc. All rights reserved.

  5. Differences in bacterial diversity of host-associated populations of Phylloxera notabilis Pergande (Hemiptera: Phylloxeridae) in pecan and water hickory.

    PubMed

    Medina, R F; Nachappa, P; Tamborindeguy, C

    2011-04-01

    Host-associated differentiation (HAD) is the presence of genetically divergent, host-associated populations. It has been suggested that microbial symbionts of insect herbivores may play a role in HAD by allowing their insect hosts to use different plant species. The objective of this study was to document if host-associated populations of Phylloxera notabilis Pergande (Hemiptera: Phylloxeridae) in pecan and water hickory corresponded with differences in the composition of their associated bacteria. To test this hypothesis, we characterized the symbionts present in P. notabilis associated with these two tree species through metagenomic analyses using 454 sequencing. Differences in bacterial diversity were found between P. notabilis populations associated with pecan and water hickory. The bacteria, Pantoea agglomerans and Serratia marcescens, were absent in the P. notabilis water hickory population, whereas both species accounted for more than 69.72% of bacterial abundance in the pecan population.

  6. Magnesium isotope fractionation in co-existing clino-pyroxene and garnet: implications for geothermometry and mantle source characterization

    NASA Astrophysics Data System (ADS)

    Chakrabarti, R.; Jacobsen, S. B.; Basu, A. R.

    2011-12-01

    It is now well established that the Mg isotopic composition of the bulk silicate Earth, as represented by olivines, peridotites and basalts is identical to bulk meteorites and the Moon. However, small differences have been documented between co-existing olivines and clino-pyroxenes in mantle xenoliths as well as co-existing hornblendes and biotites in granitoids; spinels show some of the heaviest δ26Mg (deviation of the 26Mg/24Mg ratio from the Dead Sea Metal standard). A recent study has documented a large Mg isotopic fractionation between co-existing omphacite and garnet (Δ26MgOMP-GT = δ26MgOMP - δ26MgGT ~1.14) from eclogites in the Dabie orogen of China. This large equilibrium Mg isotope fractionation is explained by the difference in coordination number of Mg in omphacite (six) and garnet (eight). We report stable Mg isotopic compositions of co-existing garnet and clino-pyroxenes from different mantle-derived rocks. Garnet-omphacite pairs analyzed are from an eclogite xenolith from the Roberts Victor kimberlite pipe, the ultra-high pressure Tso Morari eclogite from the Ladakh Himalayas and the Healdsburg eclogite from the Franciscan Subduction Complex, which have a wide range in estimated temperatures of equilibration. Although, the latter two eclogites were exhumed in orogenic belts, our selective picking of the mineral cores for analysis avoided retrograded compositions. We have also analyzed Cr-diopside and pyrope-rich garnet pairs from several southern African kimberlite pipes. These include granular garnet peridotite xenoliths (P = 30-40 kbar, T =950-10500C) as well as the deeper sheared xenoliths (P = 50-60 kbar, T = 13500C). Rapid quenching of the kimberlite-hosted xenoliths ensures minimal low temperature pervasive alteration of these samples. Also analyzed are samples from the Gore Mt. amphibolite and a wollastonite-diopside-garnet skarn from the Adirondacks with equilibration temperatures of 700-7260C. Minerals were separated by hand-picking under

  7. Co-existence of a rare dyspnea with pericardial diaphragmatic rupture and pericardial rupture: a case report.

    PubMed

    Öz, Necdet; Kargı, Ahmet Bülent; Zeybek, Arife

    2015-06-01

    Pericardial-diaphragmatic rupture is a rare condition which occurs after blunt trauma and involves the herniation of abdominal organs into the pericardium. A 77-year-old female patient presenting with complaints of palpitation and difficulty in breathing was admitted to the emergency room. Left lateral thoracotomy revealed the herniation of abdominal organs into the thorax. A pericardial-diaphragmatic rupture and a pericardial rupture were found to co-exist. The diaphragm and the pericardium were repaired primarily. The case is presented here because herniation of abdominal organs into the pleural cavity through the pericardium is a rare condition.

  8. NUMERICAL COMPUTATIONS OF CO-EXISTING SUPER-CRITICAL AND SUB-CRITICAL FLOWS BASED UPON CRD SCHEMES

    NASA Astrophysics Data System (ADS)

    Horie, Katsuya; Okamura, Seiji; Kobayashi, Yusuke; Hyodo, Makoto; Hida, Yoshihisa; Nishimoto, Naoshi; Mori, Akio

    Stream flows in steep gradient bed form complicating flow configurations, where co-exist super-critical and sub-critical flows. Computing numerically such flows are the key to successful river management. This study applied CRD schemes to 1D and 2D stream flow computations and proposed genuine ways to eliminate expansion shock waves. Through various cases of computing stream flows conducted, CRD schemes showed that i) conservativeness of discharge and accuracy of four significant figures are ensured, ii) artificial viscosity is not explicitly used for computational stabilization, and thus iii) 1D and 2D computations based upon CRD schemes are applicable to evaluating complicating stream flows for river management.

  9. ADHD in girls and boys – gender differences in co-existing symptoms and executive function measures

    PubMed Central

    2013-01-01

    Background ADHD is diagnosed and treated more often in males than in females. Research on gender differences suggests that girls may be consistently underidentified and underdiagnosed because of differences in the expression of the disorder among boys and girls. One aim of the present study was to assess in a clinical sample of medication naïve boys and girls with ADHD, whether there were significant gender x diagnosis interactions in co-existing symptom severity and executive function (EF) impairment. The second aim was to delineate specific symptom ratings and measures of EF that were most important in distinguishing ADHD from healthy controls (HC) of the same gender. Methods Thirty-seven females with ADHD, 43 males with ADHD, 18 HC females and 32 HC males between 8 and 17 years were included. Co-existing symptoms were assessed with self-report scales and parent ratings. EF was assessed with parent ratings of executive skills in everyday situations (BRIEF), and neuropsychological tests. The three measurement domains (co-existing symptoms, BRIEF, neuropsychological EF tests) were investigated using analysis of variance (ANOVA) and random forest classification. Results ANOVAs revealed only one significant diagnosis x gender interaction, with higher rates of self-reported anxiety symptoms in females with ADHD. Random forest classification indicated that co-existing symptom ratings was substantially better in distinguishing subjects with ADHD from HC in females (93% accuracy) than in males (86% accuracy). The most important distinguishing variable was self-reported anxiety in females, and parent ratings of rule breaking in males. Parent ratings of EF skills were better in distinguishing subjects with ADHD from HC in males (96% accuracy) than in females (92% accuracy). Neuropsychological EF tests had only a modest ability to categorize subjects as ADHD or HC in males (73% accuracy) and females (79% accuracy). Conclusions Our findings emphasize the combination of

  10. Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates

    PubMed Central

    Olm, Matthew R.; Brown, Christopher T.; Brooks, Brandon; Firek, Brian; Baker, Robyn; Burstein, David; Soenjoyo, Karina; Thomas, Brian C.; Morowitz, Michael; Banfield, Jillian F.

    2017-01-01

    The initial microbiome impacts the health and future development of premature infants. Methodological limitations have led to gaps in our understanding of the habitat range and subpopulation complexity of founding strains, as well as how different body sites support microbial growth. Here, we used metagenomics to reconstruct genomes of strains that colonized the skin, mouth, and gut of two hospitalized premature infants during the first month of life. Seven bacterial populations, considered to be identical given whole-genome average nucleotide identity of >99.9%, colonized multiple body sites, yet none were shared between infants. Gut-associated Citrobacter koseri genomes harbored 47 polymorphic sites that we used to define 10 subpopulations, one of which appeared in the gut after 1 wk but did not spread to other body sites. Differential genome coverage was used to measure bacterial population replication rates in situ. In all cases where the same bacterial population was detected in multiple body sites, replication rates were faster in mouth and skin compared to the gut. The ability of identical strains to colonize multiple body sites underscores the habit flexibility of initial colonists, whereas differences in microbial replication rates between body sites suggest differences in host control and/or resource availability. Population genomic analyses revealed microdiversity within bacterial populations, implying initial inoculation by multiple individual cells with distinct genotypes. Overall, however, the overlap of strains across body sites implies that the premature infant microbiome can exhibit very low microbial diversity. PMID:28073918

  11. Investigating bacterial population structure and dynamics in traditional koumiss from Inner Mongolia using single molecule real-time sequencing.

    PubMed

    Gesudu, Qimu; Zheng, Yi; Xi, Xiaoxia; Hou, Qiang Chuan; Xu, Haiyan; Huang, Weiqiang; Zhang, Heping; Menghe, Bilige; Liu, Wenjun

    2016-10-01

    Koumiss is considered as a complete dairy product high in nutrients and with medicinal properties. The bacterial communities involved in production of koumiss play a crucial role in the fermentation cycle. To reveal bacterial biodiversity in koumiss and the dynamics of succession in bacterial populations during fermentation, 22 samples were collected from 5 sampling sites and the full length of the 16S ribosomal RNA genes sequenced using single molecule real-time sequencing technology. One hundred forty-eight species were identified from 82 bacterial genera and 8 phyla. These results suggested that the structural difference in the bacterial community could be attributed to geographical location. The most significant difference in bacterial composition occurred in samples from group D compared with other groups. The sampling location of group D was distant from the city and maintained the primitive local nomadic life. The dynamics of succession in bacterial communities showed that Lactobacillus helveticus increased in abundance from 0 to 9h and reached its peak at 9h and then decreased. In contrast, Enterococcus faecalis, Enterococcus durans, and Enterococcus casseliflavus increased gradually throughout the fermentation process, and reached a maximum after 24h. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  12. Life history correlates of fecal bacterial species richness in a wild population of the blue tit Cyanistes caeruleus.

    PubMed

    Benskin, Clare McW H; Rhodes, Glenn; Pickup, Roger W; Mainwaring, Mark C; Wilson, Kenneth; Hartley, Ian R

    2015-02-01

    Very little is known about the normal gastrointestinal flora of wild birds, or how it might affect or reflect the host's life-history traits. The aim of this study was to survey the species richness of bacteria in the feces of a wild population of blue tits Cyanistes caeruleus and to explore the relationships between bacterial species richness and various life-history traits, such as age, sex, and reproductive success. Using PCR-TGGE, 55 operational taxonomic units (OTUs) were identified in blue tit feces. DNA sequencing revealed that the 16S rRNA gene was amplified from a diverse range of bacteria, including those that shared closest homology with Bacillus licheniformis, Campylobacter lari, Pseudomonas spp., and Salmonella spp. For adults, there was a significant negative relationship between bacterial species richness and the likelihood of being detected alive the following breeding season; bacterial richness was consistent across years but declined through the breeding season; and breeding pairs had significantly more similar bacterial richness than expected by chance alone. Reduced adult survival was correlated with the presence of an OTU most closely resembling C. lari; enhanced adult survival was associated with an OTU most similar to Arthrobacter spp. For nestlings, there was no significant change in bacterial species richness between the first and second week after hatching, and nestlings sharing the same nest had significantly more similar bacterial richness. Collectively, these results provide compelling evidence that bacterial species richness was associated with several aspects of the life history of their hosts.

  13. Dandruff Is Associated with Disequilibrium in the Proportion of the Major Bacterial and Fungal Populations Colonizing the Scalp

    PubMed Central

    Clavaud, Cécile; Jourdain, Roland; Bar-Hen, Avner; Tichit, Magali; Bouchier, Christiane; Pouradier, Florence; El Rawadi, Charles; Guillot, Jacques; Ménard-Szczebara, Florence; Breton, Lionel; Latgé, Jean-Paul; Mouyna, Isabelle

    2013-01-01

    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. PMID:23483996

  14. Plantago ovata in broiler chicken nutrition: Performance, carcass criteria, intestinal morphology, immunity, and intestinal bacterial population.

    PubMed

    Divani, A; Bagherzadeh-Kasmani, F; Mehri, M

    2017-06-13

    In this experiment, the effect of dietary Plantago ovata (PO) on performance, carcass criteria, intestinal morphology, immunity, and intestinal bacterial population of broiler chickens was evaluated. A total of 250 one-day-old male broiler chicks (Ross 308) were randomly assigned to five treatments containing 0, 5, 10, 15, or 20 g/kg of PO with five replicate pens and 10 birds in each replicate. Dietary PO increased body weight gain and decreased feed conversion ratio in the finisher period, improving the performance index (p < .05). Dietary treatments had no effects on carcass criteria, but breast meat percentage showed an increasing trend with incremental levels of PO in the diet (p = .069). The length of small intestine, especially jejunum section, as well as the villus height, villus width, villus area, and goblet cell numbers were significantly increased with supplemental PO (p < .05). Humoral and cellular immunity parameters, and oxidation stability of meat were improved due to use of dietary PO (p < .05). Dietary PO decreased the CFU of Escherichia coli, whereas the Lactobacilli population was increased (p = .001). Broken-line regression revealed that dietary PO at the rate of 10 g/kg may results in the best performance in broiler chickens. This study showed that PO at the level of 10 g/kg could be considered as a beneficial feed additive in broiler diet. © 2017 Blackwell Verlag GmbH.

  15. Bacterial and archaeal populations associated with freshwater ferromanganous micronodules and sediments.

    PubMed

    Stein, L Y; La Duc, M T; Grundl, T J; Nealson, K H

    2001-01-01

    Biology is believed to play a large role in the cycling of iron and manganese in many freshwater environments, but specific microbial groups indigenous to these systems have not been well characterized. To investigate the populations of Bacteria and Archaea associated with metal-rich sediments from Green Bay, WI, we extracted nucleic acids and analysed the phylogenetic relationships of cloned 16S rRNA genes. Because nucleic acids have not been routinely extracted from metal-rich samples, we investigated the bias inherent in DNA extraction and gene amplification from pure MnO2 using defined populations of whole cells or naked DNA. From the sediments, we screened for manganese-oxidizing bacteria using indicator media and found three isolates that were capable of manganese oxidation. In the phylogenetic analysis of bacterial 16S rRNA gene clones, we found two groups related to known metal-oxidizing genera, Leptothrix of the beta-Proteobacteria and Hyphomicrobium of the alpha-Proteobacteria, and a Fe(III)-reducing group related to the Magnetospirillum genus of the alpha-Proteobacteria. Groups related to the metal-reducing delta-Proteobacteria constituted 22% of the gene clones. In addition, gene sequences from one group of methanogens and a group of Crenarchaeota, identified in the archaeal gene clone library, were related to those found previously in Lake Michigan sediments.

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

    PubMed

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

    2016-12-15

    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.

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

    PubMed

    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, Pi(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.

  18. Co-existence of tic disorders and attention-deficit/hyperactivity disorder-recent advances in understanding and treatment.

    PubMed

    Rothenberger, Aribert; Roessner, Veit; Banaschewski, Tobias; Leckman, James F

    2007-06-01

    In daily clinical practice of child psychiatry tic disorders (TD) and attention-deficit/hyperactivity disorder (ADHD) as well as their co-existence are common and need careful evidence-based approaches in differential diagnostics and treatment choice. Hence, their relationship at different levels (e.g., psychopathology, neuropsychology, neurobiology, treatment) needs to be elucidated in more detail. The articles of this supplement deal with this subject. It is unclear if TD + ADHD represents an own clinical entity and which component (TD vs. ADHD) is most important in case of co-existence with respect to accompanying problems like emotional or cognitive disturbances. This editorial gives a short overview of the essential research topics concerning TD + ADHD and shows where (in this ECAP supplement and other literature) empirically based answers can be found. Probably, the identification of separate or common "endophenotypes" for TD-only, ADHD-only and for TD + ADHD would help to sort out the complexities and this supplement may nurture such a perspective of future research for a better understanding and treatment of youths with TD + ADHD and their families.

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

    PubMed

    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.

  20. Prophage-mediated dynamics of 'Candidatus Liberibacter asiaticus' populations, the destructive bacterial pathogens of citrus huanglongbing.

    PubMed

    Zhou, Lijuan; Powell, Charles A; Li, Wenbin; Irey, Mike; Duan, Yongping

    2013-01-01

    Prophages are highly dynamic components in the bacterial genome and play an important role in intraspecies variations. There are at least two prophages in the chromosomes of Candidatus Liberibacter asiaticus' (Las) Floridian isolates. Las is both unculturable and the most prevalent species of Liberibacter pathogens that cause huanglongbing (HLB), a worldwide destructive disease of citrus. In this study, seven new prophage variants resulting from two hyper-variable regions were identified by screening clone libraries of infected citrus, periwinkle and psyllids. Among them, Types A and B share highly conserved sequences and localize within the two prophages, FP1 and FP2, respectively. Although Types B and C were abundant in all three libraries, Type A was much more abundant in the libraries from the Las-infected psyllids than from the Las-infected plants, and Type D was only identified in libraries from the infected host plants but not from the infected psyllids. Sequence analysis of these variants revealed that the variations may result from recombination and rearrangement events. Conventional PCR results using type-specific molecular markers indicated that A, B, C and D are the four most abundant types in Las-infected citrus and periwinkle. However, only three types, A, B and C are abundant in Las-infected psyllids. Typing results for Las-infected citrus field samples indicated that mixed populations of Las bacteria present in Floridian isolates, but only the Type D population was correlated with the blotchy mottle symptom. Extended cloning and sequencing of the Type D region revealed a third prophage/phage in the Las genome, which may derive from the recombination of FP1 and FP2. Dramatic variations in these prophage regions were also found among the global Las isolates. These results are the first to demonstrate the prophage/phage-mediated dynamics of Las populations in plant and insect hosts, and their correlation with insect transmission and disease development.

  1. Pulsed blooms and persistent oil-degrading bacterial populations in the water column during and after the Deepwater Horizon blowout

    NASA Astrophysics Data System (ADS)

    Yang, Tingting; Nigro, Lisa M.; Gutierrez, Tony; D`Ambrosio, Lindsay; Joye, Samantha B.; Highsmith, Raymond; Teske, Andreas

    2016-07-01

    One of the defining features of the Deepwater Horizon oil spill was the rapid formation and persistence of a hydrocarbon plume in deep water. Here we use 16S rRNA gene clone libraries and pyrosequencing of 16S rRNA gene fragments to outline the temporal dynamics of the bacterial community in the water column near the Macondo wellhead. Our timeline starts with the pre-spill (March 2010) status of the water column bacterial community, continues through the bacterial enrichments dominating the hydrocarbon plume after the blowout (DWH Oceanospirillales, Cycloclasticus, Colwellia in late May 2010), and leads towards post-spill bacterial communities with molecular signatures related to degradation of phytoplankton pulses (September and October 2010; July 2011) in the water column near the Macondo wellhead. We document a dramatic transition as the complex bacterial community before the oil spill was temporarily overwhelmed by a few specialized bacterial groups responding to the massive influx of hydrocarbons in May 2010. In September and October 2010, this bacterial bloom had been replaced by a diversified bacterial community which resembled its predecessor prior to the spill. Notably, the post-plume 16S rRNA gene clone libraries and pyrosequencing datasets illustrated the continued presence of oil-degrading bacteria in the water column near the Macondo wellhead which we posit to represent an inherent signature of hydrocarbon catabolic potential to the Gulf of Mexico. The pyroseqencing results detected and tracked minority bacterial populations that were not visible in the conventional 16S rRNA gene clone libraries and allowed us to identify natural reservoirs of the Deepwater Horizon Oceanospirillales within and outside of the Gulf of Mexico.

  2. Emergence of Competitive Dominant Ammonia-Oxidizing Bacterial Populations in a Full-Scale Industrial Wastewater Treatment Plant

    PubMed Central

    Layton, Alice C.; Dionisi, Hebe; Kuo, H.-W.; Robinson, Kevin G.; Garrett, Victoria M.; Meyers, Arthur; Sayler, Gary S.

    2005-01-01

    Ammonia-oxidizing bacterial populations in an industrial wastewater treatment plant were investigated with amoA and 16S rRNA gene real-time PCR assays. Nitrosomonas nitrosa initially dominated, but over time RI-27-type ammonia oxidizers, also within the Nitrosomonas communis lineage, increased from below detection to codominance. This shift occurred even though nitrification remained constant. PMID:15691975

  3. Weighted ssGBLUP improves genomic selection accuracy for bacterial cold water disease resistance in a rainbow trout population

    USDA-ARS?s Scientific Manuscript database

    The objective of this study was to compare methods for genomic evaluation in a Rainbow Trout (Oncorhynchus mykiss) population for survival when challenged by Flavobacterium psychrophilum, the causative agent of bacterial cold water disease (BCWD). The used methods were: 1)regular ssGBLUP that assume...

  4. Association mapping of common bacterial blight resistance QTL in Ontario bean breeding populations

    PubMed Central

    2011-01-01

    Background Common bacterial blight (CBB), incited by Xanthomonas axonopodis pv. phaseoli (Xap), is a major yield-limiting factor of common bean (Phaseolus vulgaris L.) production around the world. Host resistance is practically the most effective and environmentally-sound approach to control CBB. Unlike conventional QTL discovery strategies, in which bi-parental populations (F2, RIL, or DH) need to be developed, association mapping-based strategies can use plant breeding populations to synchronize QTL discovery and cultivar development. Results A population of 469 dry bean lines of different market classes representing plant materials routinely developed in a bean breeding program were used. Of them, 395 lines were evaluated for CBB resistance at 14 and 21 DAI (Days After Inoculation) in the summer of 2009 in an artificially inoculated CBB nursery in south-western Ontario. All lines were genotyped using 132 SNPs (Single Nucleotide Polymorphisms) evenly distributed across the genome. Of the 132 SNPs, 26 SNPs had more than 20% missing data, 12 SNPs were monomorphic, and 17 SNPs had a MAF (Minor Allelic Frequency) of less than 0.20, therefore only 75 SNPs were used for association study, based on one SNP per locus. The best possible population structure was to assign 36% and 64% of the lines into Andean and Mesoamerican subgroups, respectively. Kinship analysis also revealed complex familial relationships among all lines, which corresponds with the known pedigree history. MLM (Mixed Linear Model) analysis, including population structure and kinship, was used to discover marker-trait associations. Eighteen and 22 markers were significantly associated with CBB rating at 14 and 21 DAI, respectively. Fourteen markers were significant for both dates and the markers UBC420, SU91, g321, g471, and g796 were highly significant (p ≤ 0.001). Furthermore, 12 significant SNP markers were co-localized with or close to the CBB-QTLs identified previously in bi-parental QTL mapping

  5. Impact of Bioreactor Environment and Recovery Method on the Profile of Bacterial Populations from Water Distribution Systems

    PubMed Central

    Luo, Xia; Jellison, Kristen L.; Huynh, Kevin; Widmer, Giovanni

    2015-01-01

    Multiple rotating annular reactors were seeded with biofilms flushed from water distribution systems to assess (1) whether biofilms grown in bioreactors are representative of biofilms flushed from the water distribution system in terms of bacterial composition and diversity, and (2) whether the biofilm sampling method affects the population profile of the attached bacterial community. Biofilms were grown in bioreactors until thickness stabilized (9 to 11 weeks) and harvested from reactor coupons by sonication, stomaching, bead-beating, and manual scraping. High-throughput sequencing of 16S rRNA amplicons was used to profile bacterial populations from flushed biofilms seeded into bioreactors as well as biofilms recovered from bioreactor coupons by different methods. β diversity between flushed and reactor biofilms was compared to β diversity between (i) biofilms harvested from different reactors and (ii) biofilms harvested by different methods from the same reactor. These analyses showed that average diversity between flushed and bioreactor biofilms was double the diversity between biofilms from different reactors operated in parallel. The diversity between bioreactors was larger than the diversity associated with different biofilm recovery methods. Compared to other experimental variables, the method used to recover biofilms had a negligible impact on the outcome of water biofilm analyses based on 16S amplicon sequencing. Results from this study show that biofilms grown in reactors over 9 to 11 weeks are not representative models of the microbial populations flushed from a distribution system. Furthermore, the bacterial population profile of biofilms grown in replicate reactors from the same flushed water are likely to diverge. However, four common sampling protocols, which differ with respect to disruption of bacterial cells, provide similar information with respect to the 16S rRNA population profile of the biofilm community. PMID:26196282

  6. Impact of Bioreactor Environment and Recovery Method on the Profile of Bacterial Populations from Water Distribution Systems.

    PubMed

    Luo, Xia; Jellison, Kristen L; Huynh, Kevin; Widmer, Giovanni

    2015-01-01

    Multiple rotating annular reactors were seeded with biofilms flushed from water distribution systems to assess (1) whether biofilms grown in bioreactors are representative of biofilms flushed from the water distribution system in terms of bacterial composition and diversity, and (2) whether the biofilm sampling method affects the population profile of the attached bacterial community. Biofilms were grown in bioreactors until thickness stabilized (9 to 11 weeks) and harvested from reactor coupons by sonication, stomaching, bead-beating, and manual scraping. High-throughput sequencing of 16S rRNA amplicons was used to profile bacterial populations from flushed biofilms seeded into bioreactors as well as biofilms recovered from bioreactor coupons by different methods. β diversity between flushed and reactor biofilms was compared to β diversity between (i) biofilms harvested from different reactors and (ii) biofilms harvested by different methods from the same reactor. These analyses showed that average diversity between flushed and bioreactor biofilms was double the diversity between biofilms from different reactors operated in parallel. The diversity between bioreactors was larger than the diversity associated with different biofilm recovery methods. Compared to other experimental variables, the method used to recover biofilms had a negligible impact on the outcome of water biofilm analyses based on 16S amplicon sequencing. Results from this study show that biofilms grown in reactors over 9 to 11 weeks are not representative models of the microbial populations flushed from a distribution system. Furthermore, the bacterial population profile of biofilms grown in replicate reactors from the same flushed water are likely to diverge. However, four common sampling protocols, which differ with respect to disruption of bacterial cells, provide similar information with respect to the 16S rRNA population profile of the biofilm community.

  7. Prevalence of Irritable Bowel Syndrome (IBS), Migraine and Co-Existing IBS-Migraine in Medical Students

    PubMed Central

    Parvin, Rukhsana; Saha, Madhusudan; Bari, Md. Shafiqul; Huda, Md. Nazmul; Ghosh, Mridul Kanti

    2016-01-01

    Introduction Irritable Bowel Syndrome (IBS) and migraine frequently co-exist. Stress is a major contributing factor for both. Our medical students are subjected to stress related to the implicit responsibility of courses. But the prevalence of IBS, migraine and co-existing migraine in medical students is not known. Aim To estimate the prevalence of migraine, IBS and co-existing IBS and migraine among medical students. A Cross-Sectional Survey. Materials and Methods Self-reported questionnaire based study, was conducted in which migraine was defined according to International Headache Society (IHS) criteria while IBS by both Asian criteria and Rome III criteria. Both preclinical (n=142) and clinical students (n=151) of four medical colleges (government and private) of Dhaka and Sylhet district participated in the study. Statistical Analysis: Student’s t-test and chi-square test were used to compare the distributions of continuous data and categorical data respectively with significance level set at 0.05 or less. Results Among the 293 students (mean age 21.09 ± 2.24 years) volunteered in the study (Males= 177), 14 (4.8%, 11 males, 3 females, p = 0.175) met the criteria for IBS with comparable prevalence among preclinical and clinical (4.2% vs. 5.3%, p = 0.787) students from both private and government institutions (2.1% vs. 7.2%, p = 0.055). IBS-D was the most prevalent subtype (n = 8, M = 6) and abdominal pain relieved by defecation (n = 11), was the most prevalent symptom. Fifty percent (n = 7) of IBS patients considered their bowel habit as normal. Among the 221 (75.4%) students with headache, only 51 (17.4%, 20 males and 31 females, p = 0.001) were diagnosed of migraine, with comparable prevalence among preclinical and clinical students (16.2% vs. 18.5%, p = 0.645). Only 17 (33%) subjects with migraine had accompanying aura. Common triggers were stress (n = 43), lack of sleep (n = 42), and daily life events. Twelve (23.5%) subjects with migraine had migraine

  8. Integrated kinetic and probabilistic modeling of the growth potential of bacterial populations.

    PubMed

    George, S M; Métris, A; Baranyi, J

    2015-05-01

    When bacteria are exposed to osmotic stress, some cells recover and grow, while others die or are unculturable. This leads to a viable count growth curve where the cell number decreases before the onset of the exponential growth phase. From such curves, it is impossible to estimate what proportion of the initial cells generates the growth because it leads to an ill-conditioned numerical problem. Here, we applied a combination of experimental and statistical methods, based on optical density measurements, to infer both the probability of growth and the maximum specific growth rate of the culture. We quantified the growth potential of a bacterial population as a quantity composed from the probability of growth and the "suitability" of the growing subpopulation to the new environment. We found that, for all three laboratory media studied, the probability of growth decreased while the "work to be done" by the growing subpopulation (defined as the negative logarithm of their suitability parameter) increased with NaCl concentration. The results suggest that the effect of medium on the probability of growth could be described by a simple shift parameter, a differential NaCl concentration that can be accounted for by the change in the medium composition. Finally, we highlighted the need for further understanding of the effect of the osmoprotectant glycine betaine on metabolism. Copyright © 2015, George et al.

  9. Does dormancy increase fitness of bacterial populations in time-varying environments?

    PubMed

    Malik, Tufail; Smith, Hal L

    2008-05-01

    A simple family of models of a bacterial population in a time varying environment in which cells can transit between dormant and active states is constructed. It consists of a linear system of ordinary differential equations for active and dormant cells with time-dependent coefficients reflecting an environment which may be periodic or random, with alternate periods of low and high resource levels. The focus is on computing/estimating the dominant Lyapunov exponent, the fitness, and determining its dependence on various parameters and the two strategies-responsive and stochastic-by which organisms switch between dormant and active states. A responsive switcher responds to good and bad times by making timely and appropriate transitions while a stochastic switcher switches continuously without regard to the environmental state. The fitness of a responsive switcher is examined and compared with fitness of a stochastic switcher, and with the fitness of a dormancy-incapable organism. Analytical methods show that both switching strategists have higher fitness than a dormancy-incapable organism when good times are rare and that responsive switcher has higher fitness than stochastic switcher when good times are either rare or common. Numerical calculations show that stochastic switcher can be most fit when good times are neither too rare or too common.

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

    EPA Science Inventory

    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...

  11. Interlinkages between bacterial populations dynamics and the operational parameters in a moving bed membrane bioreactor treating urban sewage.

    PubMed

    Reboleiro-Rivas, P; Martín-Pascual, J; Morillo, J A; Juárez-Jiménez, B; Poyatos, J M; Rodelas, B; González-López, J

    2016-01-01

    Bacteria are key players in biological wastewater treatments (WWTs), thus a firm knowledge of the bacterial population dynamics is crucial to understand environmental/operational factors affecting the efficiency and stability of the biological depuration process. Unfortunately, little is known about the microbial ecology of the advanced biological WWTs combining suspended biomass (SB) and attached biofilms (AB). This study explored in depth the bacterial community structure and population dynamics in each biomass fraction from a pilot-scale moving bed membrane bioreactor (MBMBR) treating municipal sewage, by means of temperature-gradient gel electrophoresis (TGGE) and 454-pyrosequencing. Eight experimental phases were conducted, combining different carrier filling ratios, hydraulic retention times and concentrations of mixed liquor total suspended solids. The bacterial community, dominated by Proteobacteria (20.9-53.8%) and Actinobacteria (20.6-57.6%), was very similar in both biomass fractions and able to maintain its functional stability under all the operating conditions, ensuring a successful and steady depuration process. Multivariate statistical analysis demonstrated that solids concentration, carrier filling ratio, temperature and organic matter concentration in the influent were the significant factors explaining population dynamics. Bacterial diversity increased as carrier filling ratio increased (from 20% to 35%, v/v), and solids concentration was the main factor triggering the shifts of the community structure. These findings provide new insights on the influence of operational parameters on the biology of the innovative MBMBRs. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Transperitoneal repair of a juxtarenal abdominal aortic aneurysm and co-existent horseshoe kidney with division of the renal isthmus

    PubMed Central

    Hajibandeh, Shahin; Hajibandeh, Shahab; Johnpulle, Michelle; Perricone, Vittorio

    2015-01-01

    The co-existence of abdominal aortic aneurysm (AAA) and horseshoe kidney (HSK) is rare. We report a 67-year-old man with an expanding juxtarenal AAA associated with a HSK. The aneurysm had a severely angulated neck and contained a significant amount of mural thrombus. The isthmus of HSK closely lied over the aneurysm, making its exposure extremely difficult. The aneurysm was successfully repaired using transperitoneal approach with division of the renal isthmus and without any need for the renal artery reconstruction. Despite the potential complications, particularly renal insufficiency, associated with division of the renal isthmus and suprarenal cross-clamping of the abdominal aorta, in our case, post-operative period was uneventful and the patient's recovery was satisfactory. PMID:26511935

  13. In-situ synthesis of Au nano particles of co-existing morphologies in liquid crystalline matrix

    SciTech Connect

    Dan, Kaustabh Datta, Alokmay

    2015-06-24

    The present study describes the in-situ synthesis of Au nano particles (Au-NP) in the room temperature nematic liquid crystalline (LC) substance MBBA (N-4 methoxybenzylidene 4 butylaniline) without any external reducing or stabilizing agents. UV-Visible absorption and fluorescence spectroscopy clearly show formation of Au-NP within the LC matrix through the plasmon resonance peak for the NPs and EDAX measurements confirm this formation. Transmission electron Microscopy shows co-existence of spherical and prismatic NPs. FTIR spectroscopy shows a considerable shift in the C=N stretch band pointing to the location of the growth centre of the NPs. Polarization microscopy data indicates a definite phase ordering and texture transformation from Nematic to highly ordered smectic mesophase.

  14. Interworking between IP security and NAT-PT under IPv4/IPv6 co-existent environments

    NASA Astrophysics Data System (ADS)

    Ye, Run-Guo; Yu, Shu-Yao; Yang, Hong-Wei; Song, Chuck

    2005-02-01

    Similar to conventional NAT gateways, NAT-PT gateways break traditional TCP/IP"s end-to-end argument property; hence, any IP-based applications protected by IPSec protocol cannot traverse NAT-PT gateways properly. The interworking issues between IPSec and NAT-PT gateways under IPv4/IPv6 co-existent environments were studied: this paper first pointed out the deficiency of current NAT-Traversal scheme when interworking with NAT-PT gateways and proposed an enhanced scheme, which enabled interworking between IPSec and NAT-PT gateways and served the following three scenarios: 1) secure communication between IPv6 hosts and IPv4 hosts; 2) secure communication between IPv6 subnets and IPv4 subnets; 3) secure communication between remote IPv6 hosts and legacy IPv4 subnets.

  15. Effect of co-existing copper and calcium on the removal of As(V) by reused aluminum oxides.

    PubMed

    Yang, J K; Park, Y J; Kim, K H; Lee, H Y; Min, K C; Lee, S M

    2013-01-01

    Among the various heavy metals, arsenic is frequently found in abandoned mine drainage and the environmental fate of arsenic in real aqueous solutions can be highly dependent on the presence of co-existing ions. In this study, removal of arsenate through adsorption on the reused aluminum oxide or through precipitation was investigated in a single and in a binary system as a function of pH and concentration. Different removal behaviors of arsenate were observed in the presence of different cations as well as a variation of the molar ratios of arsenate to cations. Co-operative effects on arsenate removal by precipitation in solution occurred with an increase of copper concentration, while a decrease of arsenate removal resulted in increasing calcium concentration. It was observed that the arsenate removal in the presence of calcium would be highly dependent on the molar ratios of both elements.

  16. Differential Gene Expression Landscape of Co-Existing Cervical Pre-Cancer Lesions Using RNA-seq

    PubMed Central

    Royse, Kathryn E.; Zhi, Degui; Conner, Michael G.; Clodfelder-Miller, Buffie; Srinivasasainagendra, Vinodh; Vaughan, Laura Kelly; Skibola, Christine F.; Crossman, David K.; Levy, Shawn; Shrestha, Sadeep

    2014-01-01

    Genetic changes occurring in different stages of pre-cancer lesions reflect causal events initiating and promoting the progression to cancer. Co-existing pre-cancerous lesions including low- and high-grade squamous intraepithelial lesion (LGSIL and HGSIL), and adjacent “normal” cervical epithelium from six formalin-fixed paraffin-embedded samples were selected. Tissues from these 18 samples were isolated using laser-capture microdissection, RNA was extracted and sequenced. RNA-sequencing generated 2.4 billion raw reads in 18 samples, of which ~50.1% mapped to known and annotated genes in the human genome. There were 40 genes up-regulated and 3 down-regulated (normal to LGSIL) in at least one-third of the sample pairs (same direction and FDR p < 0.05) including S100A7 and KLK6. Previous studies have shown that S110A7 and KLK7 are up-regulated in several other cancers, whereas CCL18, CFTR, and SLC6A14, also differentially expressed in two samples, are up-regulated specifically in cervical cancer. These differentially expressed genes in normal to LGSIL progression were enriched in pathways related to epithelial cell differentiation, keratinocyte differentiation, peptidase, and extracellular activities. In progression from LGSIL to HGSIL, two genes were up-regulated and five down-regulated in at least two samples. Further investigations using co-existing samples, which account for all internal confounders, will provide insights to better understand progression of cervical pre-cancer. PMID:25505737

  17. Bayesian risk maps for Schistosoma mansoni and hookworm mono-infections in a setting where both parasites co-exist.

    PubMed

    Raso, Giovanna; Vounatsou, Penelope; McManus, Donald P; Utzinger, Jürg

    2007-11-01

    There is growing interest in the use of Bayesian geostatistical models for predicting the spatial distribution of parasitic infections, including hookworm, Schistosoma mansoni and co-infections with both parasites. The aim of this study was to predict the spatial distribution of mono-infections with either hookworm or S. mansoni in a setting where both parasites co-exist. School-based cross-sectional parasitological and questionnaire surveys were carried out in 57 rural schools in the Man region, western Côte d'Ivoire. A single stool specimen was obtained from each schoolchild attending grades 3-5. Stool specimens were processed by the Kato-Katz technique and an ether concentration method and examined for the presence of hookworm and S. mansoni eggs. The combined results from the two diagnostic approaches were considered for the infection status of each child. Demographic data (i.e. age and sex) were obtained from readily available school registries. Each child's socio-economic status was estimated, using the questionnaire data following a household-based asset approach. Environmental data were extracted from satellite imagery. The different data sources were incorporated into a geographical information system. Finally, a Bayesian spatial multinomial regression model was constructed and the spatial patterns of S. mansoni and hookworm mono-infections were investigated using Bayesian kriging. Our approach facilitated the production of smooth risk maps for hookworm and S. mansoni mono-infections that can be utilized for targeting control interventions. We argue that in settings where S. mansoni and hookworm co-exist and control efforts are under way, there is a need for both mono- and co-infection risk maps to enhance the cost-effectiveness of control programmes.

  18. Functional Homomers and Heteromers of Dopamine D2L and D3 Receptors Co-exist at the Cell Surface

    PubMed Central

    Pou, Chantevy; Mannoury la Cour, Clotilde; Stoddart, Leigh A.; Millan, Mark J.; Milligan, Graeme

    2012-01-01

    Human dopamine D2long and D3 receptors were modified by N-terminal addition of SNAP or CLIP forms of O6-alkylguanine-DNA-alkyltransferase plus a peptide epitope tag. Cells able to express each of these four constructs only upon addition of an antibiotic were established and used to confirm regulated and inducible control of expression, the specificity of SNAP and CLIP tag covalent labeling reagents, and based on homogenous time-resolved fluorescence resonance energy transfer, the presence of cell surface D2long and D3 receptor homomers. Following constitutive expression of reciprocal constructs, potentially capable of forming and reporting the presence of cell surface D2long-D3 heteromers, individual clones were assessed for levels of expression of the constitutively expressed protomer. This was unaffected by induction of the partner protomer and the level of expression of the partner required to generate detectable cell surface D2long–D3 heteromers was defined. Such homomers and heteromers were found to co-exist and using a reconstitution of function approach both homomers and heteromers of D2long and D3 receptors were shown to be functional, potentially via trans-activation of associated G protein. These studies demonstrate the ability of dopamine D2long and D3 receptors to form both homomers and heteromers, and show that in cells expressing each subtype a complex mixture of homomers and heteromers co-exists at steady state. These data are of potential importance both to disorders in which D2long and D3 receptors are implicated, like schizophrenia and Parkinson disease, and also to drugs exerting their actions via these sites. PMID:22291025

  19. Bacterial diversity of East Calcutta Wet land area: possible identification of potential bacterial population for different biotechnological uses.

    PubMed

    Ghosh, Abhrajyoti; Maity, Bhaswar; Chakrabarti, Krishanu; Chattopadhyay, Dhrubajyoti

    2007-10-01

    The extent of microbial diversity in nature is still largely unknown, suggesting that there might be many more useful products yet to be identified from soil microorganisms. This insight provides the scientific foundation for a renewed interest in examining soil microorganisms for novel commercially important products. This has led us to access the metabolic potential of soil microorganisms via cultivation strategy. Keeping this in mind, we have performed a culture-dependent survey of important soil bacterial community diversity in East Calcutta Wetland area (Dhapa Landfill Area). We describe isolation of 38 strains, their phenotypic and biochemical characterization, and finally molecular identification by direct sequencing of polymerase chain reaction (PCR)-amplified 16S rRNA gene products. We have isolated and identified strains able to fix nitrogen, produce extracellular enzymes like protease, cellulase, xylanase, and amylase, and solubilize inorganic phosphates. Some isolates can synthesize extracellular insecticidal toxins. We find a good correlation between biochemical and phenotypic behavior and the molecular study using 16S rRNA gene of the isolates. Furthermore, our findings clearly indicate the composition of cultivable soil bacteria in East Calcutta Wetland Area.

  20. Hydrogeochemistry and coal-associated bacterial populations from a methanogenic coal bed

    DOE PAGES

    Barnhart, Elliott P.; Weeks, Edwin P.; Jones, Elizabeth J. P.; ...

    2016-05-04

    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 hydraulicmore » 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 112-120 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 dominantin situ bacterial 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 hydrocarbons

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

    PubMed

    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 < 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.

  2. Co-habiting amphibian species harbor unique skin bacterial communities in wild populations.

    PubMed

    McKenzie, Valerie J; Bowers, Robert M; Fierer, Noah; Knight, Rob; Lauber, Christian L

    2012-03-01

    Although all plant and animal species harbor microbial symbionts, we know surprisingly little about the specificity of microbial communities to their hosts. Few studies have compared the microbiomes of different species of animals, and fewer still have examined animals in the wild. We sampled four pond habitats in Colorado, USA, where multiple amphibian species were present. In total, 32 amphibian individuals were sampled from three different species including northern leopard frogs (Lithobates pipiens), western chorus frogs (Pseudacris triseriata) and tiger salamanders (Ambystoma tigrinum). We compared the diversity and composition of the bacterial communities on the skin of the collected individuals via barcoded pyrosequencing of the 16S rRNA gene. Dominant bacterial phyla included Acidobacteria, Actinobacteria, Bacteriodetes, Cyanobacteria, Firmicutes and Proteobacteria. In total, we found members of 18 bacterial phyla, comparable to the taxonomic diversity typically found on human skin. Levels of bacterial diversity varied strongly across species: L. pipiens had the highest diversity; A. tigrinum the lowest. Host species was a highly significant predictor of bacterial community similarity, and co-habitation within the same pond was not significant, highlighting that the skin-associated bacterial communities do not simply reflect those bacterial communities found in their surrounding environments. Innate species differences thus appear to regulate the structure of skin bacterial communities on amphibians. In light of recent discoveries that some bacteria on amphibian skin have antifungal activity, our finding suggests that host-specific bacteria may have a role in the species-specific resistance to fungal pathogens.

  3. Life history correlates of fecal bacterial species richness in a wild population of the blue tit Cyanistes caeruleus

    PubMed Central

    Benskin, Clare McW H; Rhodes, Glenn; Pickup, Roger W; Mainwaring, Mark C; Wilson, Kenneth; Hartley, Ian R

    2015-01-01

    Very little is known about the normal gastrointestinal flora of wild birds, or how it might affect or reflect the host's life-history traits. The aim of this study was to survey the species richness of bacteria in the feces of a wild population of blue tits Cyanistes caeruleus and to explore the relationships between bacterial species richness and various life-history traits, such as age, sex, and reproductive success. Using PCR-TGGE, 55 operational taxonomic units (OTUs) were identified in blue tit feces. DNA sequencing revealed that the 16S rRNA gene was amplified from a diverse range of bacteria, including those that shared closest homology with Bacillus licheniformis, Campylobacter lari, Pseudomonas spp., and Salmonella spp. For adults, there was a significant negative relationship between bacterial species richness and the likelihood of being detected alive the following breeding season; bacterial richness was consistent across years but declined through the breeding season; and breeding pairs had significantly more similar bacterial richness than expected by chance alone. Reduced adult survival was correlated with the presence of an OTU most closely resembling C. lari; enhanced adult survival was associated with an OTU most similar to Arthrobacter spp. For nestlings, there was no significant change in bacterial species richness between the first and second week after hatching, and nestlings sharing the same nest had significantly more similar bacterial richness. Collectively, these results provide compelling evidence that bacterial species richness was associated with several aspects of the life history of their hosts. PMID:25750710

  4. Influence of zinc on bacterial populations and their proteolytic enzyme activities in freshwater environments: a cross-site comparison.

    PubMed

    Rasmussen, Lauren; Olapade, Ola A

    2016-04-01

    Temporal responses of indigenous bacterial populations and proteolytic enzyme (i.e., aminopeptidase) activities in the bacterioplankton assemblages from 3 separate freshwater environments were examined after exposure to various zinc (Zn) concentrations under controlled microcosm conditions. Zn concentrations (ranging from 0 to 10 μmol/L) were added to water samples collected from the Kalamazoo River, Rice Creek, and Huron River and examined for bacterial abundance and aminopeptidase activities at various time intervals over a 48 h incubation period in the dark. The results showed that the Zn concentrations did not significantly influence total bacterial counts directly; however, aminopeptidase activities varied significantly to increasing zinc treatments over time. Also, analysis of variance and linear regression analyses revealed significant positive relationships between bacterial numbers and their hydrolytic enzyme activities, suggesting that both probably co-vary with increasing Zn concentrations in aquatic systems. The results from this study serve as additional evidence of the ecological role of Zn as an extracellular peptidase cofactor on the dynamics of bacterial assemblages in aquatic environments.

  5. Network-based identification of adaptive pathways in evolved ethanol-tolerant bacterial populations.

    PubMed

    Swings, Toon; Weytjens, Bram; Schalck, Thomas; Bonte, Camille; Verstraeten, Natalie; Michiels, Jan; Marchal, Kathleen

    2017-08-28

    Efficient production of ethanol for use as a renewable fuel requires organisms with a high level of ethanol tolerance. However, this trait is complex and increased tolerance therefore requires mutations in multiple genes and pathways. Here, we use experimental evolution for a system-level analysis of adaptation of Escherichia coli to high ethanol stress. As adaptation to extreme stress often results in complex mutational datasets consisting of both causal and non-causal passenger mutations, identifying the true adaptive mutations in these settings is not trivial. Therefore, we developed a novel method named IAMBEE (Identification of Adaptive Mutations in Bacterial Evolution Experiments). IAMBEE exploits the temporal profile of the acquisition of mutations during evolution in combination with the functional implications of each mutation at the protein level. These data are mapped to a genome-wide interaction network to search for adaptive mutations at the level of pathways. The 16 evolved populations in our dataset together harbored 2286 mutated genes with 4470 unique mutations. Analysis by IAMBEE significantly reduced this number and resulted in identification of 90 mutated genes and 345 unique mutations that are most likely to be adaptive. Moreover, IAMBEE not only enabled the identification of previously known pathways involved in ethanol tolerance, but also identified novel systems such as the AcrAB-TolC efflux pump and fatty acids biosynthesis and even allowed to gain insight into the temporal profile of adaptation to ethanol stress. Furthermore, this method offers a solid framework for identifying the molecular underpinnings of other complex traits as well. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  6. Effects of Aeration Cycles on Nitrifying Bacterial Populations and Nitrogen Removal in Intermittently Aerated Reactors

    PubMed Central

    Mota, Cesar; Head, Melanie A.; Ridenoure, Jennifer A.; Cheng, Jay J.; de los Reyes, Francis L.

    2005-01-01

    The effects of the lengths of aeration and nonaeration periods on nitrogen removal and the nitrifying bacterial community structure were assessed in intermittently aerated (IA) reactors treating digested swine wastewater. Five IA reactors were operated in parallel with different aeration-to-nonaeration time ratios (ANA). Populations of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) were monitored using 16S rRNA slot blot hybridizations. AOB species diversity was assessed using amoA gene denaturant gradient gel electrophoresis. Nitrosomonas and Nitrosococcus mobilis were the dominant AOB and Nitrospira spp. were the dominant NOB in all reactors, although Nitrosospira and Nitrobacter were also detected at lower levels. Reactors operated with the shortest aeration time (30 min) showed the highest Nitrosospira rRNA levels, and reactors operated with the longest anoxic periods (3 and 4 h) showed the lowest levels of Nitrobacter, compared to the other reactors. Nitrosomonas sp. strain Nm107 was detected in all reactors, regardless of the reactor's performance. Close relatives of Nitrosomonas europaea, Nitrosomonas sp. strain ENI-11, and Nitrosospira multiformis were occasionally detected in all reactors. Biomass fractions of AOB and effluent ammonia concentrations were not significantly different among the reactors. NOB were more sensitive than AOB to long nonaeration periods, as nitrite accumulation and lower total NOB rRNA levels were observed for an ANA of 1 h:4 h. The reactor with the longest nonaeration time of 4 h performed partial nitrification, followed by denitrification via nitrite, whereas the other reactors removed nitrogen through traditional nitrification and denitrification via nitrate. Superior ammonia removal efficiencies were not associated with levels of specific AOB species or with higher AOB species diversity. PMID:16332848

  7. C-reactive protein is differentially modulated by co-existing infections, vitamin deficiencies and maternal factors in pregnant and lactating indigenous Panamanian women.

    PubMed

    González-Fernández, Doris; Pons, Emérita Del Carmen; Rueda, Delfina; Sinisterra, Odalis Teresa; Murillo, Enrique; Scott, Marilyn E; Koski, Kristine G

    2017-06-02

    The usefulness of C-reactive protein (CRP) as a non-specific marker of inflammation during pregnancy and lactation is unclear in impoverished populations where co-existing infections and vitamin deficiencies are common. This cross-sectional study in Panama recruited 120 pregnant and 99 lactating Ngäbe-Buglé women from 14 communities in rural Panama. Obstetric history, indoor wood smoke exposure, fieldwork, BMI, vitamins A, B12, D, and folic acid, and inflammation markers (CRP, neutrophil/lymphocyte ratio (NLR), plateletcrit and cytokines) were measured. Multiple regressions explored both associations of CRP with other inflammatory markers and associations of CRP and elevated CRP based on trimester-specific cut-offs with maternal factors, infections and vitamin deficiencies. CRP was higher in pregnancy (51.4 ± 4.7 nmol/L) than lactation (27.8 ± 3.5 nmol/L) and was elevated above trimester specific cut-offs in 21% of pregnant and 30% of lactating women. Vitamin deficiencies were common (vitamin A 29.6%; vitamin D 68.5%; vitamin B12 68%; folic acid 25.5%) and over 50% of women had two or more concurrent deficiencies as well as multiple infections. Multiple regression models highlighted differences in variables associated with CRP between pregnancy and lactation. In pregnancy, CRP was positively associated with greater indoor wood smoke exposure, caries and hookworm and negatively associated with Ascaris and vaginal Lactobacillus and Bacteroides/Gardnerella scores. Consistent with this, greater wood smoke exposure, caries as well as higher diplococcal infection score increased the odds of trimester-elevated CRP concentrations whereas longer gestational age lowered the likelihood of a trimester-elevated CRP. During lactation, folic acid deficiency was associated with higher CRP whereas parity, number of eosinophils and Mobiluncus score were associated with lower CRP. Also, a higher BMI and Trichomonas vaginalis score increased the likelihood of an elevated

  8. Competition and co-existence of Zoophthora radicans and Pandora blunckii, two co-occurring fungal pathogens of the diamondback moth, Plutella xylostella.

    PubMed

    Guzmán-Franco, Ariel W; Clark, Suzanne J; Alderson, Peter G; Pell, Judith K

    2009-11-01

    The entomopathogenic fungi Zoophthora radicans and Pandora blunckii co-occur in field populations of Plutella xylostella and, therefore, are likely to interact during the infection process. We have investigated the possible outcomes of these interactions in the laboratory. Using four isolates, two of each fungal species, inter-specific interaction experiments were done in Petri dishes and on intact plants. In Petri dish experiments, larvae were inoculated directly using sporulating mats of mycelium, both species had the same opportunity to infect and only the relative concentration of conidia of each pathogen species applied was manipulated. In the intact plant experiments, larvae were placed onto fungus-contaminated plants, inoculation was passive and the probability of infection by either or both species of fungi depended on larval activity and proximity to inoculum. In the Petri dish experiment, the species with the largest concentration of conidia out-competed the other regardless of virulence, and results were similar in the intact plant experiment. The ecological implications for competition or co-existence of these two pathogens in the field are discussed.

  9. The role of indigenous bacterial and fungal soil populations in the biodegradation of crude oil in a desert soil.

    PubMed

    Embar, Keren; Forgacs, Chaim; Sivan, Alex

    2006-08-01

    The biodegradation capacity of indigenous microbial populations was examined in a desert soil contaminated with crude oil. To evaluate biodegradation, soil samples supplemented with 5, 10 or 20% (w/w) of crude oil were incubated for 90 days at 30 degrees C. The effect of augmentation of the soil with vermiculite (50% v/v) as a bulking agent providing increased surface/volume ratio and improved soil aeration was also tested. Maximal biodegradation (91%) was obtained in soil containing the highest concentration of crude oil (20%) and supplemented with vermiculite; only 74% of the oil was degraded in samples containing the same level of crude oil but lacking vermiculite. Gas chromatograms of distilled fractions of crude oil extracted from the soil before and after incubation demonstrated that most of the light and part of the intermediate weight fractions initially present in the oil extracts could not be detected after incubation. Monitoring of microbial population densities revealed an initial decline in bacterial viable counts after exposure to oil, presumably as a result of the crude oil's toxicity. This decline was followed by a steep recovery in microbial population density, then by a moderate increase that persisted until the end of incubation. By contrast, the inhibitory effect of crude oil on the fungal population was minimal. Furthermore, the overall increased growth response of the fungal population, at all three levels of contamination, was about one order of magnitude higher than that of the bacterial population.

  10. Structure and Origin of Xanthomonas arboricola pv. pruni Populations Causing Bacterial Spot of Stone Fruit Trees in Western Europe.

    PubMed

    Boudon, Sylvain; Manceau, Charles; Nottéghem, Jean-Loup

    2005-09-01

    ABSTRACT Xanthomonas arboricola pv. pruni, the causal agent of bacterial spot on stone fruit, was found in 1995 in several orchards in southeastern France. We studied population genetics of this emerging pathogen in comparison with populations from the United States, where the disease was first described, and from Italy, where the disease has occurred since 1920. Four housekeeping genes (atpD, dnaK, efp, and glnA) and the intergenic transcribed spacer region were sequenced from a total of 3.9 kb of sequences, and fluorescent amplified fragment length polymorphism (FAFLP) analysis was performed. A collection of 64 X. arboricola pv. pruni strains, including 23 strains from France, was analyzed. The X. arboricola pv. pruni population had a low diversity because no sequence polymorphisms were observed. Population diversity revealed by FAFLP was lower for the West European population than for the American population. The same bacterial genotype was detected from five countries on three continents, a geographic distribution that can be explained by human-aided migration of bacteria. Our data support the hypothesis that the pathogen originated in the United States and subsequently has been disseminated to other stone-fruit-growing regions of the world. In France, emergence of this disease was due to a recent introduction of the most prevalent genotype of the bacterium found worldwide.

  11. Bacterial Population Dynamics in a Laboratory Activated Sludge Reactor Monitored by Pyrosequencing of 16S rRNA

    PubMed Central

    Satoh, Hiroyasu; Oshima, Kenshiro; Suda, Wataru; Ranasinghe, Purnika; Li, Ning; Gunawardana, Egodaha Gedara Wasana; Hattori, Masahira; Mino, Takashi

    2013-01-01

    The microbial population in a laboratory activated sludge reactor was monitored for 245 d at 75 time points by pyrosequencing of 16S rRNA. Synthetic wastewater was used as the influent, and the reactor was operated under the same conditions throughout the experiment. The behaviors of different bacterial operational taxonomic units (OTUs) were observed. Multiple OTUs showed periodic propagation and recession. One of the OTUs showed sharp recession, which suggests that cells in the OTU were selectively killed. The behaviors of different phylogenetic lineages of Candidatus ‘Accumulibacter phosphatis’ were also visualized. It was clearly demonstrated that pyrosequencing with barcoded primers is a very effective tool to clarify the dynamics of the bacterial population in activated sludge. PMID:23100021

  12. Dissociation of a population of Pectobacterium atrosepticum SCRI1043 in tobacco plants: formation of bacterial emboli and dormant cells.

    PubMed

    Gorshkov, Vladimir; Daminova, Amina; Ageeva, Marina; Petrova, Olga; Gogoleva, Natalya; Tarasova, Nadezhda; Gogolev, Yuri

    2014-05-01

    The population dynamics of Pectobacterium atrosepticum SCRI1043 (Pba) within tobacco plants was monitored from the time of inoculation until after long-term preservation of microorganisms in the remnants of dead plants. We found and characterised peculiar structures that totally occlude xylem vessels, which we have named bacterial emboli. Viable but non-culturable (VBN) Pba cells were identified in the remnants of dead plants, and the conditions for resuscitation of these VBN cells were established. Our investigation shows that dissociation of the integrated bacterial population during plant colonisation forms distinct subpopulations and cell morphotypes, which are likely to perform specific functions that ensure successful completion of the life cycle within the plant.

  13. Co-existence of PHF6 and NOTCH1 mutations in adult T-cell acute lymphoblastic leukemia

    PubMed Central

    LI, MIN; XIAO, LICHAN; XU, JINGYAN; ZHANG, RUN; GUO, JINGJING; OLSON, JUSTIN; WU, YUJIE; LI, JIANYONG; SONG, CHUNHUA; GE, ZHENG

    2016-01-01

    T-cell acute lymphoblastic leukemia (T-ALL) results from the collaboration of multiple genetic abnormalities in the transformation of T-cell progenitors. Plant homeodomain finger protein 6 (PHF6) has recently been established as a key tumor suppressor, which is mutated in T-ALL; however, the clinical significance of PHF6 mutations has not been fully determined in adult T-ALL. In the present study, amplification of the PHF6 exons was performed, followed by DNA sequencing to identify the genomic mutations and examine the expression of PHF6 in adult patients with T-ALL. The correlation between PHF6 mutations and clinical features was also analyzed using a χ2 test, and between PHF6 mutations and survival curve using the Kaplan-Meier methods. PHF6 mutations were detected in 27.1% of the Chinese adults with T-ALL (16/59), 10 of which were found to be novel mutations. A significantly lower expression level of PHF6 was observed in T-ALL patients with PHF6 mutations compared with those without mutations. Of the observed mutations in PHF6, 6/16 were frame-shift mutations, indicating a PHF6 dysfunction in those patients. Of note, PHF6 mutations were found to be significantly associated with older age, lower hemoglobin levels, higher frequency of CD13 positivity and higher incidence of splenomegaly or lymphadenopathy. Furthermore, PHF6 mutations were found to be significantly correlated with Notch homolog 1, translocation-associated (Drosophila) (NOTCH1) mutations. The patients with T-ALL with co-existence of the two mutations had a significantly shorter event-free survival and a poor prognosis. The present results indicated that PHF6 is inactivated in adult T-ALL, due to its low expression and mutations. The present data indicated the synergistic effect of PHF6 and NOTCH1 mutations, as well as their co-existence, on the oncogenesis of adult T-ALL, and their potential as a prognostic marker for the disease. PMID:27347093

  14. Co-existence of PHF6 and NOTCH1 mutations in adult T-cell acute lymphoblastic leukemia.

    PubMed

    Li, Min; Xiao, Lichan; Xu, Jingyan; Zhang, Run; Guo, Jingjing; Olson, Justin; Wu, Yujie; Li, Jianyong; Song, Chunhua; Ge, Zheng

    2016-07-01

    T-cell acute lymphoblastic leukemia (T-ALL) results from the collaboration of multiple genetic abnormalities in the transformation of T-cell progenitors. Plant homeodomain finger protein 6 (PHF6) has recently been established as a key tumor suppressor, which is mutated in T-ALL; however, the clinical significance of PHF6 mutations has not been fully determined in adult T-ALL. In the present study, amplification of the PHF6 exons was performed, followed by DNA sequencing to identify the genomic mutations and examine the expression of PHF6 in adult patients with T-ALL. The correlation between PHF6 mutations and clinical features was also analyzed using a χ(2) test, and between PHF6 mutations and survival curve using the Kaplan-Meier methods. PHF6 mutations were detected in 27.1% of the Chinese adults with T-ALL (16/59), 10 of which were found to be novel mutations. A significantly lower expression level of PHF6 was observed in T-ALL patients with PHF6 mutations compared with those without mutations. Of the observed mutations in PHF6, 6/16 were frame-shift mutations, indicating a PHF6 dysfunction in those patients. Of note, PHF6 mutations were found to be significantly associated with older age, lower hemoglobin levels, higher frequency of CD13 positivity and higher incidence of splenomegaly or lymphadenopathy. Furthermore, PHF6 mutations were found to be significantly correlated with Notch homolog 1, translocation-associated (Drosophila) (NOTCH1) mutations. The patients with T-ALL with co-existence of the two mutations had a significantly shorter event-free survival and a poor prognosis. The present results indicated that PHF6 is inactivated in adult T-ALL, due to its low expression and mutations. The present data indicated the synergistic effect of PHF6 and NOTCH1 mutations, as well as their co-existence, on the oncogenesis of adult T-ALL, and their potential as a prognostic marker for the disease.

  15. Effect of Co-existing Chronic Obstructive Pulmonary Disease and Cognitive Impairment on Health Outcomes in Older Adults

    PubMed Central

    Chang, Sandy S.; Chen, Shu; McAvay, Gail J.; Tinetti, Mary E.

    2012-01-01

    Objectives To determine the extent to which the co-occurrence of chronic obstructive pulmonary disease (COPD) and cognitive impairment affect adverse health outcomes in older adults. Design Multi-center longitudinal cohort study. Setting California, Pennsylvania, Maryland, and North Carolina. Participants Three thousand ninety-three community-dwelling adults aged ≥65 from the Cardiovascular Health Study. Four hundred thirty-one participants had chronic obstructive pulmonary disease (COPD) at study baseline. Measurements Follow-up began at the second CHS visit and continued for three years. Spirometric criteria for airflow limitation served to establish COPD, using the Lambda-Mu-Sigma method, which accounts for age-related changes in lung function. Cognitive impairment was evaluated by the modified Mini Mental State Exam and claims data. Outcomes were respiratory-related and all-cause hospitalizations and death. Results Participants with co-existing COPD and cognitive impairment had the highest rates of respiratory-related (adjusted hazard ratio [HR]=4.10, 95%CI=1.86–9.05) and all-cause hospitalizations (HR= 1.34, 95%CI=1.00–1.80) and death (HR=2.29, 95%CI=1.18–4.45). In particular, individuals with both conditions had a 48% higher rate of all-cause hospitalizations (adjusted synergy index [SI]=1.48, 95%CI=0.19–11.31) and nearly a three-fold higher rate of death (SI=2.74, 95%CI=0.43–17.32) than the sum of risks for each respective outcome associated with having COPD or cognitive impairment alone. However, tests for interaction were not statistically significant for the presence of synergism between both conditions relative to any of the outcomes. Therefore, we cannot conclude that the combined effect of COPD and cognitive impairment is greater than additive. Conclusion Co-existing COPD and cognitive impairment have an additive effect on respiratory-related and all-cause hospitalizations and death. Optimizing outcomes in older adults with COPD and

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

    PubMed

    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.

  17. Short-Term Effects of South Louisiana and Kuwait Crude Oils on Glucose Utilization by Marine Bacterial Populations

    PubMed Central

    Alexander, Steve K.; Schwarz, John R.

    1980-01-01

    Two crude oils, South Louisiana and Kuwait, were examined for their impact on glucose utilization by bacterial populations from the Gulf of Mexico. The uptake and mineralization of [U-14C]glucose was assayed after a 4- to 23-h exposure to various concentrations of added crude oil (0, 0.001, 0.01, and 0.1% [vol/vol]). The effects of oil were determined in a total of 15 sediment and 13 water samples collected from offshore, open-bay, and salt marsh environments. The utilization of glucose by bacterial populations usually was not affected by added oil; in 10 sediment and 11 water samples, oil had no significant effect on either glucose uptake or mineralization. Stimulation by oil was recorded in four sediment samples. Oil inhibition occurred in one sediment and two water samples, but only in the presence of the highest concentration of added oil, i.e., 0.1%. Our data suggest that short-term exposure to either South Louisiana or Kuwait crude oil, even at 0.1%, usually has no toxic effect on glucose utilization by marine bacterial populations. Images PMID:16345613

  18. Short-term effects of South louisiana and kuwait crude oils on glucose utilization by marine bacterial populations.

    PubMed

    Alexander, S K; Schwarz, J R

    1980-08-01

    Two crude oils, South Louisiana and Kuwait, were examined for their impact on glucose utilization by bacterial populations from the Gulf of Mexico. The uptake and mineralization of [U-C]glucose was assayed after a 4- to 23-h exposure to various concentrations of added crude oil (0, 0.001, 0.01, and 0.1% [vol/vol]). The effects of oil were determined in a total of 15 sediment and 13 water samples collected from offshore, open-bay, and salt marsh environments. The utilization of glucose by bacterial populations usually was not affected by added oil; in 10 sediment and 11 water samples, oil had no significant effect on either glucose uptake or mineralization. Stimulation by oil was recorded in four sediment samples. Oil inhibition occurred in one sediment and two water samples, but only in the presence of the highest concentration of added oil, i.e., 0.1%. Our data suggest that short-term exposure to either South Louisiana or Kuwait crude oil, even at 0.1%, usually has no toxic effect on glucose utilization by marine bacterial populations.

  19. Molecular detection of marine bacterial populations on beaches contaminated by the Nakhodka tanker oil-spill accident.

    PubMed

    Kasai, Y; Kishira, H; Syutsubo, K; Harayama, S

    2001-04-01

    In January 1997, the tanker Nakhodka sank in the Japan Sea, and more than 5000 tons of heavy oil leaked. The released oil contaminated more than 500 km of the coastline, and some still remained even by June 1999. To investigate the long-term influence of the Nakhodka oil spill on marine bacterial populations, sea water and residual oil were sampled from the oil-contaminated zones 10, 18, 22 and 29 months after the accident, and the bacterial populations in these samples were analysed by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA fragments. The dominant DGGE bands were sequenced, and the sequences were compared with those in DNA sequence libraries. Most of the bacteria in the sea water samples were classified as the Cytophaga-Flavobacterium-Bacteroides phylum, alpha-Proteobacteria or cyanobacteria. The bacteria detected in the oil paste samples were different from those detected in the sea water samples; they were types related to hydrocarbon degraders, exemplified by strains closely related to Sphingomonas subarctica and Alcanivorax borkumensis. The sizes of the major bacterial populations in the oil paste samples ranged from 3.4 x 10(5) to 1.6 x 10(6) bacteria per gram of oil paste, these low numbers explaining the slow rate of natural attenuation.

  20. Population Dynamics of a Salmonella Lytic Phage and Its Host: Implications of the Host Bacterial Growth Rate in Modelling

    PubMed Central

    Santos, Sílvio B.; Carvalho, Carla; Azeredo, Joana; Ferreira, Eugénio C.

    2014-01-01

    The prevalence and impact of bacteriophages in the ecology of bacterial communities coupled with their ability to control pathogens turn essential to understand and predict the dynamics between phage and bacteria populations. To achieve this knowledge it is essential to develop mathematical models able to explain and simulate the population dynamics of phage and bacteria. We have developed an unstructured mathematical model using delay-differential equations to predict the interactions between a broad-host-range Salmonella phage and its pathogenic host. The model takes into consideration the main biological parameters that rule phage-bacteria interactions likewise the adsorption rate, latent period, burst size, bacterial growth rate, and substrate uptake rate, among others. The experimental validation of the model was performed with data from phage-interaction studies in a 5 L bioreactor. The key and innovative aspect of the model was the introduction of variations in the latent period and adsorption rate values that are considered as constants in previous developed models. By modelling the latent period as a normal distribution of values and the adsorption rate as a function of the bacterial growth rate it was possible to accurately predict the behaviour of the phage-bacteria population. The model was shown to predict simulated data with a good agreement with the experimental observations and explains how a lytic phage and its host bacteria are able to coexist. PMID:25051248

  1. Bacterial meningitis in diabetes patients: a population-based prospective study

    PubMed Central

    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

  2. Sorting out co-occurrence of rare monogenic retinopathies: Stargardt disease co-existing with congenital stationary night blindness.

    PubMed

    Huynh, Nancy; Jeffrey, Brett G; Turriff, Amy; Sieving, Paul A; Cukras, Catherine A

    2014-03-01

    Inherited retinal diseases are uncommon, and the likelihood of having more than one hereditary disorder is rare. Here, we report a case of Stargardt disease and congenital stationary night blindness (CSNB) in the same patient, and the identification of two novel in-frame deletions in the GRM6 gene. The patient underwent an ophthalmic exam and visual function testing including: visual acuity, color vision, Goldmann visual field, and electroretinography (ERG). Imaging of the retina included fundus photography, spectral-domain optical coherence tomography (OCT), and fundus autofluorescence. Genomic DNA was PCR-amplified for analysis of all coding exons and flanking splice sites of both the ABCA4 and GRM6 genes. A 46-year-old woman presented with recently reduced central vision and clinical findings of characteristic yellow flecks consistent with Stargardt disease. However, ERG testing revealed an ERG phenotype unusual for Stargardt disease but consistent with CSNB1. Genetic testing revealed two previously reported mutations in the ABCA4 gene and two novel deletions in the GRM6 gene. Diagnosis of concurrent Stargardt disease and CSNB was made on the ophthalmic history, clinical examination, ERG, and genetic testing. This case highlights that clinical tests need to be taken in context, and that co-existing retinal dystrophies and degenerations should be considered when clinical impressions and objective data do not correlate.

  3. Design of co-existence parallel periodic surface structure induced by picosecond laser pulses on the Al/Ti multilayers

    NASA Astrophysics Data System (ADS)

    Petrović, Suzana; Peruško, D.; Kovač, J.; Panjan, P.; Mitrić, M.; Pjević, D.; Kovačević, A.; Jelenković, B.

    2017-09-01

    Formation of periodic nanostructures on the Ti/5x(Al/Ti)/Si multilayers induced by picosecond laser pulses is studied in order to better understand the formation of a laser-induced periodic surface structure (LIPSS). At fluence slightly below the ablation threshold, the formation of low spatial frequency-LIPSS (LSFL) oriented perpendicular to the direction of the laser polarization is observed on the irradiated area. Prolonged irradiation while scanning results in the formation of a high spatial frequency-LIPSS (HSFL), on top of the LSFLs, creating a co-existence parallel periodic structure. HSFL was oriented parallel to the incident laser polarization. Intermixing between the Al and Ti layers with the formation of Al-Ti intermetallic compounds was achieved during the irradiation. The intermetallic region was formed mostly within the heat affected zone of the sample. Surface segregation of aluminium with partial ablation of the top layer of titanium was followed by the formation of an ultra-thin Al2O3 film on the surface of the multi-layered structure.

  4. Heterogeneous water supply affects growth and benefits of clonal integration between co-existing invasive and native Hydrocotyle species

    PubMed Central

    Wang, Yong-Jian; Bai, Yun-Fei; Zeng, Shi-Qi; Yao, Bin; Wang, Wen; Luo, Fang-Li

    2016-01-01

    Spatial patchiness and temporal variability in water availability are common in nature under global climate change, which can remarkably influence adaptive responses of clonal plants, i.e. clonal integration (translocating resources between connected ramets). However, little is known about the effects of spatial patchiness and temporal heterogeneity in water on growth and clonal integration between congeneric invasive and native Hydrocotyle species. In a greenhouse experiment, we subjected severed or no severed (intact) fragments of Hydrocotyle vulgaris, a highly invasive species in China, and its co-existing, native congener H. sibthorpioides to different spatial patchiness (homogeneous and patchy) and temporal interval (low and high interval) in water supply. Clonal integration had significant positive effects on growth of both species. In the homogeneous water conditions, clonal integration greatly improved the growth in fragments of both species under low interval in water. However, in the patchy water conditions, clonal integration significantly increased growth in both ramets and fragments of H. vulgaris under high interval in water. Therefore, spatial patchiness and temporal interval in water altered the effects of clonal integration of both species, especially for H. vulgaris. The adaptation of H. vulgaris might lead to invasive growth and potential spread under the global water variability. PMID:27439691

  5. The co-existence of depression, anxiety and post-traumatic stress symptoms in the perinatal period: A systematic review.

    PubMed

    Agius, Andee; Xuereb, Rita Borg; Carrick-Sen, Debbie; Sultana, Roberta; Rankin, Judith

    2016-05-01

    to identify and appraise the current international evidence regarding the presence and prevalence of the co-existence of depression, anxiety and post-traumatic stress symptoms in the antenatal and post partum period. using a list of keywords, Medline, CINHAL, Cochrane Library, EMBASE, PsychINFO, Web of Science and the Index of Theses and Conference Proceedings (Jan 1960 - Jan 2015) were systematically searched. Experts in the field were contacted to locate papers that were in progress or in press. Reference lists from relevant review articles were searched. Inclusion criteria included full papers published in English reporting concurrent depression, anxiety and post-traumatic stress symptoms in pregnant and post partum women. A validated data extraction review tool was used. 3424 citations were identified. Three studies met the full inclusion criteria. All reported findings in the postnatal period. No antenatal studies were identified. The prevalence of triple co-morbidity was relatively low ranging from 2% to 3%. triple co-morbidity does occur, although the prevalence appears to be low. Due to the presentation of complex symptoms, women with triple co-morbidity are likely to be difficult to identify, diagnose and treat. Clinical staff should be aware of the potential of complex symptomatology. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Newly diagnosed T1 diabetes presenting with hypoglycemia due to simultaneous co-existence of Addison disease.

    PubMed

    Glynn, Nigel; Bashir, Mohammed; Smith, Diarmuid; Thompson, Christopher J

    2014-09-01

    Type 1 diabetes mellitus (TIDM) classically presents with symptomatic hyperglycemia and many patients develop diabetic ketoacidosis prior to their diagnosis. However, non-classical presentation or co-presentation with associated diseases may delay diagnosis or lead to challenges in acute, clinical management. An 18-yr-old girl presented to hospital with severe, symptomatic hypoglycemia. Clinical history and serum electrolyte concentrations suggested a diagnosis of adrenal insufficiency. She remained hypoglycemic until glucocorticoid replacement was commenced, at which point she developed persistent hyperglycemia requiring insulin therapy. Subsequent follow up confirmed the diagnosis of Addison's disease (AD), the treatment of which unmasked co-existing type 1 diabetes. Autoimmune diseases often cluster together in affected patients and first-degree relatives. Approximately 1 in 200 patients with T1DM develop AD. However, months or more commonly years usually elapse between the presentation of different autoimmune conditions. The co-diagnosis T1DM and AD in the acute setting is rare. Moreover, the first presentation of T1DM with severe hypoglycemia is even more exceptional. This case highlights the need for vigilance during the acute, emergency management of patients with autoimmune conditions and, in particular, to consider the possibility of concurrent antibody-mediated diseases which may need to be addressed during resuscitation. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  7. Mycorrhizas and soil ecosystem function of co-existing woody vegetation islands at the alpine tree line.

    PubMed

    Wang, Lixia; Otgonsuren, Burenjargal; Godbold, Douglas L

    2017-01-01

    Picea abies, Pinus mugo and Rhododendron ferrugineum co-exist at the alpine tree line, and can have different mycorrhizal communities. The activity and diversity of mycorrhizal fungi are considered to be important factors in regulation of soil function. At a tree line site and a lower elevation site in the Austrian Alps, the community structure of ectomycorrhiza on Picea abies and Pinus mugo was determined. The activity of surface enzymes was determined on ectomycorrhizal and ericoid mycorrhizal roots. In soils, the activity of a range of enzymes, nitrogen (N) mineralization and biomass decomposition were determined. The community structure of the ectomycorrhizal community of Picea abies and Pinus mugo differed strongly, but the average activity of surface enzymes of the ectomycorrhizal communities was similar. A lower root surface enzyme activity was determined on Rhododendron ferrugineum. Soil N-mineralization under Rhododendron ferrugineum was significantly lower than under Picea abies and Pinus mugo. In soil, the activity of a range of enzymes did not differ at the tree line but differed between the tree line and the lower elevation sites. The different ectomycorrhizal communities on Picea abies and Pinus mugo and ericoid mycorrhizas on Rhododendron ferrugineum support similar ecosystem functions in soil.

  8. The co-existence of pure red cell aplasia and autoimmune haemolytic anaemia in a child with malignant lymphoma.

    PubMed

    Ahmed, Suhair Abbas; Hassan, Rosline

    2005-07-01

    The association between pure red cell aplasia (PRCA) and autoimmune haemolytic anaemia (AIHA) has rarely been reported. PRCA represents an isolated process, characterized by normochromic, normocytic anaemia, reticulocytopenia and erythroid hypoplasia in the bone marrow, and may be attributable to infection with Parvo virus B19. AIHA is a condition in which peripheral red blood cell destruction is induced by the presence of autoantibodies. However, the co-existence of these conditions is very rare, since only few cases of PRCA and AIHA associated with malignant lymphoma (ML) were reported. A case of PRCA and AIHA was detected and described, for the first time in Malaysia, in a 10-year-old child suffering from non-Hodgkin lymphoma from the Department of Haematology, Universiti Sains Malaysia. Following the induction course of chemotherapy, the patient turned anaemic, with tendency for red cell clumping, reticulocytopenia and anisocytosis. AIHA was suspected in spite of the weak Coomb reaction obtained. The bone marrow aspirate revealed the presence of giant pronormoblasts, suggesting PRCA. Serological tests for Parvo virus and other viruses were negative.

  9. Co-existence of Echinococcus granulosus infection and cancer metastasis in the liver correlates with reduced Th1 immune responses.

    PubMed

    Turhan, N; Esendagli, G; Ozkayar, O; Tunali, G; Sokmensuer, C; Abbasoglu, O

    2015-01-01

    A possible relationship between cancer and Echinococcus granulosus infection has been postulated. As T cells are critical players in immune responses against both infections and malignancies, in an experimental model of secondary echinococcosis and breast cancer, this study aims to observe the progression of cancer and to determine the characters of T-cell responses. 4T1 breast tumour cells were subcutaneously injected into mammary region, whereas protoscoleces were intraperitoneally inoculated into the mice. Hydatid cysts, tumours and metastases were determined with macroscopic and histopathological evaluation. T cells found in spleen, liver and tumour were characterised by flow cytometric analysis of CD3, CD4, CD8, CD25, CCR5, CCR3, IL-4 and IFN-γ. In the mice inoculated both with protoscoleces and with breast tumour cells, increased frequency of cancer metastasis was observed in the liver. The amount of CD4(+) T cells was increased in the liver and in the spleen of mice infected with E. granulosus. However, co-existence of echinococcosis and metastatic lesions in the liver was associated with significant reduction in the IFN-γ(+) and CCR5(+) Th1 cells and increase in the CD25(+) T cells. Our results may indicate an immunological link between cystic echinococcosis and cancer that allows tumour metastasis to flourish in the liver.

  10. Successful Outcome of Twin Gestation with Partial Mole and Co-Existing Live Fetus: A Case Report

    PubMed Central

    Rathod, Setu; Rani, Reddi; John, Lopamudra B.

    2015-01-01

    Sad fetus syndrome comprising of a live twin gestation with a hydatidiform mole is a rare entity. The condition is even rarer when the co-existing live fetus is associated with a partial mole than a complete mole. We report the case of a 24-year-old G2P1L1 at 28 weeks gestation who presented to our casualty in the second stage of labour. She had a previous ultrasound scan at 13 weeks which showed a live fetus with a focal area of multicystic placenta. She delivered an alive preterm male fetus weighing 1.32 kg vaginally. Following expulsion of normal placenta of the live fetus, partial mole was expelled. The fetus was admitted to neonatal ICU and discharged after two weeks. Soon after delivery, β-hCG (human chorionic gonadotropin) was 1,21,993 mIU/ml which decreased to 30mIU/ml within two weeks. The patient was discharged with advice of regular follow up of β-hCG reports. PMID:26436001

  11. IGH@ translocations co-exist with other primary rearrangements in B-cell precursor acute lymphoblastic leukemia

    PubMed Central

    Jeffries, Sally J.; Jones, Lisa; Harrison, Christine J.; Russell, Lisa J.

    2014-01-01

    Primary established genetic abnormalities in B-cell precursor acute lymphoblastic leukemia include high hyperdiploidy (51–65 chromosomes), the translocations t(12;21)(p13;q22)/ETV6-RUNX1 fusion and t(9;22)(q34;q11)/BCR-ABL1 fusion, MLL rearrangements and intrachromosomal amplification of chromosome 21. These rearrangements are of prognostic and therapeutic relevance and are usually mutually exclusive. We identified 28 patients at diagnosis with both a primary genetic rearrangement and an immunoglobulin heavy chain locus translocation using chromosomal analysis and fluorescence in situ hybridization. Among these patients, the immunoglobulin heavy chain locus translocation partner gene was identified in six (CRLF2, CEBPA, CEBPB, TRA/D@, IGF2BP1 and IGK@). Clonal architecture was investigated in 17 patients using multiple color interphase fluorescence in situ hybridization analysis, which showed that the translocation was acquired as a secondary abnormality in ten patients, in four patients the etiology was undetermined and in three patients it was observed in a separate clone from the primary chromosomal rearrangement. These findings demonstrate the co-existence of immunoglobulin heavy chain locus translocations with other primary chromosomal rearrangements either in the same or separate clones, which may have prognostic significance in B-cell precursor acute lymphoblastic leukemia. Clinical trials: UKALLXII: Study ID n. ISRCTN77346223 and ALL2003: Study ID n. ISRCTN07355119 PMID:24816234

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

    NASA Astrophysics Data System (ADS)

    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 the presence of 0.65 g/L of nZnO and nAg. In contrast, there was no significant difference (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. Comparison of fermentation of diets of variable composition and microbial populations in the rumen of sheep and Rusitec fermenters. II. Protozoa population and diversity of bacterial communities.

    PubMed

    Martínez, M E; Ranilla, M J; Tejido, M L; Saro, C; Carro, M D

    2010-08-01

    Four ruminally and duodenally cannulated sheep and 8 Rusitec fermenters were used to determine the effects of dietary characteristics on microbial populations and bacterial diversity. The purpose of the study was to assess how closely fermenters can mimic the differences between diets found in vivo. The 4 experimental diets contained forage to concentrate (F:C) ratios of 70:30 (high forage; HF) or 30:70 (high concentrate; HC) with either alfalfa hay (A) or grass hay (G) as the forage. Total bacterial numbers were greater in the rumen of sheep fed HF diets compared with those fed HC diets, whereas the opposite was found in fermenters. The numbers of cellulolytic bacteria were not affected by F:C ratio in any fermentation system, but cellulolytic numbers were 2.7 and 1.8 times greater in sheep than in fermenters for HF and HC diets, respectively. Neither total bacterial nor cellulolytic numbers were affected by the type of forage in sheep or fermenters. Decreasing F:C ratio increased total protozoa and Entodiniae numbers in sheep by about 29 and 25%, respectively, but it had no effect in fermenters. Isotrichidae and Ophryoscolecinae numbers in sheep were not affected by changing F:C ratio, but both disappeared completely from fermenters fed HC diets. Total protozoa and Entodiniae numbers were greater in sheep fed A diets than in those fed G diets, whereas the opposite was found in fermenters. Results indicate that under the conditions of the present study, protozoa population in Rusitec fermenters was not representative of that in the rumen of sheep fed the same diets. In addition, protozoa numbers in fermenters were 121 and 226 times lower than those in the sheep rumen for HF and HC diets, respectively. The automated ribosomal intergenic spacer analysis of the 16S ribosomal DNA was used to analyze the diversity of liquid- and solid-associated bacteria in both systems. A total of 170 peaks were detected in the automated ribosomal intergenic spacer analysis

  14. Hydrogeochemistry and coal-associated bacterial populations from a methanogenic coal bed

    USGS Publications Warehouse

    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

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

    PubMed

    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.

  16. Comparative modifications in bacterial gill-endosymbiotic populations of the two bivalves Codakia orbiculata and Lucina pensylvanica during bacterial loss and reacquisition.

    PubMed

    Elisabeth, Nathalie H; Caro, Audrey; Césaire, Thierry; Mansot, Jean-Louis; Escalas, Arthur; Sylvestre, Marie-Noëlle; Jean-Louis, Patrick; Gros, Olivier

    2014-09-01

    Until now, the culture of sulphur-oxidizing bacterial symbionts associated with marine invertebrates remains impossible. Therefore, few studies focused on symbiont's physiology under stress conditions. In this study, we carried out a comparative experiment based on two different species of lucinid bivalves (Codakia orbiculata and Lucina pensylvanica) under comparable stress factors. The bivalves were starved for 6 months in sulphide-free filtered seawater. For C. orbiculata only, starved individuals were then put back to the field, in natural sediment. We used in situ hybridization, flow cytometry and X-ray fluorescence to characterize the symbiont population hosted in the gills of both species. In L. pensylvanica, no decrease in symbiont abundance was observed throughout the starvation experiment, whereas elemental sulphur slowly decreased to zero after 3 months of starvation. Conversely, in C. orbiculata, symbiont abundance within bacteriocytes decreased rapidly and sulphur from symbionts disappeared during the first weeks of the experiment. The modifications of the cellular characteristics (SSC--relative cell size and FL1--genomic content) of the symbiotic populations along starvation were not comparable between species. Return to the sediment of starved C. orbiculata individuals led to a rapid (2-4 weeks) recovery of symbiotic cellular characteristics, comparable with unstressed symbionts. These results suggest that endosymbiotic population regulation is host-species-dependent in lucinids. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  17. Drastic changes in aquatic bacterial populations from the Cuatro Cienegas Basin (Mexico) in response to long-term environmental stress.

    PubMed

    Pajares, Silvia; Eguiarte, Luis E; Bonilla-Rosso, German; Souza, Valeria

    2013-12-01

    Understanding the changes of aquatic microbial community composition in response to changes in temperature and ultraviolet irradiation is relevant for predicting biogeochemical modifications in the functioning of natural microbial communities under global climate change scenarios. Herein we investigate shifts in the bacterioplankton composition in response to long-term changes in temperature and UV radiation. For this purpose, 15 mesocosms were seeded with composite aquatic microbial communities from natural pools within the Cuatro Cienegas Basin (Mexican Chihuahuan desert) and were subject to different temperatures and UV conditions. 16S rRNA gene clone libraries were obtained from water samples at the mid-point (4 months) and the end of the experiment (8 months). An increase in bacterial diversity over time was found in the treatment of constant temperature and UV protection, which suggests that stable environments promote the establishment of complex and diverse bacterial community. Drastic changes in the phylogenetic bacterioplankton composition and structure were observed in response to fluctuating temperature and increasing UV radiation and temperature. Fluctuating temperature induced the largest decrease of bacterial richness during the experiment, indicating that frequent temperature changes drive the reduction in abundance of several species, most notably autotrophs. The long-term impact of these environmental stresses reduced diversity and selected for generalist aquatic bacterial populations, such as Porphyrobacter. These changes at the community level occur at an ecological time scale, suggesting that under global warming scenarios cascade effects on the food web are possible if the microbial diversity is modified.

  18. Changes in the bacterial populations of the highly alkaline saline soil of the former lake Texcoco (Mexico) following flooding.

    PubMed

    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.

  19. Diversity and dynamics of rare and of resident bacterial populations in coastal sands

    PubMed Central

    Gobet, Angélique; Böer, Simone I; Huse, Susan M; van Beusekom, Justus E E; Quince, Christopher; Sogin, Mitchell L; Boetius, Antje; Ramette, Alban

    2012-01-01

    Coastal sands filter and accumulate organic and inorganic materials from the terrestrial and marine environment, and thus provide a high diversity of microbial niches. Sands of temperate climate zones represent a temporally and spatially highly dynamic marine environment characterized by strong physical mixing and seasonal variation. Yet little is known about the temporal fluctuations of resident and rare members of bacterial communities in this environment. By combining community fingerprinting via pyrosequencing of ribosomal genes with the characterization of multiple environmental parameters, we disentangled the effects of seasonality, environmental heterogeneity, sediment depth and biogeochemical gradients on the fluctuations of bacterial communities of marine sands. Surprisingly, only 3–5% of all bacterial types of a given depth zone were present at all times, but 50–80% of them belonged to the most abundant types in the data set. About 60–70% of the bacterial types consisted of tag sequences occurring only once over a period of 1 year. Most members of the rare biosphere did not become abundant at any time or at any sediment depth, but varied significantly with environmental parameters associated with nutritional stress. Despite the large proportion and turnover of rare organisms, the overall community patterns were driven by deterministic relationships associated with seasonal fluctuations in key biogeochemical parameters related to primary productivity. The maintenance of major biogeochemical functions throughout the observation period suggests that the small proportion of resident bacterial types in sands perform the key biogeochemical processes, with minimal effects from the rare fraction of the communities. PMID:21975598

  20. Bacterial population kinetics on hands during 2 consecutive surgical hand disinfection procedures.

    PubMed

    Kampf, Günter; Ostermeyer, Christiane; Kohlmann, Thomas

    2008-06-01

    Although consecutive surgical hand disinfections is common clinical practice, the effect on the bacterial density on hands has not been studied for all commonly used hand rubs. We studied the effect of 2 consecutive applications of hand rubs on resident bacterial hand flora. A propanol-based hand rub (PBHR; Sterillium) and the reference alcohol (60% n-propanol) were tested in a Latin-square design according to EN 12791. The first application of the PBHR was always for 1.5 minutes; the second application was for 1.5, 1, or 0.5 minutes. The reference alcohol was always applied for 3 minutes. Pre-values and post-values were obtained in accordance with EN 12791. The first reference disinfection reduced the bacterial density by 2.87 log(10) (immediate efficacy) and 2.27 log(10) (after 3 hours). The PBHR yielded a similar reduction. Immediately after the second reference disinfection, bacterial density was reduced by 0.45 log(10). Application of the PBHR yielded greater reductions of 0.71 log(10) (after 0.5 minute), 0.79 log(10) (after 1 minute), and 1.12 log(10) (after 1.5 minutes). The difference between all treatments was not significant (P = .089; Friedman test). After 3 hours, bacterial density was further decreased by 1.11 log(10) (reference disinfection), 1.89 log(10) (PBHR, 1 minute), 1.67 log(10) (PBHR, 1.5 minutes), and 1.08 log(10) (PBHR, 0.5 minute). The difference between all treatments was significant (P = .005), but none of the short treatments with the PBHR was significantly less effective than the reference treatment (P > .05; Wilcoxon-Wilcox test). Overall, a simple 1.5-minute application of a well-formulated PBHR for surgical hand disinfection keeps the bacterial density as low as possible ("irreducible minimum") even in 2 consecutive surgical procedures of 3 hours.

  1. Periodicity in Age-Resolved Populations

    NASA Astrophysics Data System (ADS)

    Esipov, Sergei

    We discuss the interplay between the non-linear diffusion and age-resolved population dynamics. Depending on the age properties of collective migration the system may exhibit continuous joint expansion of all ages or continuous expansion with age segregation. Between these two obvious limiting regimes there is an interesting window of periodic expansion, which has been previously used by us in modeling bacterial colonies of Proteus mirabilis. In order to test whether the age-dependent collective migration leads to periodicity in other systems we performed a Fourier analysis of historical data on ethnic expansions and found multiple co-existing periods of activity.

  2. Water use efficiency of twenty-five co-existing Patagonian species growing under different soil water availability.

    PubMed

    Golluscio, R A; Oesterheld, M

    2007-11-01

    The variation of plant water use efficiency (WUE) with water availability has two interacting components: a plastic response, evident when individuals of the same genotype are compared (e.g. wet versus dry years), and an interspecific response, evident when different species living in habitats with different water availability are compared. We analysed the WUE of 25 Patagonian species that belong to four life forms (grasses, shrubs, annual herbs and perennial herbs) in relation to the climatic conditions of 2 years and the mean historic water availability experienced by each species. To estimate water availability, we calculated the effective soil water potential (EWP) of each species, based on available information about soil water dynamics, phenology and root system structure. To estimate WUE, we used isotopic discrimination of leaf C (Delta(13)C) and mean annual water vapour difference between leaves and atmosphere (Deltae) measured in situ. For the plastic response, for every species and life form, WUE increased from the dry to the wet year. We hypothesize that photosynthesis was less nutrient limited in the wet than in the dry year, facilitating higher net photosynthesis rates per unit of stomatal conductance in the wet year. For the interspecific response, WUE was lower in species native to drier habitats than in species native to wetter habitats. This response was mostly accounted for by a decrease in Deltae with EWP. Annual herbs, which avoid drought in time (they have the earliest growth cycle), and shrubs, which avoid drought in space (they have the deepest roots), showed the highest EWP and WUE. We conclude that the conventional wisdom which states that the highest WUE occurs within a species during the driest years, and among species in the driest habitats, does not always hold true, and that co-existing life forms drastically differ in water availability and water economy.

  3. Occurrence of co-existing bla VIM-2 and bla NDM-1 in clinical isolates of Pseudomonas aeruginosa from India.

    PubMed

    Paul, Deepjyoti; Dhar, Debadatta; Maurya, Anand Prakash; Mishra, Shweta; Sharma, Gauri Dutt; Chakravarty, Atanu; Bhattacharjee, Amitabha

    2016-05-06

    bla VIM-2 harboring Pseudomonas aeruginosa has been reported worldwide and considered as the most prevalent metallo-β-lactamase after NDM which are found horizontally transferable and mostly associated with integron gene cassettes. The present study investigates the genetic background, transmission dynamics as well as stability of bla VIM-2 in clinical isolates of P. aeruginosa harbor bla NDM-1 as well which were collected from October 2012 to September 2013. Two P. aeruginosa strains harboring bla VIM-2 along with bla NDM-1 were isolated from Silchar Medical College and Hospital, India. Genetic environment of these resistance determinants was determined and transferability was checked by transformation and conjugation assay which was further confirmed by Southern hybridization. Replicon typing was performed to determine the incompatibility group of the resistant plasmid and their stability was checked by serial passage method. Antimicrobial susceptibility pattern of the isolates was determined and their clonal relatedness was checked by pulsed field gel electrophoresis. bla VIM-2 was found to be horizontally transferable through an Inc F type plasmid of approximately 30 kb in size. bla VIM-2 was found to be associated with integron gene cassette and was flanked by two different types of cassette arrays. Both the isolates were co-harboring bla NDM-1 which was carried within Inc N type of plasmid with an approximate 24 kb in size and associated with ISAba125 in their upstream region. Reduced susceptibility rate as well as high MIC range was observed in case of wild strains and transformants carrying bla VIM-2 and bla NDM-1. The detection of this co-existence of multiple carbapenem resistance genes in this part of world is worrisome and further investigation is required in order to trace the source and to initiate proper treatment option.

  4. Experimental model considerations for the study of protein-energy malnutrition co-existing with ischemic brain injury.

    PubMed

    Prosser-Loose, Erin J; Smith, Shari E; Paterson, Phyllis G

    2011-05-01

    Protein-energy malnutrition (PEM) affects ~16% of patients at admission for stroke. We previously modeled this in a gerbil global cerebral ischemia model and found that PEM impairs functional outcome and influences mechanisms of ischemic brain injury and recovery. Since this model is no longer reliable, we investigated the utility of the rat 2-vessel occlusion (2-VO) with hypotension model of global ischemia for further study of this clinical problem. Male, Sprague-Dawley rats were exposed to either control diet (18% protein) or PEM induced by feeding a low protein diet (2% protein) for 7d prior to either global ischemia or sham surgery. PEM did not significantly alter the hippocampal CA1 neuron death (p = 0.195 by 2-factor ANOVA) or the increase in dendritic injury caused by exposure to global ischemia. Unexpectedly, however, a strong trend was evident for PEM to decrease the consistency of hippocampal damage, as shown by an increased incidence of unilateral or no hippocampal damage (p=0.069 by chi-square analysis). Although PEM caused significant changes to baseline arterial blood pH, pO(2), pCO(2), and fasting glucose (p<0.05), none of these variables (nor hematocrit) correlated significantly with CA1 cell counts in the malnourished group exposed to 2-VO (p>0.269). Intra-ischemic tympanic temperature and blood pressure were strictly and equally controlled between ischemic groups. We conclude that co-existing PEM confounded the consistency of hippocampal injury in the 2-VO model. Although the mechanisms responsible were not identified, this model of brain ischemia should not be used for studying this co-morbidity factor. © 2011 Bentham Science Publishers Ltd.

  5. Identification of Bacterial Populations in Drinking Water Using 16S rRNA-Based Sequence Analyses

    EPA Science Inventory

    Intracellular RNA is rapidly degraded in stressed cells and is more unstable outside of the cell than DNA. As a result, RNA-based methods have been suggested to study the active microbial fraction in environmental matrices. The aim of this study was to identify bacterial populati...

  6. Independent Shifts of Abundant and Rare Bacterial Populations across East Antarctica Glacial Foreland

    PubMed Central

    Yan, Wenkai; Ma, Hongmei; Shi, Guitao; Li, Yuansheng; Sun, Bo; Xiao, Xiang; Zhang, Yu

    2017-01-01

    Glacial forelands are extremely sensitive to temperature changes and are therefore appropriate places to explore the development of microbial communities in response to climate-driven deglaciation. In this study, we investigated the bacterial communities that developed at the initial stage of deglaciation using space-for-time substitution in the foreland of an ice sheet in Larsemann Hills. A series of soil samples across the glacial foreland were deeply sequenced with 16S rRNA gene amplicon sequencing to determine the bacterial community, including both abundant bacteria, which contribute more to geobiochemistry, and rare bacteria, which serve as a seed bank for diversity. Our results show that abundant bacterial communities were more sensitive to changing conditions in the early stages of deglaciation than rare community members. Moreover, among the environmental parameters tested, which included total organic carbon, pH, and moisture of the soils, ice thickness was the most influential factor affecting the community structure of abundant bacteria. These results show the different effects of abundant and rare bacteria on community shifts and highlight ice thickness as the primary factor affecting the bacterial community in the early stages of deglaciation. The response of microbial community to climate change can be predicted with more certainty in this polar region. PMID:28848537

  7. Polystyrene influences bacterial assemblages in Arenicola marina-populated aquatic environments in vitro.

    PubMed

    Kesy, Katharina; Oberbeckmann, Sonja; Müller, Felix; Labrenz, Matthias

    2016-12-01

    Plastic is ubiquitous in global oceans and constitutes a newly available habitat for surface-associated bacterial assemblages. Microplastics (plastic particles <5 mm) are especially susceptible to ingestion by marine organisms, as the size of these particles makes them available also to lower trophic levels. Because many marine invertebrates harbour potential pathogens in their guts, we investigated whether bacterial assemblages on polystyrene are selectively modified during their passage through the gut of the lugworm Arenicola marina and are subsequently able to develop pathogenic biofilms. We also examined whether polystyrene acts as a vector for gut biofilm assemblages after subsequent incubation of the egested particles in seawater. Our results showed that after passage through the digestive tract of A. marina, the bacterial assemblages on polystyrene particles and reference glass beads became more similar, harbouring common sediment bacteria. By contrast, only in the presence of polystyrene the potential symbiont Amphritea atlantica was enriched in the investigated biofilms, faeces, and water. Thus, especially in areas of high polystyrene contamination, this polymer may impact the bacterial composition of different habitats, with as yet unknown consequences for the respective ecosystems.

  8. Spread and transmission of bacterial pathogens in experimental populations of the nematode Caenorhabditis elegans.

    PubMed

    Diaz, S Anaid; Restif, Olivier

    2014-09-01

    Caenorhabditis elegans is frequently used as a model species for the study of bacterial virulence and innate immunity. In recent years, diverse mechanisms contributing to the nematode's immune response to bacterial infection have been discovered. Yet despite growing interest in the biochemical and molecular basis of nematode-bacterium associations, many questions remain about their ecology. Although recent studies have demonstrated that free-living nematodes could act as vectors of opportunistic pathogens in soil, the extent to which worms may contribute to the persistence and spread of these bacteria has not been quantified. We conducted a series of experiments to test whether colonization of and transmission between C. elegans nematodes could enable two opportunistic pathogens (Salmonella enterica and Pseudomonas aeruginosa) to spread on agar plates occupied by Escherichia coli. We monitored the transmission of S. enterica and P. aeruginosa from single infected nematodes to their progeny and measured bacterial loads both within worms and on the plates. In particular, we analyzed three factors affecting the dynamics of bacteria: (i) initial source of the bacteria, (ii) bacterial species, and (iii) feeding behavior of the host. Results demonstrate that worms increased the spread of bacteria through shedding and transmission. Furthermore, we found that despite P. aeruginosa's relatively high transmission rate among worms, its pathogenic effects reduced the overall number of worms colonized. This study opens new avenues to understand the role of nematodes in the epidemiology and evolution of pathogenic bacteria in the environment.

  9. Population number, viability, and taxonomic composition of the bacterial nanoforms in iron-manganic concretions

    NASA Astrophysics Data System (ADS)

    Lysak, L. V.; Kadulin, M. S.; Konova, I. A.; Lapygina, E. V.; Ivanov, A. V.; Zvyagintsev, D. G.

    2013-06-01

    It is shown for the first time that a significant part of the bacteria (up to 40%) in the iron-manganic concretions of soddy-podzolic and soddy meadow soils are represented by nanoforms; their number reaches 600-700 million cells/g. Judging from the specific luminescent coloration, the fraction of viable cells among the bacterial nanoforms is very high in the concretions and amounts up to 88-99%. For the first time, the following phyla were identified among the bacterial nanoforms in the concretions with the use of the FISH method: Alphaproteobacteria, Betaproteobacteria, Gammaproteobateria, Deltaproteobacteria, Acidobacteria, and Planctomycetes. The Gammaproteobacteria phylum predominated in the concretions from the soddy-podzolic soil, and the Deltaproteobacteria phylum predominated in the concretions from the soddy meadow soil. In the alluvial meadow soil, the Alphaproteobacteria, Betaproteobacteria, and Acidobacteria phyla were found. The significant number and portion of bacterial nanoforms in the concretions, their high vitality, and their taxonomic diversity allow us to conclude that the bacterial nanoforms play an important role in the processes taking place in the concretions.

  10. Identification of Bacterial Populations in Drinking Water Using 16S rRNA-Based Sequence Analyses

    EPA Science Inventory

    Intracellular RNA is rapidly degraded in stressed cells and is more unstable outside of the cell than DNA. As a result, RNA-based methods have been suggested to study the active microbial fraction in environmental matrices. The aim of this study was to identify bacterial populati...

  11. Prevalence of gastrointestinal bacterial pathogens in a population of zoo animals.

    PubMed

    Stirling, J; Griffith, M; Blair, I; Cormican, M; Dooley, J S G; Goldsmith, C E; Glover, S G; Loughrey, A; Lowery, C J; Matsuda, M; McClurg, R; McCorry, K; McDowell, D; McMahon, A; Cherie Millar, B; Nagano, Y; Rao, J R; Rooney, P J; Smyth, M; Snelling, W J; Xu, J; Moore, J E

    2008-04-01

    Faecal prevalence of gastrointestinal bacterial pathogens, including Campylobacter, Escherichia coli O157:H7, Salmonella, Shigella, Yersinia, as well as Arcobacter, were examined in 317 faecal specimens from 44 animal species in Belfast Zoological Gardens, during July-September 2006. Thermophilic campylobacters including Campylobacter jejuni, Campylobacter coli and Campylobacter lari, were the most frequently isolated pathogens, where members of this genus were isolated from 11 animal species (11 of 44; 25%). Yersinia spp. were isolated from seven animal species (seven of 44; 15.9%) and included, Yersinia enterocolitica (five of seven isolates; 71.4%) and one isolate each of Yersinia frederiksenii and Yersinia kristensenii. Only one isolate of Salmonella was obtained throughout the entire study, which was an isolate of Salmonella dublin (O 1,9,12: H g, p), originating from tiger faeces after enrichment. None of the animal species found in public contact areas of the zoo were positive for any gastrointestinal bacterial pathogens. Also, water from the lake in the centre of the grounds, was examined for the same bacterial pathogens and was found to contain C. jejuni. This study is the first report on the isolation of a number of important bacterial pathogens from a variety of novel host species, C. jejuni from the red kangaroo (Macropus rufus), C. lari from a maned wolf (Chrysocyon brachyurus), Y. kristensenii from a vicugna (Vicugna vicugna) and Y. enterocolitica from a maned wolf and red panda (Ailurus fulgens). In conclusion, this study demonstrated that the faeces of animals in public contact areas of the zoo were not positive for the bacterial gastrointestinal pathogens examined. This is reassuring for the public health of visitors, particularly children, who enjoy this educational and recreational resource.

  12. Characterization of methanotrophic bacterial populations in natural and agricultural aerobic soils of the European Russia

    NASA Astrophysics Data System (ADS)

    Kravchenko, Irina; Sukhacheva, Marina; Kizilova, Anna

    2014-05-01

    Atmospheric methane contributes to about 20% of the total radiative forcing by long-lived greenhouse gases, and microbial methane oxidation in upland soils is the only biological sink of methane. Microbial methane oxidation in aerated upland soils is estimated as 15 - 45 Tg yr-1 or 3-9% of the annual sink. Therefore there is need of extensive research to characterize methanotrophic activity in various ecosystems for possible application to reduce atmospheric methane fluxes and to minimize global climate change. The vast majority of known aerobic methanotrophs belongs to the Proteobacteria and placed in the families Methylococcaceae in the Gammaproteobacteria, and Methylocystaceae and Beijerinckiaceae in the Alphaproteobacteria. Known exceptions include the phylum Verrucomicrobia and uncultured methanotrophs such as Candidatus 'Methylomirabilis oxyfera' affiliated with the 'NC10' phylum. Plenty of studies of aerobic methane oxidation and key players of the process have been performed on various types of soils, and it was found that Methylocystis spp and uncultivated methanotrophs are abundant in upland soils. Two of the uncultured groups are upland soil cluster alphaproteobacteria (USCa) and gammaproteobacteria (USCg), as revealed by cultivation-independent surveys of pmoA diversity. Russia is extremely rich in soil types due to its vast territories, and most of these soils have never been investigated from the aspect of methanotrophy. This study addresses methane oxidation activity and diversity of aerobic methanotrophic bacteria in eight types of natural aerobic soils, four of which also had been under agricultural use. Methane fluxes have been measured by in situ static chamber method and methane oxidation rates in soil samples - by radioisotope tracer (14CH4) technique. Changes in methanotroph diversity and abundance were assessed by cloning and Sanger sequencing, and quantitative real-time PCR of pmoA genes. Methanotrophic population of unmanaged soils turned

  13. Co-Existence of Acinic Cell Carcinoma - Papillary Cystic Variant and Extrapulmonary Tuberculosis – Report of A Case with Brief Review

    PubMed Central

    Vijayshankar, Shivshankar; Sanjay, Manchaiah

    2015-01-01

    Tuberculosis (TB) and cancer are two lethal diseases causing significant morbidity and mortality in developing countries like India. Co-existence of these two disease lead to diagnostic dielemma among the clinicians. Overlapping clinical manifestations lead to delay in diagnosis. We report a case of acinic cell carcinoma –papillary cystic variant of the salivary gland and extra pulmonary tuberculosis in a young female. We emphasize the importance of the awareness of the co-existence of these two diseases and the role of fine needle aspiration cytology in the initial diagnosis. PMID:26500919

  14. Application of a mathematical model to prevent in vivo amplification of antibiotic-resistant bacterial populations during therapy

    PubMed Central

    Jumbe, Nelson; Louie, Arnold; Leary, Robert; Liu, Weiguo; Deziel, Mark R.; Tam, Vincent H.; Bachhawat, Reetu; Freeman, Christopher; Kahn, James B.; Bush, Karen; Dudley, Michael N.; Miller, Michael H.; Drusano, George L.

    2003-01-01

    The worldwide increase in the prevalence of multi-antibiotic–resistant bacteria has threatened the physician’s ability to provide appropriate therapy for infections. The relationship between antimicrobial drug concentration and infecting pathogen population reduction is of primary interest. Using data derived from mice infected with the bacterium Pseudomonas aeruginosa and treated with a fluoroquinolone antibiotic, a mathematical model was developed that described relationships between antimicrobial drug exposures and changes in drug-susceptible and -resistant bacterial subpopulations at an infection site. Dosing regimens and consequent drug exposures that amplify or suppress the emergence of resistant bacterial subpopulations were identified and prospectively validated. Resistant clones selected in vivo by suboptimal regimens were characterized. No mutations were identified in the quinolone resistance–determining regions of gyrA/B or parC/E. However, all resistant clones demonstrated efflux pump overexpression. At base line, MexAB-OprM, MexCD-OprJ, and MexEF-OprN were represented in the drug-resistant population. After 28 hours of therapy, MexCD-OprJ became the predominant pump expressed in the resistant clones. The likelihood of achieving resistance-suppression exposure in humans with a clinically prescribed antibiotic dose was determined. The methods developed in this study provide insight regarding how mathematical models can be used to identify rational dosing regimens that suppress the amplification of the resistant mutant population. PMID:12865415

  15. Application of a mathematical model to prevent in vivo amplification of antibiotic-resistant bacterial populations during therapy.

    PubMed

    Jumbe, Nelson; Louie, Arnold; Leary, Robert; Liu, Weiguo; Deziel, Mark R; Tam, Vincent H; Bachhawat, Reetu; Freeman, Christopher; Kahn, James B; Bush, Karen; Dudley, Michael N; Miller, Michael H; Drusano, George L

    2003-07-01

    The worldwide increase in the prevalence of multi-antibiotic-resistant bacteria has threatened the physician's ability to provide appropriate therapy for infections. The relationship between antimicrobial drug concentration and infecting pathogen population reduction is of primary interest. Using data derived from mice infected with the bacterium Pseudomonas aeruginosa and treated with a fluoroquinolone antibiotic, a mathematical model was developed that described relationships between antimicrobial drug exposures and changes in drug-susceptible and -resistant bacterial subpopulations at an infection site. Dosing regimens and consequent drug exposures that amplify or suppress the emergence of resistant bacterial subpopulations were identified and prospectively validated. Resistant clones selected in vivo by suboptimal regimens were characterized. No mutations were identified in the quinolone resistance-determining regions of gyrA/B or parC/E. However, all resistant clones demonstrated efflux pump overexpression. At base line, MexAB-OprM, MexCD-OprJ, and MexEF-OprN were represented in the drug-resistant population. After 28 hours of therapy, MexCD-OprJ became the predominant pump expressed in the resistant clones. The likelihood of achieving resistance-suppression exposure in humans with a clinically prescribed antibiotic dose was determined. The methods developed in this study provide insight regarding how mathematical models can be used to identify rational dosing regimens that suppress the amplification of the resistant mutant population.

  16. Effect of dietary supplementation of bacteriophage on performance, egg quality and caecal bacterial populations in laying hens.

    PubMed

    Kim, J H; Kim, J W; Shin, H S; Kim, M C; Lee, J H; Kim, G-B; Kil, D Y

    2015-01-01

    1. Bacteriophages (BP) have gained increasing attention as a treatment of bacterial infection for animals. However, the data pertaining to dietary application of BP for laying hens have been limited. 2. This study aimed to investigate the effect of dietary BP on laying performance, egg quality and caecal bacterial populations in laying hens. 3. The dietary BP used in this experiment was a mixture of individual BP targeting Salmonella gallinarum, Salmonella pullorum, Salmonella typhimurium, Salmonella enteritidis, Salmonella derby and Staphylococcus aureus. 4. A total of 360 Hy-Line Brown laying hens of 32 weeks of age were allotted to one of three dietary treatments with 6 replicates in a completely randomised design. The basal diet was prepared, and 0.4 or 0.8 g/kg BP mixture was supplemented to the basal diet. Diets were fed to hens for 8 weeks. 5. Laying performance and egg quality were not affected by dietary treatments. As inclusion levels of BP mixture in diets were increased, the DNA copy numbers for Salmonella spp. in the caecal contents decreased linearly, whereas the DNA copy numbers for Escherichia coli in the caecal contents increased linearly. 6. Results indicate that dietary supplementation of BP mixture decreases the target Salmonella spp. populations but increases Escherichia coli populations in the gastrointestinal tract of laying hens with little impact on laying performance and egg quality.

  17. Analysis of bacterial, fungal and archaeal populations from a municipal wastewater treatment plant developing an innovative aerobic granular sludge process.

    PubMed

    Liu, Jun; Li, Jun; Tao, Yaqiang; Sellamuthu, Balasubramanian; Walsh, Ryan

    2017-01-01

    Mature granules and flocs from aerobic sludge were collected from the wastewater treatment plant (WWTP) treating both municipal and industrial effluents in Haining city China. This plant has been operating under conditions favoring aerobic granular sludge formation, for over 3 years, suggesting that the granules, which stably retained under changing effluent conditions, may contain unique microbial populations. Microbial analysis indicated that the granular sludge was primarily composed of Planctomycetes, Proteobacteria and Bacteroidetes from the bacterial phyla. Interestingly, microbial communities were also observed to be stratified between the structural features of the sludge. For example, Euryarchaeota was found to make up the majority of the archaea found in the granules while Methanosaeta was dominant in the flocs. Additionally, granules were found to contain, 34 phyla and 222 genera of bacteria, 4 phyla and 13 genera of fungi, and 2 phyla and 17 genera of archaea. While flocs contained, 32 phyla and 203 genera of bacteria, 6 phyla and 26 genera of fungi, and 2 phyla and 12 genera of archaea. This biodiversity signifying a preservation of bacterial and archaeal population in granules, and fungal populations in flocs may result from the sedimentary characteristics of the granules. This suggests microbes uniquely associated in the granules are playing a key role in structure formation and stability of the granular ecosystem, which is maintained by the longer sludge retention time.

  18. Effect of dietary probiotic, prebiotic and synbiotic supplementation on performance, immune responses, intestinal morphology and bacterial populations in broilers.

    PubMed

    Salehimanesh, A; Mohammadi, M; Roostaei-Ali Mehr, M

    2016-08-01

    This study was conducted to investigate the effects of probiotic (Primalac), prebiotic (TechnoMos) and synbiotic (Primalac + TechnoMos) supplementation on performance, immune responses, intestinal morphology and bacterial populations of ileum in broilers. A total of 240 one-day-old broiler chicks were randomly divided into four treatment groups which included 60 birds. Control group did not receive any treatment. The chicks in the second, third and fourth groups were fed probiotic (0.9 g/kg), prebiotic (0.9 g/kg) and probiotic (0.9 g/kg) plus probiotic (0.9 g/kg; synbiotic), respectively, at entire period. Daily feed intake, daily weight gain and feed conversion ratio were evaluated. The birds were immunized by sheep red blood cell (SRBC) on days 12 and 29 of age and serum antibody titres were measured on days 28, 35 and 42. Newcastle vaccines administered on days 9, 18 and 27 to chicks and blood samples were collected on day 42. Intestinal morphometric assessment and enumeration of intestinal bacterial populations were performed on day 42. The results indicated that consumption of probiotic, prebiotic and synbiotic had no significant effect on daily feed intake, daily body weight gain, feed conversion ratio, carcass traits, intestinal morphology and bacterial populations of ileum (p > 0.05). Consumption of prebiotic increased total and IgM anti-SRBC titres on days 28 and 42 and antibody titre against Newcastle virus disease on day 42 (p < 0.05). Synbiotic increased only total anti-SRBC on day 28 (p < 0.05). It is concluded that consumption of prebiotic increased humoral immunity in broilers. Therefore, supplementation of diet with prebiotic for improvement of humoral immune responses is superior to synbiotic supplementation. Journal of Animal Physiology and Animal Nutrition © 2016 Blackwell Verlag GmbH.

  19. Bacterial antibiotic resistance studies using in vitro dynamic models: Population analysis vs. susceptibility testing as endpoints of mutant enrichment.

    PubMed

    Firsov, Alexander A; Strukova, Elena N; Portnoy, Yury A; Shlykova, Darya S; Zinner, Stephen H

    2015-09-01

    Emergence of bacterial antibiotic resistance is usually characterised either by population analysis or susceptibility testing. To compare these endpoints in their ability to demonstrate clear relationships with the ratio of 24-h area under the concentration-time curve (AUC24) to the minimum inhibitory concentration (MIC), enrichment of ciprofloxacin-resistant mutants of four clinical isolates of Pseudomonas aeruginosa was studied in an in vitro dynamic model that simulates mono-exponential pharmacokinetics of ciprofloxacin over a wide range of the AUC24/MIC ratios. Each organism was exposed to twice-daily ciprofloxacin for 3 days. Amplification of resistant mutants was monitored by plating on media with 2×, 4×, 8× and 16× MIC of ciprofloxacin. Population analysis data were expressed by the area under the bacterial mutant concentration-time curve (AUBCM). Changes in P. aeruginosa susceptibility were examined by daily MIC determinations. To account for the different susceptibilities of P. aeruginosa strains, post-exposure MICs (MICfinal) were related to the MICs determined with the starting inoculum (MICinitial). For each organism, AUC24/MIC relationships both with AUBCM and MICfinal/MICinitial were bell-shaped, but the latter were more strain-specific than the former. Using combined data on all four isolates, AUBCM showed a better correlation than MICfinal/MICinitial (r(2)=0.75 vs. r(2)=0.53). The shift of MICfinal/MICinitial relative to AUBCM vs. AUC24/MIC curves resulted in a weak correlation between AUBCM and MICfinal/MICinitial (r(2)=0.41). These data suggest that population analysis is preferable to susceptibility testing in bacterial resistance studies and that these endpoints should not be considered interchangeable.

  20. Malaria, anaemia and under-nutrition: three frequently co-existing conditions among preschool children in rural Rwanda.

    PubMed

    Kateera, Fredrick; Ingabire, Chantal M; Hakizimana, Emmanuel; Kalinda, Parfait; Mens, Petra F; Grobusch, Martin P; Mutesa, Leon; van Vugt, Michèle

    2015-11-05

    Malaria, anaemia and under-nutrition are three highly prevalent and frequently co-existing diseases that cause significant morbidity and mortality particularly among children aged less than 5 years. Currently, there is paucity of conclusive studies on the burden of and associations between malaria, anaemia and under-nutrition in Rwanda and comparable sub-Saharan and thus, this study measured the prevalence of malaria parasitaemia, anaemia and under-nutrition among preschool age children in a rural Rwandan setting and evaluated for interactions between and risk determinants for these three conditions. A cross-sectional household (HH) survey involving children aged 6-59 months was conducted. Data on malaria parasitaemia, haemoglobin densities, anthropometry, demographics, socioeconomic status (SES) and malaria prevention knowledge and practices were collected. The prevalences of malaria parasitaemia and anaemia were 5.9 and 7.0 %, respectively, whilst the prevalence of stunting was 41.3 %. Malaria parasitaemia risk differed by age groups with odds ratio (OR) = 2.53; P = 0.04 for age group 24-35 months, OR = 3.5; P = 0.037 for age group 36-47 months, and OR = 3.03; P = 0.014 for age group 48-60 months, whilst a reduced risk was found among children living in high SES HHs (OR = 0.37; P = 0.029). Risk of anaemia was high among children aged ≥12 months, those with malaria parasitaemia (OR = 3.86; P ≤ 0.0001) and children living in HHs of lower SES. Overall, under-nutrition was not associated with malaria parasitaemia. Underweight was higher among males (OR = 1.444; P = 0.019) and children with anaemia (OR = 1.98; P = 0.004). In this study group, four in 10 and one in 10 children were found stunted and underweight, respectively, in an area of low malaria transmission. Under-nutrition was not associated with malaria risk. While the high prevalence of stunting requires urgent response, reductions in malaria parasitaemia and anaemia rates may require, in addition to

  1. Effects of petroleum mixture types on soil bacterial population dynamics associated with the biodegradation of hydrocarbons in soil environments.

    PubMed

    Hamamura, Natsuko; Ward, David M; Inskeep, William P

    2013-07-01

    Soil bacterial population dynamics were examined to assess patterns in microbial response to contamination by different petroleum mixtures with variation in n-alkane profiles or toxic constituents such as pentachlorophenol (PCP). Three soil types from distinct areas of the United States (Montana, Oregon, and Arizona) were used in controlled perturbation experiments containing crude oil, kerosene, diesel, or diesel plus PCP spiked with (14)C-hexadecane or (14)C-tridecane. After a 50-day incubation, 30-70% of added (14)C-alkanes were mineralized to (14)CO₂ in Montana and Oregon soils. In contrast, significantly lower mineralization was observed with diesel or kerosene (< 5%) compared to crude-oil treatment (~45%) in the Arizona soil. Different hydrocarbon mixtures selected both unique and common microbial populations across all three soils. Conversely, the contamination of different soils with the same mixture selected for distinct microbial populations. The most consistent genotype observed, a Rhodococcus-like population, was present in the Montana soil with all mixture types. The addition of PCP selected for PCP-tolerant alkane-degrading specialist populations. The results indicated that petroleum mixture type influenced hydrocarbon degradation rates and microbial population selection and that soil characteristics, especially organic content, could also be an important determinant of community responses to hydrocarbon perturbation. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  2. Resilience of the rhizosphere Pseudomonas and ammonia-oxidizing bacterial populations during phytoextraction of heavy metal polluted soil with poplar.

    PubMed

    Frey, Beat; Pesaro, Manuel; Rüdt, Andreas; Widmer, Franco

    2008-06-01

    We assessed the effects of phytoextraction on the dynamics of Pseudomonas spp. and ammonia-oxidizing bacterial populations in a heavy metal (HM) polluted soil. Hybrid poplars were grown in two-compartment root containers with a medium history (> 4 years) of HM pollution for 13 weeks. Bulk and poplar rhizosphere soils were analysed by denaturing gradient gel electrophoresis (DGGE) of Pseudomonas (sensu stricto) 16S rRNA and amoA gene fragments. DGGE patterns revealed that Pseudomonas and amoA-containing populations in the contaminated soils were markedly different from those in the uncontaminated soils. Pseudomonas and amoA profiles appeared to be stable over time in the bulk soils. In contrast, contaminated rhizosphere soils revealed a clear shift of populations with removal of HM becoming similar or at least shifted to the populations of the uncontaminated soils. The effect of phytoextraction was, however, not evident in the bulk samples, which still contained large amounts of HM. Cloning and sequencing of dominant DGGE bands revealed that Pseudomonas were phylogenetically related to the Pseudomonas fluorescens cluster and the amoA sequences to Nitrosospira spp. At the last sampling, major prominent band sequences from contaminated rhizosphere soils were identical to sequences obtained from uncontaminated rhizosphere soils, indicating that the populations were dominated by the same phylotypes. This study suggests that two taxonomically different populations are able to recover after the relief of HM stress by phytoextraction practices, whereas bulk microbial activities still remained depressed.

  3. The effect of wheat prebiotics on the gut bacterial population and iron status of iron deficient broiler chickens

    PubMed Central

    2014-01-01

    Background Currently, there is a lot of interest in improving gut health, and consequently increasing Fe absorption, by managing the colonic microbial population. This is traditionally done by the consumption of probiotics, live microbial food supplements. However, an alternative, and often very effective approach, is the consumption of food ingredients known as prebiotics. Fructans and arabinoxylans are naturally occurring non-digestible oligosaccharides in wheat that exhibit prebiotic properties and may enhance intestinal iron (Fe) absorption. The aim of this study was to assess the effect of prebiotics from wheat on Fe bioavailability in vitro (Caco-2 cells) and in vivo (broiler chickens, Gallus gallus). Methods In the current study, the effect of intra-amniotic administration of wheat samples extracts at 17 d of embryonic incubation on the Fe status and possible changes in the bacterial population in intestinal content of broiler hatchlings were investigated. A group of 144 eggs were injected with the specified solution (1 ml per egg) into the amniotic fluid. Immediately after hatch (21 d) and from each treatment group, 10 chicks were euthanized and their small intestine, liver and cecum were removed for relative mRNA abundance of intestinal Fe related transporters, relative liver ferritin amounts and bacterial analysis of cecal content, respectively. Results The in vivo results are in agreement with the in vitro observations, showing no differences in the hatchling Fe status between the treatment groups, as Fe bioavailability was not increased in vitro and no significant differences were measured in the intestinal expression of DMT1, Ferroportin and DcytB in vivo. However, there was significant variation in relative amounts of bifidobacteria and lactobacilli in the intestinal content between the treatments groups, with generally more bifidobacteria being produced with increased prebiotic content. Conclusions In this study we showed that prebiotics naturally

  4. The effect of wheat prebiotics on the gut bacterial population and iron status of iron deficient broiler chickens.

    PubMed

    Tako, Elad; Glahn, Raymond P; Knez, Marija; Stangoulis, James Cr

    2014-06-13

    Currently, there is a lot of interest in improving gut health, and consequently increasing Fe absorption, by managing the colonic microbial population. This is traditionally done by the consumption of probiotics, live microbial food supplements. However, an alternative, and often very effective approach, is the consumption of food ingredients known as prebiotics. Fructans and arabinoxylans are naturally occurring non-digestible oligosaccharides in wheat that exhibit prebiotic properties and may enhance intestinal iron (Fe) absorption. The aim of this study was to assess the effect of prebiotics from wheat on Fe bioavailability in vitro (Caco-2 cells) and in vivo (broiler chickens, Gallus gallus). In the current study, the effect of intra-amniotic administration of wheat samples extracts at 17 d of embryonic incubation on the Fe status and possible changes in the bacterial population in intestinal content of broiler hatchlings were investigated. A group of 144 eggs were injected with the specified solution (1 ml per egg) into the amniotic fluid. Immediately after hatch (21 d) and from each treatment group, 10 chicks were euthanized and their small intestine, liver and cecum were removed for relative mRNA abundance of intestinal Fe related transporters, relative liver ferritin amounts and bacterial analysis of cecal content, respectively. The in vivo results are in agreement with the in vitro observations, showing no differences in the hatchling Fe status between the treatment groups, as Fe bioavailability was not increased in vitro and no significant differences were measured in the intestinal expression of DMT1, Ferroportin and DcytB in vivo. However, there was significant variation in relative amounts of bifidobacteria and lactobacilli in the intestinal content between the treatments groups, with generally more bifidobacteria being produced with increased prebiotic content. In this study we showed that prebiotics naturally found in wheat grains/bread products

  5. Defining the Estimated Core Genome of Bacterial Populations Using a Bayesian Decision Model

    PubMed Central

    van Tonder, Andries J.; Mistry, Shilan; Bray, James E.; Hill, Dorothea M. C.; Cody, Alison J.; Farmer, Chris L.; Klugman, Keith P.; von Gottberg, Anne; Bentley, Stephen D.; Parkhill, Julian; Jolley, Keith A.; Maiden, Martin C. J.; Brueggemann, Angela B.

    2014-01-01

    The bacterial core genome is of intense interest and the volume of whole genome sequence data in the public domain available to investigate it has increased dramatically. The aim of our study was to develop a model to estimate the bacterial core genome from next-generation whole genome sequencing data and use this model to identify novel genes associated with important biological functions. Five bacterial datasets were analysed, comprising 2096 genomes in total. We developed a Bayesian decision model to estimate the number of core genes, calculated pairwise evolutionary distances (p-distances) based on nucleotide sequence diversity, and plotted the median p-distance for each core gene relative to its genome location. We designed visually-informative genome diagrams to depict areas of interest in genomes. Case studies demonstrated how the model could identify areas for further study, e.g. 25% of the core genes with higher sequence diversity in the Campylobacter jejuni and Neisseria meningitidis genomes encoded hypothetical proteins. The core gene with the highest p-distance value in C. jejuni was annotated in the reference genome as a putative hydrolase, but further work revealed that it shared sequence homology with beta-lactamase/metallo-beta-lactamases (enzymes that provide resistance to a range of broad-spectrum antibiotics) and thioredoxin reductase genes (which reduce oxidative stress and are essential for DNA replication) in other C. jejuni genomes. Our Bayesian model of estimating the core genome is principled, easy to use and can be applied to large genome datasets. This study also highlighted the lack of knowledge currently available for many core genes in bacterial genomes of significant global public health importance. PMID:25144616

  6. Effect of DNA extraction and sample preservation method on rumen bacterial population.

    PubMed

    Fliegerova, Katerina; Tapio, Ilma; Bonin, Aurelie; Mrazek, Jakub; Callegari, Maria Luisa; Bani, Paolo; Bayat, Alireza; Vilkki, Johanna; Kopečný, Jan; Shingfield, Kevin J; Boyer, Frederic; Coissac, Eric; Taberlet, Pierre; Wallace, R John

    2014-10-01

    The comparison of the bacterial profile of intracellular (iDNA) and extracellular DNA (eDNA) isolated from cow rumen content stored under different conditions was conducted. The influence of rumen fluid treatment (cheesecloth squeezed, centrifuged, filtered), storage temperature (RT, -80 °C) and cryoprotectants (PBS-glycerol, ethanol) on quality and quantity parameters of extracted DNA was evaluated by bacterial DGGE analysis, real-time PCR quantification and metabarcoding approach using high-throughput sequencing. Samples clustered according to the type of extracted DNA due to considerable differences between iDNA and eDNA bacterial profiles, while storage temperature and cryoprotectants additives had little effect on sample clustering. The numbers of Firmicutes and Bacteroidetes were lower (P < 0.01) in eDNA samples. The qPCR indicated significantly higher amount of Firmicutes in iDNA sample frozen with glycerol (P < 0.01). Deep sequencing analysis of iDNA samples revealed the prevalence of Bacteroidetes and similarity of samples frozen with and without cryoprotectants, which differed from sample stored with ethanol at room temperature. Centrifugation and consequent filtration of rumen fluid subjected to the eDNA isolation procedure considerably changed the ratio of molecular operational taxonomic units (MOTUs) of Bacteroidetes and Firmicutes. Intracellular DNA extraction using bead-beating method from cheesecloth sieved rumen content mixed with PBS-glycerol and stored at -80 °C was found as the optimal method to study ruminal bacterial profile. Copyright © 2013 Elsevier Ltd. All rights reserved.

  7. Defining the estimated core genome of bacterial populations using a Bayesian decision model.

    PubMed

    van Tonder, Andries J; Mistry, Shilan; Bray, James E; Hill, Dorothea M C; Cody, Alison J; Farmer, Chris L; Klugman, Keith P; von Gottberg, Anne; Bentley, Stephen D; Parkhill, Julian; Jolley, Keith A; Maiden, Martin C J; Brueggemann, Angela B

    2014-08-01

    The bacterial core genome is of intense interest and the volume of whole genome sequence data in the public domain available to investigate it has increased dramatically. The aim of our study was to develop a model to estimate the bacterial core genome from next-generation whole genome sequencing data and use this model to identify novel genes associated with important biological functions. Five bacterial datasets were analysed, comprising 2096 genomes in total. We developed a Bayesian decision model to estimate the number of core genes, calculated pairwise evolutionary distances (p-distances) based on nucleotide sequence diversity, and plotted the median p-distance for each core gene relative to its genome location. We designed visually-informative genome diagrams to depict areas of interest in genomes. Case studies demonstrated how the model could identify areas for further study, e.g. 25% of the core genes with higher sequence diversity in the Campylobacter jejuni and Neisseria meningitidis genomes encoded hypothetical proteins. The core gene with the highest p-distance value in C. jejuni was annotated in the reference genome as a putative hydrolase, but further work revealed that it shared sequence homology with beta-lactamase/metallo-beta-lactamases (enzymes that provide resistance to a range of broad-spectrum antibiotics) and thioredoxin reductase genes (which reduce oxidative stress and are essential for DNA replication) in other C. jejuni genomes. Our Bayesian model of estimating the core genome is principled, easy to use and can be applied to large genome datasets. This study also highlighted the lack of knowledge currently available for many core genes in bacterial genomes of significant global public health importance.

  8. Bacterial reduction of highly concentrated perchlorate: Kinetics and influence of co-existing electron acceptors, temperature, pH and electron donors.

    PubMed

    Zhu, Yanping; Gao, Naiyun; Chu, Wenhai; Wang, Shuaifeng; Xu, Jianhong

    2016-04-01

    Perchlorate reduction kinetics and effects of various environmental conditions on removal of perchlorate from synthetic water were investigated to seek high-strength perchlorate removal using mixed perchlorate reducing bacteria. Results demonstrated that perchlorate (50-1500 mg L(-1)) could be degraded rapidly within 28 h under the optimal conditions. The maximum specific perchlorate reduction rate (qmax) and half saturation constant (Ks) were 0.92 mg-perchlorate (mg-dry weight)(-1) h(-1) and 157.7 mg L(-1), respectively. In the ClO4(-)-NO3(-) systems obvious but recoverable lags were caused in perchlorate reduction and the lag time increased with the ratio of nitrate to perchlorate concentration increasing from 0.5 to 3. While in the ClO4(-)-SO4(2-) systems inhibitions didn't occur until the ratio of sulfate to perchlorate concentration exceeded 10. The optimum temperature and pH value were 35 °C and 6.85, respectively. The optimal acetate-to-perchlorate ratio that could consume all perchlorate and acetate simultaneously was about 2. Dechloromonas, one of the most prominent perchlorate reducing bacteria, was identified as the dominant bacterium in the acclimated culture (69.33% of the whole clones). The study demonstrated that the perchlorate-acclimated mixed microorganisms can readily and efficiently realize reduction of highly concentrated perchlorate in wastewater. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

    PubMed Central

    Maltas, Jeff; Brumm, Peter; Wood, Kevin B.

    2016-01-01

    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. PMID:27764095

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

    PubMed

    Karslake, Jason; Maltas, Jeff; Brumm, Peter; Wood, Kevin B

    2016-10-01

    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. Differences in major bacterial populations in the intestines of mature broilers after feeding virginiamycin or bacitracin methylene disalicylate.

    PubMed

    Neumann, A P; Suen, G

    2015-12-01

    The purpose of this study was to compare the effects of feeding virginiamycin or bacitracin methylene disalicylate (BMD), two in-feed antibiotics typically used by commercial poultry producers in the United States, on the chicken gastrointestinal microbiota. 454 pyrosequencing of the V6-V8 region of the 16S rRNA gene and quantitative PCR were employed to examine the bacterial microbiota and Clostridium perfringens, respectively, in the jejunum and caecum of market-age broiler chickens over four replicate grow-outs. Our results suggest that virginiamycin has a more pronounced impact on broiler gastrointestinal tract bacterial communities, relative to BMD, manifested primarily through significant enrichments in the genus Faecalibacterium in the caecum and a distinct population of Lactobacillus, OTU_02, in both the jejunum and caecum. No evidence for a difference among the diets in Cl. perfringens levels in the jejunum or caecum was observed. This work represents the highest resolution comparison to date of the jejunum and caecum microbiota in broilers fed either virginiamycin or BMD, and provides evidence for specific bacterial OTUs potentially involved in the health and performance benefits typically attributed to these in-feed antibiotics. © 2015 The Society for Applied Microbiology.

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

    PubMed Central

    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

    2015-01-01

    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. PMID:26119183

  13. Characterization of the major bacterial-fungal populations colonizing dandruff scalps in Shanghai, China, shows microbial disequilibrium.

    PubMed

    Wang, Lili; Clavaud, Cécile; Bar-Hen, Avner; Cui, Meng; Gao, Jun; Liu, Yuanyuan; Liu, Chen; Shibagaki, Nakako; Guéniche, Audrey; Jourdain, Roland; Lan, Ke; Zhang, Chiyu; Altmeyer, Ralf; Breton, Lionel

    2015-05-01

    Dandruff is a scalp disorder characterized by the formation of flaky white-yellowish scales due to an altered proliferation and differentiation status; a disrupted barrier function; a decrease in the level of hydration and of natural moisturizing factors (NMF) in the scalp, with a persistent and relapsing inflammatory condition. It was recently reported that an imbalance between bacterial and fungal species colonizing the scalp of French volunteers was associated with dandruff condition. The purpose of the present study was to analyze the major bacterial and fungal species present on the scalp surface of Chinese volunteers and to investigate possible region-related variation in the microbiota linked to dandruff condition. The data obtained from the Chinese populations were highly similar to those obtained in France, confirming that dandruff scalps are associated with a higher incidence of Malassezia restricta and Staphylococcal sp. The ratios of Malassezia to Propionibacterium and Propionibacterium to Staphylococcus were also significantly higher in the dandruff volunteers as compared to normal volunteers, suggesting that equilibrium between the major bacterial and fungal taxa found on the normal scalps is perturbed in the dandruff scalps. The main difference between the French and Shanghai subjects was in their Staphylococcal biota. The results obtained in China and in France suggest that targeting one particular Malassezia sp. by antifungals instead of using large spectrum antifungals and rebalancing the dandruff scalp microbiota could be common approach to improve dandruff condition in the two countries. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  14. Bacterial Populations Colonizing and Degrading Rice Straw in Anoxic Paddy Soil

    PubMed Central

    Weber, Sabine; Stubner, Stephan; Conrad, Ralf

    2001-01-01

    Rice straw is a major substrate for the production of methane, a greenhouse gas, in flooded rice fields. The bacterial community degrading rice straw under anoxic conditions was investigated with molecular methods. Rice straw was incubated in paddy soil anaerobically for 71 days. Denaturing gradient gel electrophoresis (DGGE) of the amplified bacterial 16S rRNA genes showed that the composition of the bacterial community changed during the first 15 days but then was stable until the end of incubation. Fifteen DGGE bands with different signal intensities were excised, cloned, and sequenced. In addition, DNA was extracted from straw incubated for 1 and 29 days and the bacterial 16S rRNA genes were amplified and cloned. From these clone libraries 16 clones with different electrophoretic mobilities on a DGGE gel were sequenced. From a total of 31 clones, 20 belonged to different phylogenetic clusters of the clostridia, i.e., clostridial clusters I (14 clones), III (1 clone), IV (1 clone), and XIVa (4 clones). One clone fell also within the clostridia but could not be affiliated to one of the clostridial clusters. Ten clones grouped closely with the genera Bacillus (3 clones), Nitrosospira (1 clone), Fluoribacter (1 clones), and Acidobacterium (2 clones) and with clone sequences previously obtained from rice field soil (3 clones). The relative abundances of various phylogenetic groups in the rice straw-colonizing community were determined by fluorescence in situ hybridization (FISH). Bacteria were detached from the incubated rice straw with an efficiency of about 80 to 90%, as determined by dot blot hybridization of 16S rRNA in extract and residue. The number of active (i.e., a sufficient number of ribosomes) Bacteria detected with a general eubacterial probe (Eub338) after 8 days of incubation was 61% of the total cell counts. This percentage decreased to 17% after 29 days of incubation. Most (55%) of the active cells on day 8 belonged to the genus Clostridium, mainly

  15. Parental Choice of Schools and Parents' Perceptions of Multicultural and Co-Existence Education: The Case of the Israeli Palestinian-Jewish Bilingual Primary Schools

    ERIC Educational Resources Information Center

    Bekerman, Zvi; Tatar, Moshe

    2009-01-01

    The present research effort aims to better understand parental choice of the Israeli Palestinian-Jewish bilingual primary schools and its implications in contributing (or not) to fostering multicultural and co-existence educational efforts in conflict-ridden societies. The manuscript offers a short description of the educational initiative under…

  16. Parental Choice of Schools and Parents' Perceptions of Multicultural and Co-Existence Education: The Case of the Israeli Palestinian-Jewish Bilingual Primary Schools

    ERIC Educational Resources Information Center

    Bekerman, Zvi; Tatar, Moshe

    2009-01-01

    The present research effort aims to better understand parental choice of the Israeli Palestinian-Jewish bilingual primary schools and its implications in contributing (or not) to fostering multicultural and co-existence educational efforts in conflict-ridden societies. The manuscript offers a short description of the educational initiative under…

  17. Molecular Characterization of Bacterial Populations in Petroleum-Contaminated Groundwater Discharged from Underground Crude Oil Storage Cavities

    PubMed Central

    Watanabe, Kazuya; Watanabe, Kanako; Kodama, Yumiko; Syutsubo, Kazuaki; Harayama, Shigeaki

    2000-01-01

    Petroleum-contaminated groundwater discharged from underground crude oil storage cavities (cavity groundwater) harbored more than 106 microorganisms ml−1, a density 100 times higher than the densities in groundwater around the cavities (control groundwater). To characterize bacterial populations growing in the cavity groundwater, 46 PCR-amplified almost full-length 16S ribosomal DNA (rDNA) fragments were cloned and sequenced, and 28 different sequences were obtained. All of the sequences were affiliated with the Proteobacteria; 25 sequences (43 clones) were affiliated with the epsilon subclass, 2 were affiliated with the beta subclass, and 1 was affiliated with the delta subclass. Two major clusters (designated clusters 1 and 2) were found for the epsilon subclass proteobacterial clones; cluster 1 (25 clones) was most closely related to Thiomicrospira denitrificans (88% identical in nucleotide sequence), while cluster 2 (11 clones) was closely related to Arcobacter spp. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rDNA fragments showed that one band was detected most strongly in cavity groundwater profiles independent of storage oil type and season. The sequence of this major band was identical to the sequences of most of the cluster 1 clones. Fluorescence in situ hybridization (FISH) indicated that the cluster 1 population accounted for 12 to 24% of the total bacterial population. This phylotype was not detected in the control groundwater by DGGE and FISH analyses. These results indicate that the novel members of the epsilon subclass of the Proteobacteria grow as major populations in the petroleum-contaminated cavity groundwater. PMID:11055927

  18. Molecular characterization of bacterial populations in petroleum-contaminated groundwater discharged from underground crude oil storage cavities.

    PubMed

    Watanabe, K; Watanabe, K; Kodama, Y; Syutsubo, K; Harayama, S

    2000-11-01

    Petroleum-contaminated groundwater discharged from underground crude oil storage cavities (cavity groundwater) harbored more than 10(6) microorganisms ml(-1), a density 100 times higher than the densities in groundwater around the cavities (control groundwater). To characterize bacterial populations growing in the cavity groundwater, 46 PCR-amplified almost full-length 16S ribosomal DNA (rDNA) fragments were cloned and sequenced, and 28 different sequences were obtained. All of the sequences were affiliated with the Proteobacteria; 25 sequences (43 clones) were affiliated with the epsilon subclass, 2 were affiliated with the beta subclass, and 1 was affiliated with the delta subclass. Two major clusters (designated clusters 1 and 2) were found for the epsilon subclass proteobacterial clones; cluster 1 (25 clones) was most closely related to Thiomicrospira denitrificans (88% identical in nucleotide sequence), while cluster 2 (11 clones) was closely related to Arcobacter spp. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rDNA fragments showed that one band was detected most strongly in cavity groundwater profiles independent of storage oil type and season. The sequence of this major band was identical to the sequences of most of the cluster 1 clones. Fluorescence in situ hybridization (FISH) indicated that the cluster 1 population accounted for 12 to 24% of the total bacterial population. This phylotype was not detected in the control groundwater by DGGE and FISH analyses. These results indicate that the novel members of the epsilon subclass of the Proteobacteria grow as major populations in the petroleum-contaminated cavity groundwater.

  19. Linking bacterial population dynamics and nutrient removal in the granular sludge biofilm ecosystem engineered for wastewater treatment.

    PubMed

    Weissbrodt, David G; Shani, Noam; Holliger, Christof

    2014-06-01

    Intensive nutrient removal from wastewater in anaerobic-aerobic systems using granular sludge should rely on optimal balances at biofilm and microbial ecology levels. This study targets the impacts of reactor characteristics and fluctuations in operation conditions on nutrient removal and bacterial community structures by means of microbial and numerical ecology methods. The dynamics of both predominant and accompanying populations were investigated with high resolution on temporal and phylogenetic scales in two reactors operated during 5 months with synthetic wastewater. Multivariate analyses highlighted significant correlations from process to microbial scales in the first reactor, whereas nitrification and phosphorus removal might have been affected by oxygen mass transfer limitations with no impact at population level in the second system. The bacterial community continuum of the first reactor was composed of two major antagonistic Accumulibacter-Nitrosomonas-Nitrospira and Competibacter-Cytophaga-Intrasporangiaceae clusters that prevailed under conditions leading to efficient P- (> 95%) and N-removal (> 65%) and altered P- (< 90%) and N-removal (< 60%), respectively. A third cluster independent of performances was dominated by Xanthomonadaceae affiliates that were on average more abundant at 25 °C (31 ± 5%) than at 20 °C (22 ± 4%). Starting from the physiological traits of the numerous phylotypes identified, a conceptual model is proposed as a base for functional analysis in the granular sludge microbiome and for future investigations with complex real wastewater. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  20. Seasonal effects of heat shock on bacterial populations, including artificial Vibrio parahaemolyticus exposure, in the Pacific oyster, Crassostrea gigas.

    PubMed

    Aagesen, Alisha M; Häse, Claudia C

    2014-04-01

    During the warmer summer months, oysters are conditioned to spawn, resulting in massive physiological efforts for gamete production. Moreover, the higher temperatures during the summer typically result in increased bacteria populations in oysters. We hypothesized that these animals are under multiple stresses that lead to possible immune system impairments during the summer months that can possibly lead to death. Here we show that in the summer and the fall animals exposed to a short heat stress respond similarly, resulting in a general trend of more bacteria being found in heat shocked animals than their non-heat shocked counterparts. We also show that naturally occurring bacterial populations are effected by a heat shock. In addition, oysters artificially contaminated with Vibrio parahaemolyticus were also affected by a heat shock. Heat shocked animals contained higher concentrations of V. parahaemolyticus in their tissues and hemolymph than control animals and this was consistent for animals examined during summer and fall. Finally, oyster hemocyte interactions with V. parahaemolyticus differed based on the time of the year. Overall, these findings demonstrate that seasonal changes and/or a short heat shock is sufficient to impact bacterial retention, particularly V. parahaemolyticus, in oysters and this line of research might lead to important considerations for animal harvesting procedures. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. Evolution in an Afternoon: Rapid Natural Selection and Adaptation of Bacterial Populations

    ERIC Educational Resources Information Center

    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…

  2. Evolution in an Afternoon: Rapid Natural Selection and Adaptation of Bacterial Populations

    ERIC Educational Resources Information Center

    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…

  3. Bacterial populations as perfect gases: genomic integrity and diversification tensions in Helicobacter pylori.

    PubMed

    Kang, Josephine; Blaser, Martin J

    2006-11-01

    Microorganisms that persist in single hosts face particular challenges. Helicobacter pylori, an obligate bacterial parasite of the human stomach, has evolved a lifestyle that features interstrain competition and intraspecies cooperation, both of which involve horizontal gene transfer. Microbial species must maintain genomic integrity, yet H. pylori has evolved a complex nonlinear system for diversification that exists in dynamic tension with the mechanisms for ensuring fidelity. Here, we review these tensions and propose that they create a dynamic pool of genetic variants that is sufficiently genetically diverse to allow H. pylori to occupy all of the potential niches in the stomach.

  4. Population Structure of the Bacterial Pathogen Xylella fastidiosa among Street Trees in Washington D.C.

    PubMed Central

    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. PMID:25815838

  5. Population dynamics of an algal bacterial cenosis in closed ecological system

    NASA Astrophysics Data System (ADS)

    Pisman, T. I.; Galayda, Ya. V.; Loginova, N. S.

    The paper deals with microalgae-bacteria interrelationships in the "autotroph-heterotroph" aquatic biotic cycle. Explanations of why and how algal-bacterial ecosystems are formed still remain controversial. The paper presents results of experimental and theoretical investigations of the functioning of the algal-bacterial cenosis (the microalga Chlorella vulgaris and concomitant microflora). The Chlorella microbial community is dominated by representatives of the genus Pseudomonas. Experiments with non-sterile batch cultures of Chlorella on Tamiya medium showed that the biomass of microorganisms increases simultaneously with the increase in microalgal biomass. The microflora of Chlorella can grow on organic substances released by photosynthesizing Chlorella. Microorganisms can also use dying Chlorella cells, i.e. form a "producer-reducer" biocycle. To get a better insight into the cenosis-forming role of microalgae, a mathematical model of the "autotroph-heterotroph" aquatic biotic cycle has been constructed, taking into account the utilization of Chlorella photosynthates and dead cells by microorganisms and the contribution of the components to the nitrogen cycle. A theoretical study showed that the biomass of concomitant bacteria grown on glucose and detritus is larger than the biomass of bacteria utilizing only microalgal photosynthates, which agrees well with the experimental data.

  6. Bacterial and archaeal populations at two shallow hydrothermal vents off Panarea Island (Eolian Islands, Italy).

    PubMed

    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.

  7. Population structure of the bacterial pathogen Xylella fastidiosa among street trees in Washington D.C.

    PubMed

    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.

  8. Bacterial Population in Intestines of Litopenaeus vannamei Fed Different Probiotics or Probiotic Supernatant.

    PubMed

    Sha, Yujie; Liu, Mei; Wang, Baojie; Jiang, Keyong; Qi, Cancan; Wang, Lei

    2016-10-28

    The interactions of microbiota in the gut play an important role in promoting or maintaining the health of hosts. In this study, in order to investigate and compare the effects of dietary supplementation with Lactobacillus pentosus HC-2 (HC-2), Enterococcus faecium NRW-2, or the bacteria-free supernatant of a HC-2 culture on the bacterial composition of Litopenaeus vannamei, Illumina sequencing of the V1-V2 region of the 16S rRNA gene was used. The results showed that unique species exclusively existed in specific dietary groups, and the abundance of Actinobacteria was significantly increased in the intestinal bacterial community of shrimp fed with the bacteria-free supernatant of an HC-2 culture compared with the control. In addition, the histology of intestines of the shrimp from the four dietary groups was also described, but no obvious improvements in the intestinal histology were observed. The findings in this work will help to promote the understanding of the roles of intestinal bacteria in shrimps when fed with probiotics or probiotic supernatant.

  9. Vertical distribution of nitrifying populations in bacterial biofilms from a full-scale nitrifying trickling filter.

    PubMed

    Lydmark, Pär; Lind, Magnus; Sörensson, Fred; Hermansson, Malte

    2006-11-01

    Cryosectioned biofilm from three depths (0.5, 3.0 and 6.0 m) in a full-scale nitrifying trickling filter (NTF) were studied using fluorescence in situ hybridization (FISH). A large number of sections were used to determine how the biofilm thickness, structure and community composition varied with depth along the ammonium concentration gradient in the NTF, and how the ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) were distributed vertically within the biofilm. Both the biofilm thickness and relative biomass content of the biofilm decreased with depth, along with structural differences such as void size and surface roughness. Four AOB populations were found, with two Nitrosomonas oligotropha populations dominating at all depths. A smaller population of Nitrosomonas europaea was present only at 0.5 m, while a population of Nitrosomonas communis increased with depth. The two N. oligotropha populations showed different vertical distribution patterns within the biofilm, indicating different ecophysiologies even though they belong to the same AOB lineage. All NOB were identified as Nitrospira sp., and were generally more associated with the biofilm base than the surface-associated dominating AOB population. Additionally, a small population of anaerobic ammonia-oxidizers was found at 6.0 m, even though the biofilm was well aerated.

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

    NASA Astrophysics Data System (ADS)

    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.

  11. Study on the bacterial midgut microbiota associated to different Brazilian populations of Lutzomyia longipalpis (Lutz & Neiva) (Diptera: Psychodidae).

    PubMed

    Gouveia, Cheryl; Asensi, Marise D; Zahner, Viviane; Rangel, Elizabeth F; Oliveira, Sandra M P de

    2008-01-01

    The bacterial community associated with the midgut of three Brazilian Lutzomyia longipalpis (Lutz & Neiva) populations, two from endemic areas for visceral leishmaniasis (Jacobina, Bahia State and São Luís, Maranhão State) and one from a non-endemic area (Lapinha Cave, Minas Gerais State), was identified. Five groups, 35 females each, from each population were separated; a total of 175 females per collecting area were analyzed. The species identification was based on molecular and traditional bacteriological methods. All bacteria were either affiliated to non-Enterobacteriaceae, such as Acinetobacter, Burkholderia, Flavimonas, Pseudomonas and Stenotrophomonas, or and to Enterobacteriaceae, such as Citrobacter, Enterobacter, Escherichia, Klebsiella, Serratia, Pantoea, Morganella and Weeksella. Stenotrophomonas was found to be associated with all three populations studied. In addition, Serratia spp., which are well documented as laboratory contaminant of insects, were detected only in the Jacobina population. We also discuss the impact of the colonization of insect gut by bacteria on the development and transmission of pathogens.

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

    PubMed Central

    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

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

    PubMed

    Mathis, Roland; Ackermann, Martin

    2016-04-12

    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.

  14. In vitro bacterial growth and in vivo ruminal microbiota populations associated with bloat in steers grazing wheat forage.

    PubMed

    Min, B R; Pinchak, W E; Anderson, R C; Hume, M E

    2006-10-01

    on d 50 for bloated than for nonbloated steers when grazing wheat forage. The molecular analysis of the 16S rDNA showed that 2 different ruminal microbiota populations developed between bloated and nonbloated animals grazing wheat forage. Bloat in cattle grazing wheat pastures may be caused by increased production of biofilm, resulting from a diet-influenced switch in the rumen bacterial population.

  15. Spatial Heterogeneity of Bacterial Populations along an Environmental Gradient at a Shallow Submarine Hydrothermal Vent near Milos Island (Greece)

    PubMed Central

    Sievert, Stefan M.; Brinkhoff, Thorsten; Muyzer, Gerard; Ziebis, Wiebke; Kuever, Jan

    1999-01-01

    The spatial heterogeneity of bacterial populations at a shallow-water hydrothermal vent in the Aegean Sea close to the island of Milos (Greece) was examined at two different times by using acridine orange staining for total cell counts, cultivation-based techniques, and denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rRNA gene fragments. Concurrent with measurements of geochemical parameters, samples were taken along a transect from the center of the vent to the surrounding area. Most-probable-number (MPN) counts of metabolically defined subpopulations generally constituted a minor fraction of the total cell counts; both counting procedures revealed the highest cell numbers in a transition zone from the strongly hydrothermally influenced sediments to normal sedimentary conditions. Total cell counts ranged from 3.2 × 105 cells ml−1 in the water overlying the sediments to 6.4 × 108 cells g (wet weight) of sediment−1. MPN counts of chemolithoautotrophic sulfur-oxidizing bacteria varied between undetectable and 1.4 × 106 cells g−1. MPN counts for sulfate-reducing bacteria and dissimilatory iron-reducing bacteria ranged from 8 to 1.4 × 105 cells g−1 and from undetectable to 1.4 × 106 cells g−1, respectively. DGGE revealed a trend from a diverse range of bacterial populations which were present in approximately equal abundance in the transition zone to a community dominated by few populations close to the center of the vent. Temperature was found to be an important parameter in determining this trend. However, at one sampling time this trend was not discernible, possibly due to storm-induced disturbance of the upper sediment layers. PMID:10473383

  16. Light Suppresses Bacterial Population through the Accumulation of Hydrogen Peroxide in Tobacco Leaves Infected with Pseudomonas syringae pv. tabaci

    PubMed Central

    Cheng, Dan-Dan; Liu, Mei-Jun; Sun, Xing-Bin; Zhao, Min; Chow, Wah S.; Sun, Guang-Yu; Zhang, Zi-Shan; Hu, Yan-Bo

    2016-01-01

    Pseudomonas syringae pv. tabaci (Pst) is a hemibiotrophic bacterial pathogen responsible for tobacco wildfire disease. Although considerable research has been conducted on the tobacco plant’s tolerance to Pst, the role of light in the responses of the photosystems to Pst infection is poorly understood. This study aimed to elucidate the underlying mechanisms of the reduced photosystem damage in tobacco leaves due to Pst infection under light conditions. Compared to dark conditions, Pst infection under light conditions resulted in less chlorophyll degradation and a smaller decline in photosynthetic function. Although the maximal quantum yield of photosystem II (PSII) and the activity of the photosystem I (PSI) complex decreased as Pst infection progressed, damage to PSI and PSII after infection was reduced under light conditions compared to dark conditions. Pst was 17-fold more abundant in tobacco leaves under dark compared to light conditions at 3 days post inoculation (dpi). Additionally, H2O2 accumulated to a high level in tobacco leaves after Pst infection under light conditions; although to a lesser extent, H2O2 accumulation was also significant under dark conditions. Pretreatment with H2O2 alleviated chlorotic lesions and decreased Pst abundance in tobacco leaves at 3 dpi under dark conditions. MV pretreatment had the same effects under light conditions, whereas 3-(3,4-dichlorophenyl)-1,1-dimethylurea pretreatment aggravated chlorotic lesions and increased the Pst population. These results indicate that chlorotic symptoms and the size of the bacterial population are each negatively correlated with H2O2 accumulation. In other words, light appears to suppress the Pst population in tobacco leaves through the accumulation of H2O2 during infection. PMID:27148334

  17. Bacterial Community and “Candidatus Accumulibacter” Population Dynamics in Laboratory-Scale Enhanced Biological Phosphorus Removal Reactors ▿ †

    PubMed Central

    He, Shaomei; Bishop, Forrest I.; McMahon, Katherine D.

    2010-01-01

    “Candidatus Accumulibacter” and total bacterial community dynamics were studied in two lab-scale enhanced biological phosphorus removal (EBPR) reactors by using a community fingerprint technique, automated ribosomal intergenic spacer analysis (ARISA). We first evaluated the quantitative capability of ARISA compared to quantitative real-time PCR (qPCR). ARISA and qPCR provided comparable relative quantification of the two dominant “Ca. Accumulibacter” clades (IA and IIA) detected in our reactors. The quantification of total “Ca. Accumulibacter” 16S rRNA genes relative to that from the total bacterial community was highly correlated, with ARISA systematically underestimating “Ca. Accumulibacter” abundance, probably due to the different normalization techniques applied. During 6 months of normal (undisturbed) operation, the distribution of the two clades within the total “Ca. Accumulibacter” population was quite stable in one reactor while comparatively dynamic in the other reactor. However, the variance in the clade distribution did not appear to affect reactor performance. Instead, good EBPR activity was positively associated with the abundance of total “Ca. Accumulibacter.” Therefore, we concluded that the different clades in the system provided functional redundancy. We disturbed the reactor operation by adding nitrate together with acetate feeding in the anaerobic phase to reach initial reactor concentrations of 10 mg/liter NO3-N for 35 days. The reactor performance deteriorated with a concomitant decrease in the total “Ca. Accumulibacter” population, suggesting that a population shift was the cause of performance upset after a long exposure to nitrate in the anaerobic phase. PMID:20601516

  18. Diversity of Endophytic Bacterial Populations and Their Interaction with Xylella fastidiosa in Citrus Plants

    PubMed Central

    Araújo, Welington L.; Marcon, Joelma; Maccheroni, Walter; van Elsas, Jan Dirk; van Vuurde, Jim W. L.; Azevedo, João Lúcio

    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 cultivation-independent techniques. The endophytic communities were assessed in surface-disinfected citrus branches by plating and denaturing gradient gel electrophoresis (DGGE). Dominant isolates were characterized by fatty-acid methyl ester analysis as Bacillus pumilus, Curtobacterium flaccumfaciens, Enterobacter cloacae, Methylobacterium spp. (including Methylobacterium extorquens, M. fujisawaense, M. mesophilicum, M. radiotolerans, and M. zatmanii), Nocardia sp., Pantoea agglomerans, and Xanthomonas campestris. We observed a relationship between CVC symptoms and the frequency of isolation of species of Methylobacterium, the genus that we most frequently isolated from symptomatic plants. In contrast, we isolated C. flaccumfaciens significantly more frequently from asymptomatic plants than from those with symptoms of CVC while P. agglomerans was frequently isolated from tangerine (Citrus reticulata) and sweet-orange (C. sinensis) plants, irrespective of whether the plants were symptomatic or asymptomatic or showed symptoms of CVC. DGGE analysis of 16S rRNA gene fragments amplified from total plant DNA resulted in several bands that matched those from the bacterial isolates, indicating that DGGE profiles can be used to detect some endophytic bacteria of citrus plants. However, some bands had no match with any isolate, suggesting the occurrence of other, nonculturable or as yet uncultured, endophytic bacteria. A specific band with a high G+C ratio was observed only in asymptomatic plants. The higher frequency of C. flaccumfaciens in asymptomatic plants suggests a role for this organism in the resistance of plants to CVC. PMID:12324338

  19. Diversity of endophytic bacterial populations and their interaction with Xylella fastidiosa in citrus plants.

    PubMed

    Araújo, Welington L; Marcon, Joelma; Maccheroni, Walter; Van Elsas, Jan Dirk; Van Vuurde, Jim W L; Azevedo, João Lúcio

    2002-10-01

    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 cultivation-independent techniques. The endophytic communities were assessed in surface-disinfected citrus branches by plating and denaturing gradient gel electrophoresis (DGGE). Dominant isolates were characterized by fatty-acid methyl ester analysis as Bacillus pumilus, Curtobacterium flaccumfaciens, Enterobacter cloacae, Methylobacterium spp. (including Methylobacterium extorquens, M. fujisawaense, M. mesophilicum, M. radiotolerans, and M. zatmanii), Nocardia sp., Pantoea agglomerans, and Xanthomonas campestris. We observed a relationship between CVC symptoms and the frequency of isolation of species of Methylobacterium, the genus that we most frequently isolated from symptomatic plants. In contrast, we isolated C. flaccumfaciens significantly more frequently from asymptomatic plants than from those with symptoms of CVC while P. agglomerans was frequently isolated from tangerine (Citrus reticulata) and sweet-orange (C. sinensis) plants, irrespective of whether the plants were symptomatic or asymptomatic or showed symptoms of CVC. DGGE analysis of 16S rRNA gene fragments amplified from total plant DNA resulted in several bands that matched those from the bacterial isolates, indicating that DGGE profiles can be used to detect some endophytic bacteria of citrus plants. However, some bands had no match with any isolate, suggesting the occurrence of other, nonculturable or as yet uncultured, endophytic bacteria. A specific band with a high G+C ratio was observed only in asymptomatic plants. The higher frequency of C. flaccumfaciens in asymptomatic plants suggests a role for this organism in the resistance of plants to CVC.

  20. The Population Structure of Antibiotic-Producing Bacterial Symbionts of Apterostigma dentigerum Ants: Impacts of Coevolution and Multipartite Symbiosis

    PubMed Central

    Caldera, Eric J.; Currie, Cameron R.

    2016-01-01

    Fungus-growing ants (Attini) are part of a complex symbiosis with Basidiomycetous fungi, which the ants cultivate for food, Ascomycetous fungal pathogens (Escovopsis), which parasitize cultivars, and Actinobacteria, which produce antibiotic compounds that suppress pathogen growth. Earlier studies that have characterized the association between attine ants and their bacterial symbionts have employed broad phylogenetic approaches, with conclusions ranging from a diffuse coevolved mutualism to no specificity being reported. However, the geographic mosaic theory of coevolution proposes that coevolved interactions likely occur at a level above local populations but within species. Moreover, the scale of population subdivision is likely to impact coevolutionary dynamics. Here, we describe the population structure of bacteria associated with the attine Apterostigma dentigerum across Central America using multilocus sequence typing (MLST) of six housekeeping genes. The majority (90%) of bacteria that were isolated grouped into a single clade within the genus Pseudonocardia. In contrast to studies that have suggested that Pseudonocardia dispersal is high and therefore unconstrained by ant associations, we found highly structured (FST = 0.39) and dispersal-limited (i.e., significant isolation by distance; r = 0.517, P = .05) populations over even a relatively small scale (e.g., within the Panama Canal Zone). Estimates of recombination versus mutation were uncharacteristically low compared with estimates for free-living Actinobacteria (e.g., ρ/θ = 0.028 in La Selva, Costa Rica), which suggests that recombination is constrained by association with ant hosts. Furthermore, Pseudonocardia population structure was correlated with that of Escovopsis species (r = 0.67, P = .02), supporting the bacteria's role in disease suppression. Overall, the population dynamics of symbiotic Pseudonocardia are more consistent with a specialized mutualistic association than with recently

  1. Culture History and Population Heterogeneity as Determinants of Bacterial Adaptation: the Adaptomics of a Single Environmental Transition

    PubMed Central

    Ryall, Ben; Eydallin, Gustavo

    2012-01-01

    Summary: Diversity in adaptive responses is common within species and populations, especially when the heterogeneity of the frequently large populations found in environments is considered. By focusing on events in a single clonal population undergoing a single transition, we discuss how environmental cues and changes in growth rate initiate a multiplicity of adaptive pathways. Adaptation is a comprehensive process, and stochastic, regulatory, epigenetic, and mutational changes can contribute to fitness and overlap in timing and frequency. We identify culture history as a major determinant of both regulatory adaptations and microevolutionary change. Population history before a transition determines heterogeneities due to errors in translation, stochastic differences in regulation, the presence of aged, damaged, cheating, or dormant cells, and variations in intracellular metabolite or regulator concentrations. It matters whether bacteria come from dense, slow-growing, stressed, or structured states. Genotypic adaptations are history dependent due to variations in mutation supply, contingency gene changes, phase variation, lateral gene transfer, and genome amplifications. Phenotypic adaptations underpin genotypic changes in situations such as stress-induced mutagenesis or prophage induction or in biofilms to give a continuum of adaptive possibilities. Evolutionary selection additionally provides diverse adaptive outcomes in a single transition and generally does not result in single fitter types. The totality of heterogeneities in an adapting population increases the chance that at least some individuals meet immediate or future challenges. However, heterogeneity complicates the adaptomics of single transitions, and we propose that subpopulations will need to be integrated into future population biology and systems biology predictions of bacterial behavior. PMID:22933562

  2. The population structure of antibiotic-producing bacterial symbionts of Apterostigma dentigerum ants: impacts of coevolution and multipartite symbiosis.

    PubMed

    Caldera, Eric J; Currie, Cameron R

    2012-11-01

    Fungus-growing ants (Attini) are part of a complex symbiosis with Basidiomycetous fungi, which the ants cultivate for food, Ascomycetous fungal pathogens (Escovopsis), which parasitize cultivars, and Actinobacteria, which produce antibiotic compounds that suppress pathogen growth. Earlier studies that have characterized the association between attine ants and their bacterial symbionts have employed broad phylogenetic approaches, with conclusions ranging from a diffuse coevolved mutualism to no specificity being reported. However, the geographic mosaic theory of coevolution proposes that coevolved interactions likely occur at a level above local populations but within species. Moreover, the scale of population subdivision is likely to impact coevolutionary dynamics. Here, we describe the population structure of bacteria associated with the attine Apterostigma dentigerum across Central America using multilocus sequence typing (MLST) of six housekeeping genes. The majority (90%) of bacteria that were isolated grouped into a single clade within the genus Pseudonocardia. In contrast to studies that have suggested that Pseudonocardia dispersal is high and therefore unconstrained by ant associations, we found highly structured ([Formula: see text]) and dispersal-limited (i.e., significant isolation by distance; [Formula: see text], [Formula: see text]) populations over even a relatively small scale (e.g., within the Panama Canal Zone). Estimates of recombination versus mutation were uncharacteristically low compared with estimates for free-living Actinobacteria (e.g., [Formula: see text] in La Selva, Costa Rica), which suggests that recombination is constrained by association with ant hosts. Furthermore, Pseudonocardia population structure was correlated with that of Escovopsis species ([Formula: see text], [Formula: see text]), supporting the bacteria's role in disease suppression. Overall, the population dynamics of symbiotic Pseudonocardia are more consistent with a

  3. Phage mutations in response to CRISPR diversification in a bacterial population.

    PubMed

    Sun, Christine L; Barrangou, Rodolphe; Thomas, Brian C; Horvath, Philippe; Fremaux, Christophe; Banfield, Jillian F

    2013-02-01

    Interactions between bacteria and their coexisting phage populations impact evolution and can strongly influence biogeochemical processes in natural ecosystems. Periodically, mutation or migration results in exposure of a host to a phage to which it has no immunity; alternatively, a phage may be exposed to a host it cannot infect. To explore the processes by which coexisting, co-evolving hosts and phage populations establish, we cultured Streptococcus thermophilus DGCC7710 with phage 2972 and tracked CRISPR (clustered regularly interspaced short palindromic repeats) diversification and host-phage co-evolution in a population derived from a colony that acquired initial CRISPR-encoded immunity. After 1 week of co-culturing, the coexisting host-phage populations were metagenomically characterized using 454 FLX Titanium sequencing. The evolved genomes were compared with reference genomes to identify newly incorporated spacers in S. thermophilus DGCC7710 and recently acquired single-nucleotide polymorphisms (SNPs) in phage 2972. Following phage exposure, acquisition of immune elements (spacers) led to a genetically diverse population with multiple subdominant strain lineages. Phage mutations that circumvented three early immunization events were localized in the proto-spacer adjacent motif (PAM) or near the PAM end of the proto-spacer, suggesting a strong selective advantage for the phage that mutated in this region. The sequential fixation or near fixation of these single mutations indicates selection events so severe that single phage genotypes ultimately gave rise to all surviving lineages and potentially carried traits unrelated to immunity to fixation.

  4. A heterogeneous population model for the analysis of bacterial growth kinetics.

    PubMed

    McKellar, R C

    1997-05-20

    A two-compartment, heterogeneous population model (HPM) was derived using the simulation software SB ModelMaker to describe the growth of Listeria monocytogenes in bacteriological media at 5-35 degrees C. The model assumed that, at time t = 0, the inoculum was distributed between two distinct compartments, Non-Growing and Growing, and that growth could be described by four parameters: initial total cell population (N0), final maximum cell population (Nmax), maximum specific growth rate (mu(max)), and initial cell population in the Growing compartment (G0). The model was fitted to the data by optimizing the four parameters, and lag phase duration (lambda) was calculated. The resulting values of mu(max) and lambda were similar to those determined using the modified Gompertz equation. A new parameter, w0, was defined which relates to the proportion of the initial cell population capable of growth, and is a measure of the initial physiological state of the cells. A modified model in which mu(max) was replaced with a temperature function, and w0 replaced G0, was used to predict the effect of temperature on the growth of L. monocytogenes. The results of this study raise questions concerning the current definition of the lag phase.

  5. Enumerating Virus-Like Particles and Bacterial Populations in the Sinuses of Chronic Rhinosinusitis Patients Using Flow Cytometry

    PubMed Central

    Carlson-Jones, Jessica A. P.; Paterson, James S.; Newton, Kelly; Smith, Renee J.; Dann, Lisa M.; Speck, Peter; Mitchell, James G.; Wormald, Peter-John

    2016-01-01

    There is increasing evidence to suggest that the sinus microbiome plays a role in the pathogenesis of chronic rhinosinusitis (CRS). However, the concentration of these microorganisms within the sinuses is still unknown. We show that flow cytometry can be used to enumerate bacteria and virus-like particles (VLPs) in sinus flush samples of CRS patients. This was achieved through trialling 5 sample preparation techniques for flow cytometry. We found high concentrations of bacteria and VLPs in these samples. Untreated samples produced the highest average bacterial and VLP counts with 3.3 ± 0.74 x 107 bacteria ml-1 and 2.4 ± 1.23 x 109 VLP ml-1 of sinus flush (n = 9). These counts were significantly higher than most of the treated samples (p < 0.05). Results showed 103 and 104 times inter-patient variation for bacteria and VLP concentrations. This wide variation suggests that diagnosis and treatment need to be personalised and that utilising flow cytometry is useful and efficient for this. This study is the first to enumerate bacterial and VLP populations in the maxillary sinus of CRS patients. The relevance of enumeration is that with increasing antimicrobial resistance, antibiotics are becoming less effective at treating bacterial infections of the sinuses, so alternative therapies are needed. Phage therapy has been proposed as one such alternative, but for dosing, the abundance of bacteria is required. Knowledge of whether phages are normally present in the sinuses will assist in gauging the safety of applying phage therapy to sinuses. Our finding, that large numbers of VLP are frequently present in sinuses, indicates that phage therapy may represent a minimally disruptive intervention towards the nasal microbiome. We propose that flow cytometry can be used as a tool to assess microbial biomass dynamics in sinuses and other anatomical locations where infection can cause disease. PMID:27171169

  6. Identification and characterization of metabolic properties of bacterial populations recovered from arsenic contaminated ground water of North East India (Assam).

    PubMed

    Ghosh, Soma; Sar, Pinaki

    2013-12-01

    Diversity of culturable bacterial populations within the Arsenic (As) contaminated groundwater of North Eastern state (Assam) of India is studied. From nine As contaminated samples 89 bacterial strains are isolated. 16S rRNA gene sequence analysis reveals predominance of Brevundimonas (35%) and Acidovorax (23%) along with Acinetobacter (10%), Pseudomonas (9%) and relatively less abundant (<5%) Undibacterium, Herbaspirillum, Rhodococcus, Staphylococcus, Bosea, Bacillus, Ralstonia, Caulobacter and Rhizobiales members. High As(III) resistance (MTC 10-50 mM) is observed for the isolates obtained from As(III) enrichment, particularly for 3 isolates of genus Brevundimonas (MTC 50 mM). In contrast, high resistance to As(V) (MTC as high as 550 mM) is present as a ubiquitous property, irrespective of isolates' enrichment condition. Bacterial genera affiliated to other groups showed relatively lower degree of As resistance [MTCs of 15-20 mM As(III) and 250-350 mM As(V)]. As(V) reductase activity is detected in strains with high As(V) as well as As(III) resistance. A strong correlation could be established among isolates capable of reductase activity and siderophore production as well as As(III) tolerance. A large number of isolates (nearly 50%) is capable of anaerobic respiration using alternate inorganic electron acceptors [As(V), Se(VI), Fe(III), [NO(3)(2), SO(4)(2), S(2)O(3)(2). Ability to utilize different carbon sources ranging from C2-C6 compounds along with some complex sugars is also observed. Particularly, a number of strains is found to possess ability to grow chemolithotrophically using As(III) as the electron donor. The study reports for the first time the identity and metabolic abilities of bacteria in As contaminated ground water of North East India, useful to elucidate the microbial role in influencing mobilization of As in the region.

  7. Molecular diversity analysis and bacterial population dynamics of an adapted seawater microbiota during the degradation of Tunisian zarzatine oil.

    PubMed

    Zrafi-Nouira, Ines; Guermazi, Sonda; Chouari, Rakia; Safi, Nimer M D; Pelletier, Eric; Bakhrouf, Amina; Saidane-Mosbahi, Dalila; Sghir, Abdelghani

    2009-07-01

    The indigenous microbiota of polluted coastal seawater in Tunisia was enriched by increasing the concentration of zarzatine crude oil. The resulting adapted microbiota was incubated with zarzatine crude oil as the only carbon and energy source. Crude oil biodegradation capacity and bacterial population dynamics of the microbiota were evaluated every week for 28 days (day 7, day 14, day 21, and day 28). Results show that the percentage of petroleum degradation was 23.9, 32.1, 65.3, and 77.8%, respectively. At day 28, non-aromatic and aromatic hydrocarbon degradation rates reached 92.6 and 68.7%, respectively. Bacterial composition of the adapted microflora was analysed by 16S rRNA gene cloning and sequencing, using total genomic DNA extracted from the adapted microflora at days 0, 7, 14, 21, and 28. Five clone libraries were constructed and a total of 430 sequences were generated and grouped into OTUs using the ARB software package. Phylogenetic analysis of the adapted microbiota shows the presence of four phylogenetic groups: Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Diversity indices show a clear decrease in bacterial diversity of the adapted microflora according to the incubation time. The Proteobacteria are the most predominant (>80%) at day 7, day 14 and day 21 but not at day 28 for which the microbiota was reduced to only one OTU affiliated with the genus Kocuria of the Actinobacteria. This study shows that the degradation of zarzatine crude oil components depends on the activity of a specialized and dynamic seawater consortium composed of different phylogenetic taxa depending on the substrate complexity.

  8. Diversity of bacterial communities in the midgut of Bactrocera cucurbitae (Diptera: Tephritidae) populations and their potential use as attractants.

    PubMed

    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.

  9. Hierarchical nested trial design (HNTD) for demonstrating treatment efficacy of new antibacterial drugs in patient populations with emerging bacterial resistance.

    PubMed

    Huque, Mohammad F; Valappil, Thamban; Soon, Guoxing Greg

    2014-11-10

    In the last decade or so, pharmaceutical drug development activities in the area of new antibacterial drugs for treating serious bacterial diseases have declined, and at the same time, there are worries that the increased prevalence of antibiotic-resistant bacterial infections, especially the increase in drug-resistant Gram-negative infections, limits available treatment options . A recent CDC report, 'Antibiotic Resistance Threats in the United States', indicates that antimicrobial resistance is one of our most serious health threats. However, recently, new ideas have been proposed to change this situation. An idea proposed in this regard is to conduct randomized clinical trials in which some patients, on the basis of a diagnostic test, may show presence of bacterial pathogens that are resistant to the control treatment, whereas remaining patients would show pathogens that are susceptible to the control. The control treatment in such trials can be the standard of care or the best available therapy approved for the disease. Patients in the control arm with resistant pathogens can have the option for rescue therapies if their clinical signs and symptoms worsen. A statistical proposal for such patient populations is to use a hierarchical noninferiority-superiority nested trial design that is informative and allows for treatment-to-control comparisons for the two subpopulations without any statistical penalty. This design can achieve in the same trial dual objectives: (i) to show that the new drug is effective for patients with susceptible pathogens on the basis of a noninferiority test and (ii) to show that it is superior to the control in patients with resistant pathogens. This paper addresses statistical considerations and methods for achieving these two objectives for this design. Published 2014. This article is a U.S. Government work and is in the public domain in the USA. Published 2014. This article is a U.S. Government work and is in the public domain in the

  10. BACTERIAL POPULATION SHIFTS IN THE RUMEN OF LACTATING DAIRY COWS WITHIN AND ACROSS FEEDING CYCLES

    USDA-ARS?s Scientific Manuscript database

    While species composition of the ruminal microflora is thought to change during the feeding cycle due to variations in feed intake and ruminal environmental conditions, no studies have systematically characterized these purported population shifts. We used PCR amplification and automated ribosomal ...

  11. Bacterial populations within copper mine tailings: long-term effects of amendment with Class A biosolids

    USDA-ARS?s Scientific Manuscript database

    This study evaluates the effect of surface application of dried Class A biosolids on microbial populations within copper mine tailings. Methods and Results: Mine tailing sites were established at ASARCO Mission Mine close to Sahuarita, Arizona. Site 1 (Dec. 1998) was amended with 248 tons ha-1 of C...

  12. Distribution, fluxes and bacterial consumption of total organic carbon in a populated Mediterranean Gulf

    NASA Astrophysics Data System (ADS)

    Zeri, C.; Kontoyiannis, H.; Giannakourou, A.

    2009-04-01

    Saronikos Gulf (Greece) practically constitutes the sea border of the metropolitan city of Athens and the alongshore outskirts, and it receives the treated wastes of ˜4 million people from a point source that discharges on the sea bottom at ˜65 m water depth. Total organic carbon (TOC) was measured in 477 seawater samples collected in the Saronikos Gulf, during 10 cruises, from August 2001 to May 2004 and analyzed with the High Temperature Catalytic Oxidation method (HTCO). TOC concentrations ranged from 49 to 198 μmol C L -1 in agreement with other Mediterranean coastal waters. The highest TOC concentrations were found in the upper waters (0-75 m), whereas in the deeper parts of the Gulf (between 100 and 400 m) TOC concentrations were kept constantly low (49-70 μmol C L -1). A general pattern towards higher TOC concentrations during summer was also observed. Calculations of non-refractory (labile+semi-labile) organic material based on a one-dimensional (1D) conceptual model showed that it corresponds to 33% of the bulk TOC during summer and to 27% during winter. Bacterial production (BP) was measured at selected stations of ˜70-80 m depth using the [ 3H] leucine method. Depth integrated BP values varied from 2.8 to 10.9 mmol m -2 d -1, whereas extraordinary high integrated BP values (126 and 140 mmol m -2 d -1) were observed at the station over the treated sewage outflow. From the turnover time, τ, of the non-refractory TOC by bacteria it was implied that organic matter in the effluents is extremely labile (2-58 days). Moreover, τ values at the other sites showed that during summer non-refractory organic material resisted bacterial degradation (1-8 months), whereas during early spring it was easily degradable (20-50 days). The balance of TOC fluxes for the Inner Gulf for June and September 2003 showed that the Inner Gulf acts as a net producer of TOC during summer. Our results suggest that the presence of the Athens treated sewage outfall does not

  13. Two novel temperate bacteriophages co-existing in Aeromonas sp. ARM81 - characterization of their genomes, proteomes and DNA methyltransferases.

    PubMed

    Dziewit, Lukasz; Radlinska, Monika

    2016-08-01

    Aeromonas species are causative agents of a wide spectrum of diseases in animals and humans. Although these bacteria are commonly found in various environments, little is known about their phages. Thus far, only one temperate Aeromonas phage has been characterized. Whole-genome sequencing of an Aeromonas sp. strain ARM81 revealed the presence of two prophage clusters. One of them is integrated into the chromosome and the other was maintained as an extrachromosomal, linear plasmid-like prophage encoding a protelomerase. Both prophages were artificially and spontaneously inducible. We separately isolated both phages and compared their genomes with other known viruses. The novel phages show no similarity to the previously characterized Aeromonas phages and might represent new evolutionary lineages of viruses infecting Aeromonadaceae. Apart from the comparative genomic analyses of these phages, complemented with their structural and molecular characterization, a functional analysis of four DNA methyltransferases encoded by these viruses was conducted. One of the investigated N6-adenine-modifying enzymes shares sequence specificity with a Dam-like methyltransferase of its bacterial host, while another one is non-specific, as it catalyzes adenine methylation in various sequence contexts. The presented results shed new light on the diversity of Aeromonas temperate phages.

  14. HRT dependent performance and bacterial community population of granular hydrogen-producing mixed cultures fed with galactose.

    PubMed

    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.

  15. Carbon transformations by attached bacterial populations in granitic groundwater from deep crystalline bed-rock of the Stripa research mine.

    PubMed

    Ekendahl, S; Pedersen, K

    1994-07-01

    This paper presents and compares the assimilation rates of CO2 and lactate, and the lactate respiration rates, of attached bacterial populations growing in slowly flowing groundwater (1-3 mm s-1) from deep crystalline bed-rock of the Stripa research mine, Sweden. The bacteria studied grew in anoxic, high-pH (9-10) and low-redox artesian groundwater flowing up through tubing from two levels of a borehole designated V2, 812-820 m and 970-1240 m below ground. Bacteria were allowed to attach to and grow on sterile glass microscope slides in laminar-flow reactors connected to the flowing groundwater. Total numbers of bacteria were counted by acridine orange direct counts. The bacteria grew slowly, with doubling times of 34 d at 10 degrees C for the 812-820 m population, 23 d for the 970-1240 m population at 10 degrees C and 16 d for this population at 20 degrees C. Numbers of attached bacteria reached between 10(6) and 10(7) bacteria cm-2. The populations at the two levels of the borehole were different in physiology as well as in phylogeny and reflected the heterogeneity between the sampling levels. The earlier proposed presence of sulphate-reducing bacteria could not be confirmed. This is discussed in relation to results from 16S rRNA gene sequencing studies. The CO2 assimilation rates (as mol CO2 cm-2 h-1, using liquid scintillation techniques) increased with depth and temperature.(ABSTRACT TRUNCATED AT 250 WORDS)

  16. Measuring the Rate of Conjugal Plasmid Transfer and Phage Infection in a Bacterial Population Using Quantitative PCR

    NASA Astrophysics Data System (ADS)

    Wan, Zhenmao; Goddard, Noel

    2012-02-01

    Horizontal gene transfer between species is an important mechanism for bacterial genome evolution. In Escherichia coli, conjugation is the transfer from a donor(F^+) to a recipient(F^-) cell through cell-to-cell contact. We demonstrate a novel qPCR method for quantifying the transfer kinetics of the F plasmid in a population by enumerating the relative abundance of genetic loci unique to the plasmid and the chromosome. This approach allows us to query the plasmid transfer rate without the need for selective culturing with unprecedented single locus resolution. It also allows us to investigate the inhibition of conjugation in the presence of filamentous bacteriophages M13. Experimental data is then compared with numerical simulation using a mass action, resource limited model.

  17. Bacterial populations and metabolites in the feces of free roaming and captive grizzly bears.

    PubMed

    Schwab, Clarissa; Cristescu, Bogdan; Boyce, Mark S; Stenhouse, Gordon B; Gänzle, Michael

    2009-12-01

    Gut physiology, host phylogeny, and diet determine the composition of the intestinal microbiota. Grizzly bears (Ursus arctos horribilis) belong to the Order Carnivora, yet feed on an omnivorous diet. The role of intestinal microflora in grizzly bear digestion has not been investigated. Microbiota and microbial activity were analysed from the feces of wild and captive grizzly bears. Bacterial composition was determined using culture-dependent and culture-independent methods. The feces of wild and captive grizzly bears contained log 9.1 +/- 0.5 and log 9.2 +/- 0.3 gene copies x g(-1), respectively. Facultative anaerobes Enterobacteriaceae and enterococci were dominant in wild bear feces. Among the strict anaerobes, the Bacteroides-Prevotella-Porphyromonas group was most prominent. Enterobacteriaceae were predominant in the feces of captive grizzly bears, at log 8.9 +/- 0.5 gene copies x g(-1). Strict anaerobes of the Bacteroides-Prevotella-Porphyromonas group and the Clostridium coccoides cluster were present at log 6.7 +/- 0.9 and log 6.8 +/- 0.8 gene copies x g(-1), respectively. The presence of lactate and short-chain fatty acids (SCFAs) verified microbial activity. Total SCFA content and composition was affected by diet. SCFA composition in the feces of captive grizzly bears resembled the SCFA composition of prey-consuming wild animals. A consistent data set was obtained that associated fecal microbiota and metabolites with the distinctive gut physiology and diet of grizzly bears.

  18. Microbial Diversity Analysis of the Bacterial and Archaeal Population in Present Day Stromatolites

    NASA Technical Reports Server (NTRS)

    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.

  19. Modeling Physiological Processes That Relate Toxicant Exposure and Bacterial Population Dynamics

    PubMed Central

    Klanjscek, Tin; Nisbet, Roger M.; Priester, John H.; Holden, Patricia A.

    2012-01-01

    Quantifying effects of toxicant exposure on metabolic processes is crucial to predicting microbial growth patterns in different environments. Mechanistic models, such as those based on Dynamic Energy Budget (DEB) theory, can link physiological processes to microbial growth. Here we expand the DEB framework to include explicit consideration of the role of reactive oxygen species (ROS). Extensions considered are: (i) additional terms in the equation for the “hazard rate” that quantifies mortality risk; (ii) a variable representing environmental degradation; (iii) a mechanistic description of toxic effects linked to increase in ROS production and aging acceleration, and to non-competitive inhibition of transport channels; (iv) a new representation of the “lag time” based on energy required for acclimation. We estimate model parameters using calibrated Pseudomonas aeruginosa optical density growth data for seven levels of cadmium exposure. The model reproduces growth patterns for all treatments with a single common parameter set, and bacterial growth for treatments of up to 150 mg(Cd)/L can be predicted reasonably well using parameters estimated from cadmium treatments of 20 mg(Cd)/L and lower. Our approach is an important step towards connecting levels of biological organization in ecotoxicology. The presented model reveals possible connections between processes that are not obvious from purely empirical considerations, enables validation and hypothesis testing by creating testable predictions, and identifies research required to further develop the theory. PMID:22328915

  20. Collective Bacterial Dynamics Revealed Using a Three-Dimensional Population-Scale Defocused Particle Tracking Technique

    PubMed Central

    Wu, Mingming; Roberts, John W.; Kim, Sue; Koch, Donald L.; DeLisa, Matthew P.

    2006-01-01

    An ability to monitor bacterial locomotion and collective dynamics is crucial to our understanding of a number of well-characterized phenotypes including biofilm formation, chemotaxis, and virulence. Here, we report the tracking of multiple swimming Escherichia coli cells in three spatial dimensions and at single-cell resolution using a novel three-dimensional (3D) defocused particle tracking (DPT) method. The 3D trajectories were generated for wild-type Escherichia coli strain RP437 as well as for isogenic derivatives that display smooth swimming due to a cheA deletion (strain RP9535) or incessant tumbling behavior due to a cheZ deletion (strain RP1616). The 3D DPT method successfully differentiated these three modes of locomotion and allowed direct calculation of the diffusion coefficient for each strain. As expected, we found that the smooth swimmer diffused more readily than the wild type, and both the smooth swimmer and the wild-type cells exhibited diffusion coefficients that were at least two orders of magnitude larger than that of the tumbler. Finally, we found that the diffusion coefficient increased with increasing cell density, a phenomenon that can be attributed to the hydrodynamic disturbances caused by neighboring bacteria. PMID:16820497

  1. Different Bacterial Populations Associated with the Roots and Rhizosphere of Rice Incorporate Plant-Derived Carbon

    PubMed Central

    Hernández, Marcela; Yuan, Quan; Conrad, Ralf

    2015-01-01

    Microorganisms associated with the roots of plants have an important function in plant growth and in soil carbon sequestration. Rice cultivation is the second largest anthropogenic source of atmospheric CH4, which is a significant greenhouse gas. Up to 60% of fixed carbon formed by photosynthesis in plants is transported below ground, much of it as root exudates that are consumed by microorganisms. A stable isotope probing (SIP) approach was used to identify microorganisms using plant carbon in association with the roots and rhizosphere of rice plants. Rice plants grown in Italian paddy soil were labeled with 13CO2 for 10 days. RNA was extracted from root material and rhizosphere soil and subjected to cesium gradient centrifugation followed by 16S rRNA amplicon pyrosequencing to identify microorganisms enriched with 13C. Thirty operational taxonomic units (OTUs) were labeled and mostly corresponded to Proteobacteria (13 OTUs) and Verrucomicrobia (8 OTUs). These OTUs were affiliated with the Alphaproteobacteria, Betaproteobacteria, and Deltaproteobacteria classes of Proteobacteria and the “Spartobacteria” and Opitutae classes of Verrucomicrobia. In general, different bacterial groups were labeled in the root and rhizosphere, reflecting different physicochemical characteristics of these locations. The labeled OTUs in the root compartment corresponded to a greater proportion of the 16S rRNA sequences (∼20%) than did those in the rhizosphere (∼4%), indicating that a proportion of the active microbial community on the roots greater than that in the rhizosphere incorporated plant-derived carbon within the time frame of the experiment. PMID:25616793

  2. Revisiting the co-existence of Attention-Deficit/Hyperactivity Disorder and Chronic Tic Disorder in childhood—The case of colour discrimination, sustained attention and interference control

    PubMed Central

    Rothenberger, Aribert; Fillmer-Heise, Anke; Roessner, Veit; Sergeant, Joseph; Tannock, Rosemary; Banaschewski, Tobias

    2017-01-01

    Objective Attention Deficit / Hyperactivity Disorder (ADHD) and Chronic Tic Disorder (CTD) are two common and frequently co-existing disorders, probably following an additive model. But this is not yet clear for the basic sensory function of colour processing sensitive to dopaminergic functioning in the retina and higher cognitive functions like attention and interference control. The latter two reflect important aspects for psychoeducation and behavioural treatment approaches. Methods Colour discrimination using the Farnsworth-Munsell 100-hue Test, sustained attention during the Frankfurt Attention Inventory (FAIR), and interference liability during Colour- and Counting-Stroop-Tests were assessed to further clarify the cognitive profile of the co-existence of ADHD and CTD. Altogether 69 children were classified into four groups: ADHD (N = 14), CTD (N = 20), ADHD+CTD (N = 20) and healthy Controls (N = 15) and compared in cognitive functioning in a 2×2-factorial statistical model. Results Difficulties with colour discrimination were associated with both ADHD and CTD factors following an additive model, but in ADHD these difficulties tended to be more pronounced on the blue-yellow axis. Attention problems were characteristic for ADHD but not CTD. Interference load was significant in both Colour- and Counting-Stroop-Tests and unrelated to colour discrimination. Compared to Controls, interference load in the Colour-Stroop was higher in pure ADHD and in pure CTD, but not in ADHD+CTD, following a sub-additive model. In contrast, interference load in the Counting-Stroop did not reveal ADHD or CTD effects. Conclusion The co-existence of ADHD and CTD is characterized by additive as well as sub-additive performance impairments, suggesting that their co-existence may show simple additive characteristics of both disorders or a more complex interaction, depending on demand. The equivocal findings on interference control may indicate limited validity of the Stroop-Paradigm for

  3. Smoking and smoking cessation in relation to the development of co-existing non-small cell lung cancer with chronic obstructive pulmonary disease.

    PubMed

    Zhai, Rihong; Yu, Xiaojin; Wei, Yongyue; Su, Li; Christiani, David C

    2014-02-15

    Previous studies have identified a mixed-phenotype of non-small cell lung cancer (NSCLC) with co-existing chronic obstructive pulmonary disease (COPD). Although NSCLC and COPD share a common risk factor in smoking, whether and how smoking may contribute to the coexistence of NSCLC with COPD (NSCLC-COPD) is unclear. Our study suggests that cigarette smoking is the major risk factor for the development of NSCLC-COPD, especially in females and among patients with squamous cell carcinoma subtype.

  4. Taxonomic structure and stability of the bacterial community in belgian sourdough ecosystems as assessed by culture and population fingerprinting.

    PubMed

    Scheirlinck, Ilse; Van der Meulen, Roel; Van Schoor, Ann; Vancanneyt, Marc; De Vuyst, Luc; Vandamme, Peter; Huys, Geert

    2008-04-01

    A total of 39 traditional sourdoughs were sampled at 11 bakeries located throughout Belgium which were visited twice with a 1-year interval. The taxonomic structure and stability of the bacterial communities occurring in these traditional sourdoughs were assessed using both culture-dependent and culture-independent methods. A total of 1,194 potential lactic acid bacterium (LAB) isolates were tentatively grouped and identified by repetitive element sequence-based PCR, followed by sequence-based identification using 16S rRNA and pheS genes from a selection of genotypically unique LAB isolates. In parallel, all samples were analyzed by denaturing gradient gel electrophoresis (DGGE) of V3-16S rRNA gene amplicons. In addition, extensive metabolite target analysis of more than 100 different compounds was performed. Both culturing and DGGE analysis showed that the species Lactobacillus sanfranciscensis, Lactobacillus paralimentarius, Lactobacillus plantarum, and Lactobacillus pontis dominated the LAB population of Belgian type I sourdoughs. In addition, DGGE band sequence analysis demonstrated the presence of Acetobacter sp. and a member of the Erwinia/Enterobacter/Pantoea group in some samples. Overall, the culture-dependent and culture-independent approaches each exhibited intrinsic limitations in assessing bacterial LAB diversity in Belgian sourdoughs. Irrespective of the LAB biodiversity, a large majority of the sugar and amino acid metabolites were detected in all sourdough samples. Principal component-based analysis of biodiversity and metabolic data revealed only little variation among the two samples of the sourdoughs produced at the same bakery. The rare cases of instability observed could generally be linked with variations in technological parameters or differences in detection capacity between culture-dependent and culture-independent approaches. Within a sampling interval of 1 year, this study reinforces previous observations that the bakery environment

  5. Effects of Antibiotics on Bacterial Species Composition and Metabolic Activities in Chemostats Containing Defined Populations of Human Gut Microorganisms

    PubMed Central

    Newton, Dorothy F.; Macfarlane, George T.

    2013-01-01

    The composition and metabolic activities of the human colonic microbiota are modulated by a number of external factors, including diet and antibiotic therapy. Changes in the structure and metabolism of the gut microbiota may have long-term consequences for host health. The large intestine harbors a complex microbial ecosystem comprising several hundreds of different bacterial species, which complicates investigations on intestinal physiology and ecology. To facilitate such studies, a highly simplified microbiota consisting of 14 anaerobic and facultatively anaerobic organisms (Bacteroides thetaiotaomicron, Bacteroides vulgatus, Bifidobacterium longum, Bifidobacterium infantis, Bifidobacterium pseudolongum, Bifidobacterium adolescentis, Clostridium butyricum, C. perfringens, C. bifermentans, C. innocuum, Escherichia coli, Enterococcus faecalis, Enterococcus faecium, Lactobacillus acidophilus) was used in this investigation. Ampicillin [9.2 μg (ml culture)−1] was added to two chemostats operated at different dilution rates (D; 0.10 h−1 and 0.21 h−1), and metronidazole [76.9 μg (ml culture)−1] was added to a third vessel (D = 0.21 h−1). Perturbations in bacterial physiology and metabolism were sampled over a 48-h period. Lactobacillus acidophilus and C. bifermentans populations did not establish in the fermentors under the imposed growth conditions. Ampicillin resulted in substantial reductions in bacteroides and C. perfringens populations at both dilution rates. Metronidazole strongly affected bacteroides communities but had no effect on bifidobacterial communities. The bacteriostatic effect of ampicillin on bifidobacterial species was growth rate dependent. Several metabolic activities were affected by antibiotic addition, including fermentation product formation and enzyme synthesis. The growth of antibiotic-resistant bifidobacteria in the large bowel may enable them to occupy ecological niches left vacant after antibiotic administration, preventing

  6. The effect of polymer addition on granulation in an anaerobic baffled reactor (ABR). Part II: compartmentalization of bacterial populations.

    PubMed

    Uyanik, S; Sallis, P J; Anderson, G K

    2002-02-01

    The microbial ecology of wastewater treatment plants remains one of the least understood aspects in both aerobic and anaerobic systems, despite the fact that both processes are ultimately dependent on an active biomass for operational efficiency. Ultimately, future developments in anaerobic treatment processes will require a much greater understanding of the fundamental relationships between bacterial populations within the biomass if optimum process efficiency is to be fully realised. This study assesses the influence of polymer addition on granule formation within an ABR and compares the ecology of the biomass in each compartment of two ABRs treating ice-cream wastewater. To our knowledge, this is the first reported characterisation of the microbiology of acidogenic and methanogenic bacteria in the individual compartments of an ABR. The polymer-amended reactor contained sludge that had a greater density of anaerobic bacteria and larger and denser granules than the control reactor, indicating that polymer addition possibly contributed to the retention of active biomass within the ABR. The average fraction of autofluorescent methanogens was lower, with 1.5% being in the initial compartments of the ABRs, compared to the last compartment which had 15%, showing that each compartment of an ABR had a unique microbial composition. Partial spatial separation of anaerobic bacteria appeared to have taken place with acidogenic bacteria predominating in the initial compartments and methanogenic bacteria predominating in the final compartments. Scanning electron micrographs have revealed that the dominant bacteria in the initial compartments of the ABR (Compartments 1 and 2) were those which could consume H2/CO2 and formate as substrate, i.e. Methanobrevibacter, Methanococcus, with populations shifting to acetate utilisers, i.e. Methanosaeta, Methanosarcina, in the final compartments (Compartments 3 and 4). In addition, there appeared to be a stratified structure to the

  7. Paradoxical co-existing base metal sulphides in the mantle: The multi-event record preserved in Loch Roag peridotite xenoliths, North Atlantic Craton

    NASA Astrophysics Data System (ADS)

    Hughes, Hannah S. R.; McDonald, Iain; Loocke, Matthew; Butler, Ian B.; Upton, Brian G. J.; Faithfull, John W.

    2017-04-01

    The role of the subcontinental lithospheric mantle as a source of precious metals for mafic magmas is contentious and, given the chalcophile (and siderophile) character of metals such as the platinum-group elements (PGE), Se, Te, Re, Cu and Au, the mobility of these metals is intimately linked with that of sulphur. Hence the nature of the host phase(s), and their age and stability in the subcontinental lithospheric mantle may be of critical importance. We investigate the sulphide mineralogy and sulphide in situ trace element compositions in base metal sulphides (BMS) in a suite of spinel lherzolite mantle xenoliths from northwest Scotland (Loch Roag, Isle of Lewis). This area is situated on the margin of the North Atlantic Craton which has been overprinted by a Palaeoproterozoic orogenic belt, and occurs in a region which has undergone magmatic events from the Palaeoproterozoic to the Eocene. We identify two populations of co-existing BMS within a single spinel lherzolite xenolith (LR80) and which can also be recognised in the peridotite xenolith suite as a whole. Both populations consist of a mixture of Fe-Ni-Cu sulphide minerals, and we distinguished between these according to BMS texture, petrographic setting (i.e., location within the xenolith in terms of 'interstitial' or within feldspar-spinel symplectites, as demonstrated by X-ray Computed Microtomography) and in situ trace element composition. Group A BMS are coarse, metasomatic, have low concentrations of total PGE (< 40 ppm) and high (Re/Os)N (ranging 1 to 400). Group B BMS strictly occur within symplectites of spinel and feldspar, are finer-grained rounded droplets, with micron-scale PtS (cooperite), high overall total PGE concentrations (15-800 ppm) and low (Re/Os)N ranging 0.04 to 2. Group B BMS sometimes coexist with apatite, and both the Group B BMS and apatite can preserve rounded micron-scale Ca-carbonate inclusions indicative of sulphide-carbonate-phosphate immiscibility. This carbonate

  8. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem

    SciTech Connect

    Johnston, Eric R.; Rodriguez-R, Luis M.; Luo, Chengwei; Yuan, Mengting M.; Wu, Liyou; He, Zhili; Schuur, Edward A. G.; Luo, Yiqi; Tiedje, James M.; Zhou, Jizhong; Konstantinidis, Konstantinos T.

    2016-04-25

    How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1-2 g) are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth) by sequencing, and the recovery of 27 high-quality, almost complete ( > 80% completeness) population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100-530 km apart) tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity). Collectively, our results revealed that

  9. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem.

    PubMed

    Johnston, Eric R; Rodriguez-R, Luis M; Luo, Chengwei; Yuan, Mengting M; Wu, Liyou; He, Zhili; Schuur, Edward A G; Luo, Yiqi; Tiedje, James M; Zhou, Jizhong; Konstantinidis, Konstantinos T

    2016-01-01

    How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1-2 g) are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth) by sequencing, and the recovery of 27 high-quality, almost complete (>80% completeness) population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100-530 km apart) tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity). Collectively, our results revealed that

  10. Co-existence of phenylketonuria either with maple syrup urine disease or Sandhoff disease in two patients from Iran: emphasizing the role of consanguinity.

    PubMed

    Abiri, Maryam; Talebi, Saeed; Uitto, Jouni; Youssefian, Leila; Vahidnezhad, Hassan; Shirzad, Tina; Salehpour, Shadab; Zeinali, Sirous

    2016-10-01

    Most inborn errors of metabolism (IEMs) are inherited in an autosomal recessive manner. IEMs are one of the major concerns in Iran due to its extensive consanguineous marriages. Herein, we report two patients with two co-existent IEMs: a girl affected by classic phenylketonuria (PKU) and maple syrup urine disease (MSUD) and a male patient affected with Sandhoff disease and PKU, where Sandhoff disease was suspected due to the presence of a cherry-red spot in the eyes at 6 months which is unrelated to PKU. Sequencing of candidate genes in the first patient revealed one novel and three recurrent compound heterozygous mutations of p.Ser231Pro and p.Ala300Ser in the PAH gene and p.Glu330Lys and p.Arg170Cys mutations in the BCKDHB gene. Genetic testing results in the second patient showed previously reported homozygous mutations of p.Arg261Gln in the PAH and p.Arg533Cys mutation in the HEXB gene. Genetic testing confirmed the clinical diagnosis of both diseases in both patients. To the best of our knowledge; this is the first report of the co-existence of two distinct genetic disorders in two individuals from Iran. Co-existent different IEMs in patients complicated the clinical diagnosis and management of the diseases.

  11. Large scale analysis of co-existing post-translational modifications in histone tails reveals global fine structure of cross-talk.

    PubMed

    Schwämmle, Veit; Aspalter, Claudia-Maria; Sidoli, Simone; Jensen, Ole N

    2014-07-01

    Mass spectrometry (MS) is a powerful analytical method for the identification and quantification of co-existing post-translational modifications in histone proteins. One of the most important challenges in current chromatin biology is to characterize the relationships between co-existing histone marks, the order and hierarchy of their deposition, and their distinct biological functions. We developed the database CrossTalkDB to organize observed and reported co-existing histone marks as revealed by MS experiments of histone proteins and their derived peptides. Statistical assessment revealed sample-specific patterns for the co-frequency of histone post-translational modifications. We implemented a new method to identify positive and negative interplay between pairs of methylation and acetylation marks in proteins. Many of the detected features were conserved between different cell types or exist across species, thereby revealing general rules for cross-talk between histone marks. The observed features are in accordance with previously reported examples of cross-talk. We observed novel types of interplay among acetylated residues, revealing positive cross-talk between nearby acetylated sites but negative cross-talk for distant ones, and for discrete methylation states at Lys-9, Lys-27, and Lys-36 of histone H3, suggesting a more differentiated functional role of methylation beyond the general expectation of enhanced activity at higher methylation states.

  12. Greenhouse gas, animal performance, and bacterial population structure responses to dietary monensin fed to dairy cows.

    PubMed

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

    2010-01-01

    The present study investigated the effects of a feed additive and rumen microbial modifier, monensin sodium (monensin), on selected variables in lactating dairy cows. Monensin fed cows (MON, 600 mg d(-1)) were compared with untreated control cows (CON, 0 mg d(-1)) with respect to the effects of monensin on the production of three greenhouse gases (GHG), methane (CH(4)), nitrous oxide (N(2)O), and carbon dioxide (CO(2)), along with animal performance (dry matter intake; DMI), milk production, milk components, plasma urea nitrogen (PUN), milk urea nitrogen (MUN), and the microbial population structure of fresh feces. Measurements of GHG were collected at Days 14 and 60 in an environmental chamber simulating commercial dairy freestall housing conditions. Milk production and DMI measurements were collected twice daily over the 60-d experimental period; milk components, PUN, and MUN were measured on Days 14 and 60. The microbial population structure of feces from 6 MON and 6 CON cows was examined on three different occasions (Days 14, 30, and 60). Monensin did not affect emissions of methane (CH(4)), nitrous oxide (N(2)O), and carbon dioxide (CO(2)). Over a 24-h period, emissions of CH(4), N(2)O, and CO(2) decreased in both MON and CON groups. Animal performance and the microbial population structure of the animal fresh waste were also unaffected for MON vs. CON cows.

  13. Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations

    DOE PAGES

    Xue, Hong; Cordero, Otto X.; Camas, Francisco M.; ...

    2015-05-05

    Although plasmids and other episomes are recognized as key players in horizontal gene transfer among microbes, their diversity and dynamics among ecologically structured host populations in the wild remain poorly understood. Here, we show that natural populations of marine Vibrionaceae bacteria host large numbers of families of episomes, consisting of plasmids and a surprisingly high fraction of plasmid-like temperate phages. Episomes are unevenly distributed among host populations, and contrary to the notion that high-density communities in biofilms act as hot spots of gene transfer, we identified a strong bias for episomes to occur in free-living as opposed to particle-attached cells.more » Mapping of episomal families onto host phylogeny shows that, with the exception of all phage and a few plasmid families, most are of recent evolutionary origin and appear to have spread rapidly by horizontal transfer. Such high eco-evolutionary turnover is particularly surprising for plasmids that are, based on previously suggested categorization, putatively nontransmissible, indicating that this type of plasmid is indeed frequently transferred by currently unknown mechanisms. Finally, analysis of recent gene transfer among plasmids reveals a network of extensive exchange connecting nearly all episomes. Genes functioning in plasmid transfer and maintenance are frequently exchanged, suggesting that plasmids can be rapidly transformed from one category to another. The broad distribution of episomes among distantly related hosts and the observed promiscuous recombination patterns show how episomes can offer their hosts rapid assembly and dissemination of novel functions.« less

  14. Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations

    SciTech Connect

    Xue, Hong; Cordero, Otto X.; Camas, Francisco M.; Trimble, William; Meyer, Folker; Guglielmini, Julien; Rocha, Eduardo P. C.; Polz, Martin F.

    2015-05-05

    Although plasmids and other episomes are recognized as key players in horizontal gene transfer among microbes, their diversity and dynamics among ecologically structured host populations in the wild remain poorly understood. Here, we show that natural populations of marine Vibrionaceae bacteria host large numbers of families of episomes, consisting of plasmids and a surprisingly high fraction of plasmid-like temperate phages. Episomes are unevenly distributed among host populations, and contrary to the notion that high-density communities in biofilms act as hot spots of gene transfer, we identified a strong bias for episomes to occur in free-living as opposed to particle-attached cells. Mapping of episomal families onto host phylogeny shows that, with the exception of all phage and a few plasmid families, most are of recent evolutionary origin and appear to have spread rapidly by horizontal transfer. Such high eco-evolutionary turnover is particularly surprising for plasmids that are, based on previously suggested categorization, putatively nontransmissible, indicating that this type of plasmid is indeed frequently transferred by currently unknown mechanisms. Finally, analysis of recent gene transfer among plasmids reveals a network of extensive exchange connecting nearly all episomes. Genes functioning in plasmid transfer and maintenance are frequently exchanged, suggesting that plasmids can be rapidly transformed from one category to another. The broad distribution of episomes among distantly related hosts and the observed promiscuous recombination patterns show how episomes can offer their hosts rapid assembly and dissemination of novel functions.

  15. [Burkholderia cepacia under different ecological conditions: the amount and variability of the bacterial population].

    PubMed

    Pushkareva, V I; Velichko, V V; Kaminskaia, A A; Alekseeva, N V; Litvin, V Iu

    2005-01-01

    In a series of prolonged experiments with the use of the bacteriological method and PCR analysis the amount and state of B. cepacia population, associated and not associated with infusoria Tetrahymena pyriformis, were dynamically evaluated under different conditions: in water, brain heart broth, soil extract and at different temperature (4 degrees C and 25 degrees C). In soil extract at 25 degrees C B. cepacia existed in the vegetative state for the period of up to 3 months, while at 4 degrees C, in the absence of protozoa, the transition of these microorganisms into the uncultivable forms occurred in 9 days, and they could be detected only with the use of PCR. Protozoa maintained the existence of the vegetative bacteria for as long as 2 months, and in 3-4 months uncultivable forms of B. cepacia cells were registered. In water at low temperature B. cepacia disappeared in 2 months, evidently, eaten up by infusoria. The population variability of B. cepacia under different conditions of their existence was established: S-R dissociation, a decrease in biochemical activity, growth deceleration. A high level of cytopathogenicity in B. cepacia pigment-forming clones was noted. In the process of transition into the uncultivable state pigment formation in B. cepacia population decreased up. The ecological plasticity and multi-pathogenicity of B. cepacia as phytopathogens and the causative agents of human diseases are discussed.

  16. Housefly Larva Vermicomposting Efficiently Attenuates Antibiotic Resistance Genes in Swine Manure, with Concomitant Bacterial Population Changes.

    PubMed

    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 < 0.05), while those of genes encoding sulfonamide resistance (sul1 and sul2) were increased (P < 0.05) when normalized to 16S rRNA. The abundances of tetracycline 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.

  17. Bacterial populations and environmental factors controlling cellulose degradation in an acidic Sphagnum peat.

    PubMed

    Pankratov, Timofey A; Ivanova, Anastasia O; Dedysh, Svetlana N; Liesack, Werner

    2011-07-01

    Northern peatlands represent a major global carbon store harbouring approximately one-third of the global reserves of soil organic carbon. A large proportion of these peatlands consists of acidic Sphagnum-dominated ombrotrophic bogs, which are characterized by extremely low rates of plant debris decomposition. The degradation of cellulose, the major component of Sphagnum-derived litter, was monitored in long-term incubation experiments with acidic (pH 4.0) peat extracts. This process was almost undetectable at 10°C and occurred at low rates at 20°C, while it was significantly accelerated at both temperature regimes by the addition of available nitrogen. Cellulose breakdown was only partially inhibited in the presence of cycloheximide, suggesting that bacteria participated in this process. We aimed to identify these bacteria by a combination of molecular and cultivation approaches and to determine the factors that limit their activity in situ. The indigenous bacterial community in peat was dominated by Alphaproteobacteria and Acidobacteria. The addition of cellulose induced a clear shift in the community structure towards an increase in the relative abundance of the Bacteroidetes. Increasing temperature and nitrogen availability resulted in a selective development of bacteria phylogenetically related to Cytophaga hutchinsonii (94-95% 16S rRNA gene sequence similarity), which densely colonized microfibrils of cellulose. Among isolates obtained from this community only some subdivision 1 Acidobacteria were capable of degrading cellulose, albeit at a very slow rate. These Acidobacteria represent indigenous cellulolytic members of the microbial community in acidic peat and are easily out-competed by Cytophaga-like bacteria under conditions of increased nitrogen availability. Members of the phylum Firmicutes, known to be key players in cellulose degradation in neutral habitats, were not detected in the cellulolytic community enriched at low pH.

  18. Housefly Larva Vermicomposting Efficiently Attenuates Antibiotic Resistance Genes in Swine Manure, with Concomitant Bacterial Population Changes

    PubMed Central

    Wang, Hang; Li, Hongyi; Gilbert, Jack A.; Li, Haibo; Wu, Longhua; Liu, Meng; Wang, Liling; Zhou, Qiansheng; Yuan, Junxiang

    2015-01-01

    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 < 0.05), while those of genes encoding sulfonamide resistance (sul1 and sul2) were increased (P < 0.05) when normalized to 16S rRNA. The abundances of tetracycline 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. PMID:26296728

  19. Housefly Larva Vermicomposting Efficiently Attenuates Antibiotic Resistance Genes in Swine Manure, with Concomitant Bacterial Population Changes

    SciTech Connect

    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 < 0.05), while those of genes encoding sulfonamide resistance (sul1 and sul2) were increased (P < 0.05) when normalized to 16S rRNA. The abundances of tetracycline 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.

  20. Experimental approach for bacteriophage susceptibility testing of planktonic and sessile bacterial populations – Study protocol

    PubMed Central

    Neguţ, Alina Cristina; Săndulescu, Oana; Popa, Marcela; Streinu-Cercel, Anca; Alavidze, Zemphira; Berciu, Ioana; Bleotu, Coralia; Popa, Mircea Ioan; Chifiriuc, Mariana Carmen; Streinu-Cercel, Adrian

    2014-01-01

    Introduction Antimicrobial resistance is a growing threat for all clinical branches. This phenomenon poses important challenges in controlling infectious diseases. However, multidrug resistance is not the only issue, as bacteria that are otherwise susceptible to common antibiotics express other patterns for evading antibiotherapy, for example they can aggregate within a self-produced matrix to form biofilm. Methods We intend to perform a prospective laboratory study of the germs isolated from different samples collected from patients admitted with infectious pathology in reference hospitals in Romania. We will perform antibiotic resistance testing as well as phage testing, both on solid and liquid growth medium, for Staphylococcus spp., Enterococcus spp., and Pseudomonas spp. We intend to collect data for 150 patients with different infections with these identified pathogens. Phage susceptibility testing will be performed using 5 types of strain-specific bacteriophage mixtures: PYO, INTESTI, STAPHYLOCOCCAL (Eliava BioPreparations, Tbilisi, Georgia), PHAGYO, PHAGESTI (JSC “Biochimpharm”, Tbilisi, Georgia). For phage-susceptible strains, we will evaluate biofilm formation in the presence of phages, as well as phage effect on already formed biofilm. Expected results Through this study, we intend to provide the first set of results on bacteriophage-susceptibility of bacteria isolated from patients with hard to treat infections, from reference hospitals in Romania. By evaluating a large number of bacterial strains we aim to predict and project biofilm kinetics, while adding binary phage dilutions at key timepoints during biofilm formation. Acknowledgments POSDRU/159/1.5/S/141531; Carol Davila University of Medicine and Pharmacy, Young Researchers Grant no. 28341/2013. PMID:25505742

  1. Identification of bacterial plasmids based on mobility and plasmid population biology.

    PubMed

    Garcillán-Barcia, Maria Pilar; Alvarado, Andrés; de la Cruz, Fernando

    2011-09-01

    Plasmids contain a backbone of core genes that remains relatively stable for long evolutionary periods, making sense to speak about plasmid species. The identification and characterization of the core genes of a plasmid species has a special relevance in the study of its epidemiology and modes of transmission. Besides, this knowledge will help to unveil the main routes that genes, for example antibiotic resistance (AbR) genes, use to travel from environmental reservoirs to human pathogens. Global dissemination of multiple antibiotic resistances and virulence traits by plasmids is an increasing threat for the treatment of many bacterial infectious diseases. To follow the dissemination of virulence and AbR genes, we need to identify the causative plasmids and follow their path from reservoirs to pathogens. In this review, we discuss how the existing diversity in plasmid genetic structures gives rise to a large diversity in propagation strategies. We would like to propose that, using an identification methodology based on plasmid mobility types, we can follow the propagation routes of most plasmids in Gammaproteobacteria, as well as their cargo genes, in complex ecosystems. Once the dissemination routes are known, designing antidissemination drugs and testing their efficacy will become feasible. We discuss in this review how the existing diversity in plasmid genetic structures gives rise to a large diversity in propagation strategies. We would like to propose that, by using an identification methodology based on plasmid mobility types, we can follow the propagation routes of most plasmids in ?-proteobacteria, as well as their cargo genes, in complex ecosystems.

  2. Seasonal and annual reoccurrence in betaproteobacterial ammonia-oxidizing bacterial population structure.

    PubMed

    Bouskill, Nicholas J; Eveillard, Damien; O'Mullan, Gregory; Jackson, George A; Ward, Bess B

    2011-04-01

    Microbes exhibit remarkably high genetic diversity compared with plant and animal species. Many phylogenetically diverse but apparently functionally redundant microbial taxa are detectable within a cubic centimetre of mud or a millilitre of water, and the significance of this diversity, in terms of ecosystem function, has been difficult to understand. Thus it is not known whether temporal and spatial differences in microbial community composition are linked to particular environmental factors or might modulate ecosystem response to environmental change. Fifty-three water and sediment samples from upper and lower Chesapeake Bay were analysed in triplicate arrays to determine temporal and spatial patterns and relationships between ammonia-oxidizing bacterial (AOB) communities and environmental variables. Thirty-three water samples (three depths) collected during April, August and October, 2001-2004, from the oligohaline upper region of the Bay were analysed to investigate temporal patterns in archetype distribution. Using a combination of a non-weighted discrimination analysis and principal components analysis of community composition data obtained from functional gene microarrays, it was found that co-varying AOB assemblages reoccurred seasonally in concert with specific environmental conditions, potentially revealing patterns of niche differentiation. Among the most notable patterns were correlations of AOB archetypes with temperature, DON and ammonium concentrations. Different AOB archetypes were more prevalent at certain times of the year, e.g. some were more abundant every autumn and others every spring. This data set documents the successional return to an indigenous community following massive perturbation (hurricane induced flooding) as well as the seasonal reoccurrence of specific lineages, identified by key functional genes, associated with the biogeochemically important process nitrification.

  3. Different bacterial populations associated with the roots and rhizosphere of rice incorporate plant-derived carbon.

    PubMed

    Hernández, Marcela; Dumont, Marc G; Yuan, Quan; Conrad, Ralf

    2015-03-01

    Microorganisms associated with the roots of plants have an important function in plant growth and in soil carbon sequestration. Rice cultivation is the second largest anthropogenic source of atmospheric CH4, which is a significant greenhouse gas. Up to 60% of fixed carbon formed by photosynthesis in plants is transported below ground, much of it as root exudates that are consumed by microorganisms. A stable isotope probing (SIP) approach was used to identify microorganisms using plant carbon in association with the roots and rhizosphere of rice plants. Rice plants grown in Italian paddy soil were labeled with (13)CO2 for 10 days. RNA was extracted from root material and rhizosphere soil and subjected to cesium gradient centrifugation followed by 16S rRNA amplicon pyrosequencing to identify microorganisms enriched with (13)C. Thirty operational taxonomic units (OTUs) were labeled and mostly corresponded to Proteobacteria (13 OTUs) and Verrucomicrobia (8 OTUs). These OTUs were affiliated with the Alphaproteobacteria, Betaproteobacteria, and Deltaproteobacteria classes of Proteobacteria and the "Spartobacteria" and Opitutae classes of Verrucomicrobia. In general, different bacterial groups were labeled in the root and rhizosphere, reflecting different physicochemical characteristics of these locations. The labeled OTUs in the root compartment corresponded to a greater proportion of the 16S rRNA sequences (∼20%) than did those in the rhizosphere (∼4%), indicating that a proportion of the active microbial community on the roots greater than that in the rhizosphere incorporated plant-derived carbon within the time frame of the experiment. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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

    NASA Technical Reports Server (NTRS)

    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. Composition of Bacterial Communities Associated with Aurelia aurita Changes with Compartment, Life Stage, and Population

    PubMed Central

    Weiland-Bräuer, Nancy; Neulinger, Sven C.; Pinnow, Nicole; Künzel, Sven; Baines, John F.

    2015-01-01

    The scyphozoan Aurelia aurita is recognized as a key player in marine ecosystems and a driver of ecosystem change. It is thus intensely studied to address ecological questions, although its associations with microorganisms remain so far undescribed. In the present study, the microbiota associated with A. aurita was visualized with fluorescence in situ hybridization (FISH) analysis, and community structure was analyzed with respect to different life stages, compartments, and populations of A. aurita by 16S rRNA gene amplicon sequencing. We demonstrate that the composition of the A. aurita microbiota is generally highly distinct from the composition of communities present in ambient water. Comparison of microbial communities from different developmental stages reveals evidence for life stage-specific community patterns. Significant restructuring of the microbiota during strobilation from benthic polyp to planktonic life stages is present, arguing for a restructuring during the course of metamorphosis. Furthermore, the microbiota present in different compartments of the adult medusa (exumbrella mucus and gastric cavity) display significant differences, indicating body part-specific colonization. A novel Mycoplasma strain was identified in both compartment-specific microbiota and is most likely present inside the epithelium as indicated by FISH analysis of polyps, indicating potential endosymbiosis. Finally, comparison of polyps of different populations kept under the same controlled laboratory conditions in the same ambient water showed population-specific community patterns, most likely due the genetic background of the host. In conclusion, the presented data indicate that the associated microbiota of A. aurita may play important functional roles, e.g., during the life cycle. PMID:26116680

  6. Bacterial population development and chemical characteristics of refuse decomposition in a simulated sanitary landfill

    SciTech Connect

    Barlaz, M.A.; Schaefer, D.M.; Ham, R.K. )

    1989-01-01

    Population development of key groups of bacteria involved in municipal refuse conversion to methane was measured from the time of initial incubation through the onset of methane production. Hemicellulolytic bacteria, cellulolytic bacteria, hydrogen-producing acetogens, and acetate-and H{sub 2}-plus-CO{sub 2}-utilizing methanogens were enumerated by the most-probable-number technique with media containing oat spelt xylan, ball-milled cellulose, butyrate, acetate, and H{sub 2} plus CO{sub 2}, respectively. The methane concentration of the sampled containers increased to 64% by day 69, at which time the maximum methane production rate, 929 liters of CH{sub 4} per day kg-year, was measured. Population increases of 2, 4, 5, 5, and 6 orders of magnitude were measured between fresh refuse and the methane production phase for the hemicellulolytic bacteria, cellulolytic bacteria, butyrate-catabolizing acetogens, and acetate- and H{sub 2}-CO{sub 2}-utilizing methanogens, respectively. The cellulolytic bacteria and acetogens increased more slowly than the methanogens and only after the onset of methane production. The initial decrease in the pH of the refuse ecosystem from 7.5 to 5.7 was attributed to the accumulation of acidic end products of sugar fermentation, to the low acid-consuming activity of the acetogenic and methanogenic bacteria, and to levels of oxygen and nitrate in the fresh refuse sufficient for oxidation of only 8% of the sugars to carbon dioxide and water. Cellulose and hemicellulose decomposition was most rapid after establishment of the methanogenic and acetogenic populations and a reduction in the initial accumulation of carboxylic acids. Initially acetate utilization, but ultimately polymer hydrolysis, limited the rate of refuse conversion to methane.

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

    NASA Technical Reports Server (NTRS)

    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.

  8. Effect of probiotics on bacterial population and health status of shrimp in culture pond ecosystem.

    PubMed

    Dalmin, G; Kathiresan, K; Purushothaman, A

    2001-09-01

    The artificially manufactured probiotics having beneficial bacteria, Bacillus spp. was applied regularly in a modified extensive shrimp (Penaeus monodon) culture pond, located on the bank of Vellar estuary, Parangipettai. The populations of total heterotrophic bacteria (THB), beneficial bacteria (Bacillus spp.) and pathogenic bacteria (vibrios) were monitored in water and sediment of the pond. The results were compared with a control pond, situated in the same location having same water spread area, stocking density, species managed with same technologies and optimum environmental parameters in which no probiotic was applied. The populations of THB and Bacillus spp. in the experimental pond increased and the vibrios decreased after each application of probiotics. But the result of the control pond showed an increasing trend of the populations of THB, Bacillus spp. and vibrios towards days of culture. The control pond had lower levels of THB and Bacillus spp. and higher levels of vibrios than the probiotic applied (experimental) pond. Also the probiotics maintained optimum transparency and low organic load in the experimental pond as compared to control. In general, water and sediment had almost equal number of Bacillus spp. and vibrios, but sediment had higher THB load than water. The applications of probiotics lesser pathogenic vibrios and enhance beneficial bacilli in the culture leading to improved water quality, promoted growth and survival rates and increased the health status of the shrimp without stress and disease outbreaks. Thus the application of probiotics could lead to disease-free and profitable shrimp culture operations which will be helpful for shrimp farmers as most of them are now-a-days severely affected by microbial diseases.

  9. Metagenomics Reveals Pervasive