WorldWideScience

Sample records for understand bacterial collective

  1. Collective decisions among bacterial viruses

    Science.gov (United States)

    Joh, Richard; Mileyko, Yuriy; Voit, Eberhard; Weitz, Joshua

    2010-03-01

    For many temperate bacteriophages, the decision of whether to kill hosts or enter a latent state depends on the multiplicity of infection. In this talk, I present a quantitative model of gene regulatory dynamics to describe how phages make collective decisions within host cells. Unlike most previous studies, the copy number of viral genomes is treated as a variable. In the absence of feedback loops, viral mRNA transcription is expected to be proportional to the viral copy number. However, when there are nonlinear feedback loops in viral gene regulation, our model shows that gene expression patterns are sensitive to changes in viral copy number and there can be a domain of copy number where the system becomes bistable. Hence, the viral copy number is a key control parameter determining host cell fates. This suggests that bacterial viruses can respond adaptively to changes in population dynamics, and can make alternative decisions as a bet-hedging strategy. Finally, I present a stochastic version of viral gene regulation and discuss speed-accuracy trade-offs in the context of cell fate determination by viruses.

  2. Correlation properties of collective motion in bacterial suspensions

    International Nuclear Information System (INIS)

    Ryan, Shawn D; Berlyand, Leonid; Sokolov, Andrey; Aranson, Igor S

    2013-01-01

    The study of collective motion in bacterial suspensions has been of significant recent interest. To better understand the non-trivial spatio-temporal correlations emerging in the course of collective swimming in suspensions of motile bacteria, a simple model is employed: a bacterium is represented as a force dipole with size, through the use of a short-range repelling potential, and shape. The model emphasizes two fundamental mechanisms: dipolar hydrodynamic interactions and short-range bacterial collisions. Using direct particle simulations validated by a dedicated experiment, we show that changing the swimming speed or concentration alters the time scale of sustained collective motion, consistent with experiment. Also, the correlation length in the collective state is almost constant as concentration and swimming speed change even though increasing each greatly increases the input of energy to the system. We demonstrate that the particle shape is critical for the onset of collective effects. In addition, new experimental results are presented illustrating the onset of collective motion with an ultrasound technique. This work exemplifies the delicate balance between various physical mechanisms governing collective motion in bacterial suspensions and provides important insights into its mesoscopic nature. (paper)

  3. Understanding Collective Activities of People from Videos.

    Science.gov (United States)

    Wongun Choi; Savarese, Silvio

    2014-06-01

    This paper presents a principled framework for analyzing collective activities at different levels of semantic granularity from videos. Our framework is capable of jointly tracking multiple individuals, recognizing activities performed by individuals in isolation (i.e., atomic activities such as walking or standing), recognizing the interactions between pairs of individuals (i.e., interaction activities) as well as understanding the activities of group of individuals (i.e., collective activities). A key property of our work is that it can coherently combine bottom-up information stemming from detections or fragments of tracks (or tracklets) with top-down evidence. Top-down evidence is provided by a newly proposed descriptor that captures the coherent behavior of groups of individuals in a spatial-temporal neighborhood of the sequence. Top-down evidence provides contextual information for establishing accurate associations between detections or tracklets across frames and, thus, for obtaining more robust tracking results. Bottom-up evidence percolates upwards so as to automatically infer collective activity labels. Experimental results on two challenging data sets demonstrate our theoretical claims and indicate that our model achieves enhances tracking results and the best collective classification results to date.

  4. From organized internal traffic to collective navigation of bacterial swarms

    International Nuclear Information System (INIS)

    Ariel, Gil; Shklarsh, Adi; Kalisman, Oren; Ben-Jacob, Eshel; Ingham, Colin

    2013-01-01

    Bacterial swarming resulting in collective navigation over surfaces provides a valuable example of cooperative colonization of new territories. The social bacterium Paenibacillus vortex exhibits successful and diverse swarming strategies. When grown on hard agar surfaces with peptone, P. vortex develops complex colonies of vortices (rotating bacterial aggregates). In contrast, during growth on Mueller–Hinton broth gelled into a soft agar surface, a new strategy of multi-level organization is revealed: the colonies are organized into a special network of swarms (or ‘snakes’ of a fraction of millimeter in width) with intricate internal traffic. More specifically, cell movement is organized in two or three lanes of bacteria traveling between the back and the front of the swarm. This special form of cellular logistics suggests new methods in which bacteria can share resources and risk while searching for food or migrating into new territories. While the vortices-based organization on hard agar surfaces has been modeled before, here, we introduce a new multi-agent bacterial swarming model devised to capture the swarms-based organization on soft surfaces. We test two putative generic mechanisms that may underlie the observed swarming logistics: (i) chemo-activated taxis in response to chemical cues and (ii) special align-and-push interactions between the bacteria and the boundary of the layer of lubricant collectively generated by the swarming bacteria. Using realistic parameters, the model captures the observed phenomena with semi-quantitative agreement in terms of the velocity as well as the dynamics of the swarm and its envelope. This agreement implies that the bacteria interactions with the swarm boundary play a crucial role in mediating the interplay between the collective movement of the swarm and the internal traffic dynamics. (paper)

  5. Understanding the National Domestic Waste Collection Standards

    CSIR Research Space (South Africa)

    Oelofse, Suzanna HH

    2011-05-01

    Full Text Available The Department of Environmental Affairs with the assistance of the CSIR, developed the National Domestic Waste Collection Standards, which contain a range of service standards appropriate to different contexts. The standards, which came into effect...

  6. Understanding and Developing Black Popular Music Collections.

    Science.gov (United States)

    Murray, James Briggs

    1983-01-01

    Enumerates types of black popular music (work songs, spirituals, gospel music, blues, race records, rock and roll, soul, funk, disco, Caribbean, and African) and discusses collection development (current, retrospective, monographs, periodicals, sheet music, motion picture film, photographs, oral history), cataloging, and preservation. A 229-item…

  7. Towards understanding the molecular basis of bacterial DNA segregation

    DEFF Research Database (Denmark)

    Leonard, Thomas A.; Møller-Jensen, Jakob; Löwe, Jan

    2005-01-01

    Bacteria ensure the fidelity of genetic inheritance by the coordinated control of chromosome segregation and cell division. Here, we review the molecules and mechanisms that govern the correct subcellular positioning and rapid separation of newly replicated chromosomes and plasmids towards the cell...... poles and, significantly, the emergence of mitotic-like machineries capable of segregating plasmid DNA. We further describe surprising similarities between proteins involved in DNA partitioning (ParA/ParB) and control of cell division (MinD/MinE), suggesting a mechanism for intracellular positioning...... common to the two processes. Finally, we discuss the role that the bacterial cytoskeleton plays in DNA partitioning and the missing link between prokaryotes and eukaryotes that is bacterial mechano-chemical motor proteins. Udgivelsesdato: Mar 29...

  8. Sponge-specific unknown bacterial groups detected in marine sponges collected from Korea through barcoded pyrosequencing.

    Science.gov (United States)

    Jeong, Jong-Bin; Kim, Kyoung-Ho; Park, Jin-Sook

    2015-01-01

    The bacterial diversity of 10 marine sponges belonging to the species Cliona celata, an unidentified Cliona species, Haliclona cinerea, Halichondria okadai, Hymeniacidon sinapium, Lissodendoryx isodictyalis, Penares incrustans, Spirastrella abata, and Spirastrella panis collected from Jeju Island and Chuja Island was investigated using amplicon pyrosequencing of the 16S rRNA genes. The microbial diversity of these sponges has as of yet rarely or never been investigated. All sponges, except Cliona celata, Lissodendoryx isodictyalis, and Penares incrustans, showed simple bacterial diversity, in which one or two bacterial OTUs occupied more than 50% of the pyrosequencing reads and their OTU rank abundance curves saturated quickly. Most of the predominant OTUs belonged to Alpha-, Beta-, or Gammaproteobacteria. Some of the OTUs from the sponges with low diversity were distantly (88%~89%) or moderately (93%~97%) related to known sequences in the GenBank nucleotide database. Phylogenetic analysis showed that many of the representative sequences of the OTUs were related to the sequences originating from sponges and corals, and formed sponge-specific or -related clades. The marine sponges investigated herein harbored unexplored bacterial diversity, and further studies should be done to understand the microbes present in sponges.

  9. Understanding bacterial resistance to antimicrobial peptides: From the surface to deep inside.

    Science.gov (United States)

    Maria-Neto, Simone; de Almeida, Keyla Caroline; Macedo, Maria Ligia Rodrigues; Franco, Octávio Luiz

    2015-11-01

    Resistant bacterial infections are a major health problem in many parts of the world. The major commercial antibiotic classes often fail to combat common bacteria. Although antimicrobial peptides are able to control bacterial infections by interfering with microbial metabolism and physiological processes in several ways, a large number of cases of resistance to antibiotic peptide classes have also been reported. To gain a better understanding of the resistance process various technologies have been applied. Here we discuss multiple strategies by which bacteria could develop enhanced antimicrobial peptide resistance, focusing on sub-cellular regions from the surface to deep inside, evaluating bacterial membranes, cell walls and cytoplasmic metabolism. Moreover, some high-throughput methods for antimicrobial resistance detection and discrimination are also examined. This article is part of a Special Issue entitled: Bacterial Resistance to Antimicrobial Peptides. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Teaching with Technology: Using Websites and Videos to Increase Understanding of Bacterial Transformation

    Science.gov (United States)

    McCormack, Stephanie; Ross, Donna L.

    2010-01-01

    Technology can be a powerful tool to increase motivation, engagement, and achievement (Park, Khan, and Petrina 2009). In this article, the authors describe their collaborative approach to integrating technology with a lab on bacterial transformation. Students view websites and create videos to increase their conceptual understanding. Although the…

  11. Characterization of CCN and IN activity of bacterial isolates collected in Atlanta, GA

    Science.gov (United States)

    Purdue, Sara; Waters, Samantha; Karthikeyan, Smruthi; Konstantinidis, Kostas; Nenes, Athanasios

    2016-04-01

    Characterization of CCN activity of bacteria, other than a few select types such as Pseudomonas syringae, is limited, especially when looked at in conjunction with corresponding IN activity. The link between these two points is especially important for bacteria as those that have high CCN activity are likely to form an aqueous phase required for immersion freezing. Given the high ice nucleation temperature of bacterial cells, especially in immersion mode, it is important to characterize the CCN and IN activity of many different bacterial strains. To this effect, we developed a droplet freezing assay (DFA) which consists of an aluminum cold plate, cooled by a continuous flow of an ethylene glycol-water mixture, in order to observe immersion freezing of the collected bacteria. Here, we present the initial results on the CCN and IN activities of bacterial samples we have collected in Atlanta, GA. Bacterial strains were collected and isolated from rainwater samples taken from different storms throughout the year. We then characterized the CCN activity of each strain using a DMT Continuous Flow Streamwise Thermal Gradient CCN Counter by exposing the aerosolized bacteria to supersaturations ranging from 0.05% to 0.6%. Additionally, using our new DFA, we characterized the IN activity of each bacterial strain at temperatures ranging from -20oC to 0oC. The combined CCN and IN activity gives us valuable information on how some uncharacterized bacteria contribute to warm and mixed-phase cloud formation in the atmosphere.

  12. Understanding collective dynamics of soft active colloids by binary scattering.

    Science.gov (United States)

    Hanke, Timo; Weber, Christoph A; Frey, Erwin

    2013-11-01

    Collective motion in actively propelled particle systems is triggered on the very local scale by nucleation of coherently moving units consisting of just a handful of particles. These units grow and merge over time, ending up in a long-range ordered, coherently moving state. So far, there exists no bottom-up understanding of how the microscopic dynamics and interactions between the constituents are related to the system's ordering instability. In this paper, we study a class of models for propelled colloids allowing an explicit treatment of the microscopic details of the collision process. Specifically, the model equations are Newtonian equations of motion with separate force terms for particles' driving, dissipation, and interaction forces. Focusing on dilute particle systems, we analyze the binary scattering behavior for these models and determine-based on the microscopic dynamics-the corresponding "collision rule," i.e., the mapping of precollisional velocities and impact parameter on postcollisional velocities. By studying binary scattering we also find that the considered models for active colloids share the same principle for parallel alignment: The first incoming particle (with respect to the center of collision) is aligned to the second particle as a result of the encounter. This behavior distinctively differs from alignment in nondriven dissipative gases. Moreover, the obtained collision rule lends itself as a starting point to apply kinetic theory for propelled particle systems in order to determine the phase boundary to a long-range ordered, coherently moving state. The microscopic origin of the collision rule offers the opportunity to quantitatively scrutinize the predictions of kinetic theory for propelled particle systems through direct comparison with multiparticle simulations. We identify local precursor correlations at the onset of collective motion to constitute the essential determinant for a qualitative and quantitative validity of kinetic

  13. Active depinning of bacterial droplets: the collective surfing of Bacillus subtilis

    Science.gov (United States)

    Hennes, Marc; Tailleur, Julien; Daerr, Adrian

    2016-11-01

    How systems are endowed with migration capacity is a fascinating question with implications ranging from the design of novel active systems to the control of microbial populations. Bacteria, which can be found in a variety of environments, have developed among the richest set of locomotion mechanisms both at the microscopic and collective levels. Here, we uncover experimentally a new mode of collective bacterial motility in humid environment through the depinning of bacterial droplets. While capillary forces are notoriously enormous at the bacterial scale, even capable of pinning water droplets of millimetric size on inclined surfaces, we show that bacteria are able to harness a variety of mechanisms to unpin contact lines, hence inducing a collective sliding of the colony. Contrary to flagella-dependent migration modes like swarming we show that this much faster colony surfing still occurs in mutant strains of Bacillus subtilis lacking flagella. The diversity of mechanisms involved in the active unpinning seen in our experiments suggests that collective surfing should be a generic mode of migration of microorganisms in humid environments. Bacttern Grant.

  14. Toward a Metagenomic Understanding on the Bacterial Composition and Resistome in Hong Kong Banknotes.

    Science.gov (United States)

    Heshiki, Yoshitaro; Dissanayake, Thrimendra; Zheng, Tingting; Kang, Kang; Yueqiong, Ni; Xu, Zeling; Sarkar, Chinmoy; Woo, Patrick C Y; Chow, Billy K C; Baker, David; Yan, Aixin; Webster, Christopher J; Panagiotou, Gianni; Li, Jun

    2017-01-01

    Currency is possibly one of the main media transmitting pathogens and drug resistance due to its wide circulation in daily life. In this study, we made a comprehensive characterization of the bacterial community present on banknotes collected from different geographical regions of Hong Kong (HK) by performing in vitro characterization of the bacterial presence and resistome profile, as well as metagenomic analysis including microbial diversity, the prevalence of potential pathogens, the dissemination potential of antibiotic-resistance genes (ARGs), among others. When comparing the bacterial community of HK banknotes with other HK environmental samples, including water and marine sediment, we revealed that HK banknotes cover nearly 50% of total genera found in all the environmental samples, implying that banknotes harbor diverse bacteria originated from a variety of environments. Furthermore, the banknotes have higher abundance of potential pathogenic species (~5 times more) and ARGs (~5 times more) with higher dissemination potential (~48 times more) compared with other environmental samples. These findings unveiled the capabilities of this common medium of exchange to accommodate various bacteria, and transmit pathogens and antibiotic resistance. Furthermore, the observed independence of microbiome profile from the city's topological indices led us to formulate a hypothesis that due to their high circulation banknotes may harbor a homogenized microbiome.

  15. Bacterial Stigmergy: An Organising Principle of Multicellular Collective Behaviours of Bacteria

    Directory of Open Access Journals (Sweden)

    Erin S. Gloag

    2015-01-01

    Full Text Available The self-organisation of collective behaviours often manifests as dramatic patterns of emergent large-scale order. This is true for relatively “simple” entities such as microbial communities and robot “swarms,” through to more complex self-organised systems such as those displayed by social insects, migrating herds, and many human activities. The principle of stigmergy describes those self-organised phenomena that emerge as a consequence of indirect communication between individuals of the group through the generation of persistent cues in the environment. Interestingly, despite numerous examples of multicellular behaviours of bacteria, the principle of stigmergy has yet to become an accepted theoretical framework that describes how bacterial collectives self-organise. Here we review some examples of multicellular bacterial behaviours in the context of stigmergy with the aim of bringing this powerful and elegant self-organisation principle to the attention of the microbial research community.

  16. X-ray crystallography and its impact on understanding bacterial cell wall remodeling processes.

    Science.gov (United States)

    Büttner, Felix Michael; Renner-Schneck, Michaela; Stehle, Thilo

    2015-02-01

    The molecular structure of matter defines its properties and function. This is especially true for biological macromolecules such as proteins, which participate in virtually all biochemical processes. A three dimensional structural model of a protein is thus essential for the detailed understanding of its physiological function and the characterization of essential properties such as ligand binding and reaction mechanism. X-ray crystallography is a well-established technique that has been used for many years, but it is still by far the most widely used method for structure determination. A particular strength of this technique is the elucidation of atomic details of molecular interactions, thus providing an invaluable tool for a multitude of scientific projects ranging from the structural classification of macromolecules over the validation of enzymatic mechanisms or the understanding of host-pathogen interactions to structure-guided drug design. In the first part of this review, we describe essential methodological and practical aspects of X-ray crystallography. We provide some pointers that should allow researchers without a background in structural biology to assess the overall quality and reliability of a crystal structure. To highlight its potential, we then survey the impact X-ray crystallography has had on advancing an understanding of a class of enzymes that modify the bacterial cell wall. A substantial number of different bacterial amidase structures have been solved, mostly by X-ray crystallography. Comparison of these structures highlights conserved as well as divergent features. In combination with functional analyses, structural information on these enzymes has therefore proven to be a valuable template not only for understanding their mechanism of catalysis, but also for targeted interference with substrate binding. Copyright © 2015 Elsevier GmbH. All rights reserved.

  17. Understanding cellular responses to toxic agents: a model for mechanism-choice in bacterial metal resistance.

    Science.gov (United States)

    Rouch, D A; Lee, B T; Morby, A P

    1995-02-01

    Bacterial resistances to metals are heterogeneous in both their genetic and biochemical bases. Metal resistance may be chromosomally-, plasmid- or transposon-encoded, and one or more genes may be involved: at the biochemical level at least six different mechanisms are responsible for resistance. Various types of resistance mechanisms can occur singly or in combination and for a particular metal different mechanisms of resistance can occur in the same species. To understand better the diverse responses of bacteria to metal ion challenge we have constructed a qualitative model for the selection of metal resistance in bacteria. How a bacterium becomes resistant to a particular metal depends on the number and location of cellular components sensitive to the specific metal ion. Other important selective factors include the nature of the uptake systems for the metal, the role and interactions of the metal in the normal metabolism of the cell and the availability of plasmid (or transposon) encoded resistance mechanisms. The selection model presented is based on the interaction of these factors and allows predictions to be made about the evolution of metal resistance in bacterial populations. It also allows prediction of the genetic basis and of mechanisms of resistance which are in substantial agreement with those in well-documented populations. The interaction of, and selection for resistance to, toxic substances in addition to metals, such as antibiotics and toxic analogues, involve similar principles to those concerning metals. Potentially, models for selection of resistance to any substance can be derived using this approach.

  18. Multidisciplinary approaches to understanding collective cell migration in developmental biology.

    Science.gov (United States)

    Schumacher, Linus J; Kulesa, Paul M; McLennan, Rebecca; Baker, Ruth E; Maini, Philip K

    2016-06-01

    Mathematical models are becoming increasingly integrated with experimental efforts in the study of biological systems. Collective cell migration in developmental biology is a particularly fruitful application area for the development of theoretical models to predict the behaviour of complex multicellular systems with many interacting parts. In this context, mathematical models provide a tool to assess the consistency of experimental observations with testable mechanistic hypotheses. In this review, we showcase examples from recent years of multidisciplinary investigations of neural crest cell migration. The neural crest model system has been used to study how collective migration of cell populations is shaped by cell-cell interactions, cell-environmental interactions and heterogeneity between cells. The wide range of emergent behaviours exhibited by neural crest cells in different embryonal locations and in different organisms helps us chart out the spectrum of collective cell migration. At the same time, this diversity in migratory characteristics highlights the need to reconcile or unify the array of currently hypothesized mechanisms through the next generation of experimental data and generalized theoretical descriptions. © 2016 The Authors.

  19. ANTIMICROBIAL POTENCIAL OF SCHINUS TEREBENTHIFOLIUS ON BACTERIAL COLONIES COLLECTED BY PRESSURE ULCERS

    OpenAIRE

    Emiliana de Omena Bomfim; Giani Maria Cavalcante; Marcileide da Silva Santos

    2012-01-01

    The aim of this study is investigate the antimicrobial potential of plant species Schinus terebenthifolius, aroeira-red, on bacterial colonies of the exudate from pressure ulcers. Clinical samples were collected from pressure ulcers of 6 patients of ADEFAL, plated on blood agar and after incubation an aliquot of suspension (in the range of 0.5 Mac Farland) was sown in Mueller-Hinton. The plant extracts were ground and standardized with the aid of sieves of 150 and 75 micrometers. The re...

  20. ANTIMICROBIAL POTENCIAL OF SCHINUS TEREBENTHIFOLIUS ON BACTERIAL COLONIES COLLECTED BY PRESSURE ULCERS

    Directory of Open Access Journals (Sweden)

    Emiliana de Omena Bomfim

    2012-08-01

    Full Text Available The aim of this study is investigate the antimicrobial potential of plant species Schinus terebenthifolius, aroeira-red, on bacterial colonies of the exudate from pressure ulcers. Clinical samples were collected from pressure ulcers of 6 patients of ADEFAL, plated on blood agar and after incubation an aliquot of suspension (in the range of 0.5 Mac Farland was sown in Mueller-Hinton. The plant extracts were ground and standardized with the aid of sieves of 150 and 75 micrometers. The resulting powder was mixed with distilled water (10% m.v-1. To evaluate the antimicrobial activity, the disks were sterile filter paper saturat results referring to antibacterial activity of Schinus terebenthifolius (leaf indicate an average inhibition zone of bacterial growth of 10.8 mm. Regarding Schinus terebenthifolius (stem this study reveals Potencial antimicrobiano de extrato vegetal the inefficiency of 10% of the extract as antimicrobial agent. This fact legitimizes the literature findings which show antimicrobial activity of plant extract Schinus terebenthifolius (stem, only when tested at a concentration above 10. The efficiency of the leaves of Schinus terebenthifolius supports the use of this product to minimize bacterial colonization and future infections. However, the results that showed antibacterial inactivity of Schinus terebenthifolius (stem makes impracticable use this part of plant to treat pressure ulcers use of the extract of this plant a concentration of 10%.

  1. Pooling the ground: Understanding and coordination in collective sense making.

    Directory of Open Access Journals (Sweden)

    Joanna eRaczaszek-Leonardi

    2014-11-01

    Full Text Available Common ground is most often understood as the sum of mutually known beliefs, knowledge and suppositions among the participants in a conversation. It explains why participants do not mention things that should be obvious to both. In some accounts of communication, reaching a mutual understanding, i.e., broadening the common ground, is posed as the ultimate goal of linguistic interactions. Yet, congruent with the more pragmatic views of linguistic behavior, in which language is treated as social coordination, understanding each other is not the purpose (or not the sole purpose of linguistic interactions. This purpose is seen as at least twofold (e.g. Fusaroli, Rączaszek-Leonardi & Tylén, 2014: to maintain the systemic character of a conversing dyad and to organize it into a functional synergy in the face of tasks posed for a dyadic system as a whole. It seems that the notion of common ground may not be sufficient to address this dual character of interaction. In situated communication, in which meaning is created in the very process of interaction, both common (sameness and privileged (diversity information must be pooled task-dependently and across participants. In this paper, we analyze the definitions of common and privileged ground and propose extensions that may facilitate a theoretical account of agents that coordinate via linguistic communication. To illustrate the usefulness of this augmented framework, we apply it to one of the recurrent issues in psycholinguistic research, namely the problem of perspective-taking in dialogue, and draw conclusions for the broader problem of audience design.

  2. Pooling the ground: understanding and coordination in collective sense making

    Science.gov (United States)

    Rączaszek-Leonardi, Joanna; Dębska, Agnieszka; Sochanowicz, Adam

    2014-01-01

    Common ground is most often understood as the sum of mutually known beliefs, knowledge, and suppositions among the participants in a conversation. It explains why participants do not mention things that should be obvious to both. In some accounts of communication, reaching a mutual understanding, i.e., broadening the common ground, is posed as the ultimate goal of linguistic interactions. Yet, congruent with the more pragmatic views of linguistic behavior, in which language is treated as social coordination, understanding each other is not the purpose (or not the sole purpose) of linguistic interactions. This purpose is seen as at least twofold (e.g., Fusaroli et al., 2014): to maintain the systemic character of a conversing dyad and to organize it into a functional synergy in the face of tasks posed for a dyadic system as a whole. It seems that the notion of common ground is not sufficient to address the latter character of interaction. In situated communication, in which meaning is created in a distributed way in the very process of interaction, both common (sameness) and privileged (diversity) information must be pooled task-dependently across participants. In this paper, we analyze the definitions of common and privileged ground and propose a conceptual extension that may facilitate a theoretical account of agents that coordinate via linguistic communication. To illustrate the usefulness of this augmented framework, we apply it to one of the recurrent issues in psycholinguistic research, namely the problem of perspective-taking in dialog, and draw conclusions for the broader problem of audience design. PMID:25426087

  3. Detection of human bacterial pathogens in ticks collected from Louisiana black bears (Ursus americanus luteolus).

    Science.gov (United States)

    Leydet, Brian F; Liang, Fang-Ting

    2013-04-01

    There are 4 major human-biting tick species in the northeastern United States, which include: Amblyomma americanum, Amblyomma maculatum, Dermacentor variabilis, and Ixodes scapularis. The black bear is a large mammal that has been shown to be parasitized by all the aforementioned ticks. We investigated the bacterial infections in ticks collected from Louisiana black bears (Ursus americanus subspecies luteolus). Eighty-six ticks were collected from 17 black bears in Louisiana from June 2010 to March 2011. All 4 common human-biting tick species were represented. Each tick was subjected to polymerase chain reaction (PCR) targeting select bacterial pathogens and symbionts. Bacterial DNA was detected in 62% of ticks (n=53). Rickettsia parkeri, the causative agent of an emerging spotted fever group rickettsiosis, was identified in 66% of A. maculatum, 28% of D. variabilis, and 11% of I. scapularis. The Lyme disease bacterium, Borrelia burgdorferi, was detected in 2 I. scapularis, while one A. americanum was positive for Borrelia bissettii, a putative human pathogen. The rickettsial endosymbionts Candidatus Rickettsia andeanae, rickettsial endosymbiont of I. scapularis, and Rickettsia amblyommii were detected in their common tick hosts at 21%, 39%, and 60%, respectively. All ticks were PCR-negative for Anaplasma phagocytophilum, Ehrlichia spp., and Babesia microti. This is the first reported detection of R. parkeri in vector ticks in Louisiana; we also report the novel association of R. parkeri with I. scapularis. Detection of both R. parkeri and B. burgdorferi in their respective vectors in Louisiana demands further investigation to determine potential for human exposure to these pathogens. Copyright © 2013 Elsevier GmbH. All rights reserved.

  4. Understanding recurrent crime as system-immanent collective behavior.

    Directory of Open Access Journals (Sweden)

    Matjaž Perc

    Full Text Available Containing the spreading of crime is a major challenge for society. Yet, since thousands of years, no effective strategy has been found to overcome crime. To the contrary, empirical evidence shows that crime is recurrent, a fact that is not captured well by rational choice theories of crime. According to these, strong enough punishment should prevent crime from happening. To gain a better understanding of the relationship between crime and punishment, we consider that the latter requires prior discovery of illicit behavior and study a spatial version of the inspection game. Simulations reveal the spontaneous emergence of cyclic dominance between "criminals", "inspectors", and "ordinary people" as a consequence of spatial interactions. Such cycles dominate the evolutionary process, in particular when the temptation to commit crime or the cost of inspection are low or moderate. Yet, there are also critical parameter values beyond which cycles cease to exist and the population is dominated either by a stable mixture of criminals and inspectors or one of these two strategies alone. Both continuous and discontinuous phase transitions to different final states are possible, indicating that successful strategies to contain crime can be very much counter-intuitive and complex. Our results demonstrate that spatial interactions are crucial for the evolutionary outcome of the inspection game, and they also reveal why criminal behavior is likely to be recurrent rather than evolving towards an equilibrium with monotonous parameter dependencies.

  5. The gut bacterial communities associated with lab-raised and field-collected ants of Camponotus fragilis (Formicidae: Formicinae).

    Science.gov (United States)

    He, Hong; Wei, Cong; Wheeler, Diana E

    2014-09-01

    Camponotus is the second largest ant genus and known to harbor the primary endosymbiotic bacteria of the genus Blochmannia. However, little is known about the effect of diet and environment changes on the gut bacterial communities of these ants. We investigated the intestinal bacterial communities in the lab-raised and field-collected ants of Camponotus fragilis which is found in the southwestern United States and northern reaches of Mexico. We determined the difference of gut bacterial composition and distribution among the crop, midgut, and hindgut of the two types of colonies. Number of bacterial species varied with the methods of detection and the source of the ants. Lab-raised ants yielded 12 and 11 species using classical microbial culture methods and small-subunit rRNA genes (16S rRNAs) polymerase chain reaction-restriction fragment-length polymorphism analysis, respectively. Field-collected ants yielded just 4 and 1-3 species using the same methods. Most gut bacterial species from the lab-raised ants were unevenly distributed among the crop, midgut, and hindgut, and each section had its own dominant bacterial species. Acetobacter was the prominent bacteria group in crop, accounting for about 55 % of the crop clone library. Blochmannia was the dominant species in midgut, nearly reaching 90 % of the midgut clone library. Pseudomonas aeruginosa dominated the hindgut, accounting for over 98 % of the hindgut clone library. P. aeruginosa was the only species common to all three sections. A comparison between lab-raised and field-collected ants, and comparison with other species, shows that gut bacterial communities vary with local environment and diet. The bacterial species identified here were most likely commensals with little effect on their hosts or mild pathogens deleterious to colony health.

  6. Diversity and localization of bacterial endosymbionts from whitefly species collected in Brazil.

    Science.gov (United States)

    Marubayashi, Julio Massaharu; Kliot, Adi; Yuki, Valdir Atsushi; Rezende, Jorge Alberto Marques; Krause-Sakate, Renate; Pavan, Marcelo Agenor; Ghanim, Murad

    2014-01-01

    Whiteflies (Hemiptera: Aleyrodidae) are sap-sucking insect pests, and some cause serious damage in agricultural crops by direct feeding and by transmitting plant viruses. Whiteflies maintain close associations with bacterial endosymbionts that can significantly influence their biology. All whitefly species harbor a primary endosymbiont, and a diverse array of secondary endosymbionts. In this study, we surveyed 34 whitefly populations collected from the states of Sao Paulo, Bahia, Minas Gerais and Parana in Brazil, for species identification and for infection with secondary endosymbionts. Sequencing the mitochondrial Cytochrome Oxidase I gene revealed the existence of five whitefly species: The sweetpotato whitefly Bemisia tabaci B biotype (recently termed Middle East-Asia Minor 1 or MEAM1), the greenhouse whitefly Trialeurodes vaporariorum, B. tabaci A biotype (recently termed New World 2 or NW2) collected only from Euphorbia, the Acacia whitefly Tetraleurodes acaciae and Bemisia tuberculata both were detected only on cassava. Sequencing rRNA genes showed that Hamiltonella and Rickettsia were highly prevalent in all MEAM1 populations, while Cardinium was close to fixation in only three populations. Surprisingly, some MEAM1 individuals and one NW2 population were infected with Fritschea. Arsenopnohus was the only endosymbiont detected in T. vaporariorum. In T. acaciae and B. tuberculata populations collected from cassava, Wolbachia was fixed in B. tuberculata and was highly prevalent in T. acaciae. Interestingly, while B. tuberculata was additionally infected with Arsenophonus, T. acaciae was infected with Cardinium and Fritschea. Fluorescence in situ hybridization analysis on representative individuals showed that Hamiltonella, Arsenopnohus and Fritschea were localized inside the bacteriome, Cardinium and Wolbachia exhibited dual localization patterns inside and outside the bacteriome, and Rickettsia showed strict localization outside the bacteriome. This study is

  7. Critical sources of bacterial contamination and adoption of standard sanitary protocol during semen collection and processing in Semen Station

    Directory of Open Access Journals (Sweden)

    Chandrahas Sannat

    2015-05-01

    Full Text Available Aim: The present investigation was conducted to locate the critical sources of bacterial contamination and to evaluate the standard sanitation protocol so as to improve the hygienic conditions during collection, evaluation, and processing of bull semen in the Semen Station. Materials and Methods: The study compared two different hygienic procedures during the collection, evaluation and processing of semen in Central Semen Station, Anjora, Durg. Routinely used materials including artificial vagina (AV inner liner, cone, semen collection tube, buffer, extender/diluter, straws; and the laboratory environment like processing lab, pass box and laminar air flow (LAF cabinet of extender preparation lab, processing lab, sealing filling machine, and bacteriological lab were subjected to bacteriological examination in two phases of study using two different sanitary protocols. Bacterial load in above items/environment was measured using standard plate count method and expressed as colony forming unit (CFU. Results: Bacterial load in a laboratory environment and AV equipments during two different sanitary protocol in present investigation differed highly significantly (p<0.001. Potential sources of bacterial contamination during semen collection and processing included laboratory environment like processing lab, pass box, and LAF cabinets; AV equipments, including AV Liner and cone. Bacterial load was reduced highly significantly (p<0.001 in AV liner (from 2.33±0.67 to 0.50±0.52, cone (from 4.16±1.20 to 1.91±0.55, and extender (from 1.33±0.38 to 0 after application of improved practices of packaging, handling, and sterilization in Phase II of study. Glasswares, buffers, and straws showed nil bacterial contamination in both the phases of study. With slight modification in fumigation protocol (formalin @600 ml/1000 ft3, bacterial load was significantly decreased (p<0.001 up to 0-6 CFU in processing lab (from 6.43±1.34 to 2.86±0.59, pass box (from 12

  8. Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species

    OpenAIRE

    Luo, Chengwei; Walk, Seth T.; Gordon, David M.; Feldgarden, Michael; Tiedje, James M.; Konstantinidis, Konstantinos T.

    2011-01-01

    Defining bacterial species remains a challenging problem even for the model bacterium Escherichia coli and has major practical consequences for reliable diagnosis of infectious disease agents and regulations for transport and possession of organisms of economic importance. E. coli traditionally is thought to live within the gastrointestinal tract of humans and other warm-blooded animals and not to survive for extended periods outside its host; this understanding is the basis for its widesprea...

  9. Physicochemical and Bacterial Properties of Pasteurized Milk Samples Collected from Tabriz, Northwestern Iran

    Directory of Open Access Journals (Sweden)

    Aida Farhoodi

    2016-03-01

    Full Text Available Milk and dairy products are important components of a balanced diet. Milk does have distinct physicochemical, biological and microbial characteristics. The bacterial contamination of milk not only reduces the nutritional quality but its consumption threatens health of the society. In this study, 100 pasteurized milk samples were collected randomly from Tabriz City, northwestern and were analyzed for total plate count (TPC, coliform, E. coli and some physicochemical properties (pH, titratable acidity and density. 33.3% of samples had unacceptable microbial contamination in both warm and cold seasons. E. coli contamination was not detected in all milk samples, but 54% of pasteurized milk samples were contaminated with coliforms. The pH value (6.6-6.8 and titratable acidity (0.14-0.16% were in acceptable range. The means value of samples’ density was 1028.79±1.04. Lower microbial contamination level in this area indicates that the dairy factories are concerned about appropriate sanitary practice and pasteurization process.

  10. An Inquiry-Based Laboratory Module to Promote Understanding of the Scientific Method and Bacterial Conjugation

    Directory of Open Access Journals (Sweden)

    Melanie B. Berkmen

    2014-08-01

    Full Text Available Students are engaged and improve their critical thinking skills in laboratory courses when they have the opportunity to design and conduct inquiry-based experiments that generate novel results. A discovery-driven project for a microbiology, genetics, or multidisciplinary research laboratory course was developed to familiarize students with the scientific method. In this multi-lab module, students determine whether their chosen stress conditions induce conjugation and/or cell death of the model BSL-1 Gram-positive bacterium Bacillus subtilis. Through consultation of the primary literature, students identify conditions or chemicals that can elicit DNA damage, the SOS response, and/or cellular stress.  In groups, students discuss their selected conditions, develop their hypotheses and experimental plans, and formulate their positive and negative controls. Students then subject the B. subtilis donor cells to the stress conditions, mix donors with recipients to allow mating, and plate serial dilutions of the mixtures on selective plates to measure how the treatments affect conjugation frequency and donor cell viability.  Finally, students analyze and discuss their collective data in light of their controls. The goals of this module are to encourage students to be actively involved in the scientific process while contributing to our understanding of the conditions that stimulate horizontal gene transfer in bacteria.

  11. Pigments Characterization and Molecular Identification of Bacterial Symbionts of Brown Algae Padinasp. Collected from Karimunjawa Island

    Directory of Open Access Journals (Sweden)

    Damar Bayu Murti

    2016-06-01

    Full Text Available The search for carotenoids in nature has been extensively studied because of their applications in foods. One treasure of the biopigment source is symbiotic-microorganisms with marine biota. The advantages of symbiont bacteria are easy to culture and sensitize pigments. The use of symbiont bacteria helps to conserve fish, coral reefs, seagrass, and seaweed. Therefore, the bacteria keeps their existence in their ecosystems. In this study, bacterial symbionts were successfully isolated from brown algae Padina sp. The bacterial symbionts had yellow pigment associated with carotenoids. The pigments were characterized using High Performance Liquid Chromatography (HPLC with a Photo Diode Array (PDA detector. The carotenoid pigments in the bacterial symbionts were identified as dinoxanthin, lutein and neoxanthin. Molecular identification by using a 16S rRNA gene sequence method, reveals that the bacterial symbionts were closely related to Bacillus marisflavi with a homology of 99%. Keywords :carotenoid pigments, brown algae, Padina, bacterial symbionts, 16S rRNA

  12. Understanding the bacterial polysaccharide antigenicity of Streptococcus agalactiae versus Streptococcus pneumoniae.

    Science.gov (United States)

    Kadirvelraj, Renuka; Gonzalez-Outeiriño, Jorge; Foley, B Lachele; Beckham, Meredith L; Jennings, Harold J; Foote, Simon; Ford, Michael G; Woods, Robert J

    2006-05-23

    Bacterial surface capsular polysaccharides (CPS) that are similar in carbohydrate sequence may differ markedly in immunogenicity and antigenicity. The structural origin of these phenomena is poorly understood. Such a case is presented by the Gram-positive bacteria Streptococcus agalactiae (Group B Streptococcus; GBS) type III (GBSIII) and Streptococcus pneumoniae (Pn) type 14 (Pn14), which share closely related CPS sequences. Nevertheless, antibodies (Abs) against GBSIII rarely cross-react with the CPS from Pn14. To establish the origin for the variation in CPS antigenicity, models for the immune complexes of CPS fragments from GBSIII and Pn14, with the variable fragment (Fv) of a GBS-specific mAb (mAb 1B1), are presented. The complexes are generated through a combination of comparative Ab modeling and automated ligand docking, followed by explicitly solvated 10-ns molecular dynamics simulations. The relationship between carbohydrate sequence and antigenicity is further quantified through the computation of interaction energies using the Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) method, augmented by conformational entropy estimates. Despite the electrostatic differences between Pn14 and GBSIII CPS, analysis indicates that entropic penalties are primarily responsible for the loss of affinity of the highly flexible Pn14 CPS for mAb 1B1. The similarity of the solution conformation of the relatively rigid GBSIII CPS with that in the immune complex characterizes the previously undescribed 3D structure of the conformational epitope. The analysis provides a comprehensive interpretation for a large body of biochemical and immunological data related to Ab recognition of bacterial polysaccharides and should be applicable to other Ab-carbohydrate interactions.

  13. Bacterial communities in the collection and chlorinated distribution sections of a drinking water system in Budapest, Hungary.

    Science.gov (United States)

    Homonnay, Zalán G; Török, György; Makk, Judit; Brumbauer, Anikó; Major, Eva; Márialigeti, Károly; Tóth, Erika

    2014-07-01

    Bacterial communities of a bank-filtered drinking water system were investigated by aerobic cultivation and clone library analysis. Moreover, bacterial communities were compared using sequence-aided terminal restriction fragment length polymorphism (T-RFLP) fingerprinting at ten characteristic points located at both the collecting and the distributing part of the water supply system. Chemical characteristics of the samples were similar, except for the presence of chlorine residuals in the distribution system and increased total iron concentration in two of the samples. Assimilable organic carbon (AOC) concentration increased within the collection system, it was reduced by chlorination and it increased again in the distribution system. Neither fecal indicators nor pathogens were detected by standard cultivation techniques. Chlorination reduced bacterial diversity and heterotrophic plate counts. Community structures were found to be significantly different before and after chlorination: the diverse communities in wells and the collection system were dominated by chemolithotrophic (e.g., Gallionella and Nitrospira) and oligocarbophilic-heterotrophic bacteria (e.g., Sphingomonas, Sphingopyxis, and Bradyrhizobium). After chlorination in the distribution system, the most characteristic bacterium was related to the facultative methylotrophic Methylocella spp. Communities changed within the distribution system too, Mycobacterium spp. or Sphingopyxis spp. became predominant in certain samples. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Utilizing the Theoretical Framework of Collective Identity to Understand Processes in Youth Programs

    Science.gov (United States)

    Futch, Valerie A.

    2016-01-01

    This article explores collective identity as a useful theoretical framework for understanding social and developmental processes that occur in youth programs. Through narrative analysis of past participant interviews (n = 21) from an after-school theater program, known as "The SOURCE", it was found that participants very clearly describe…

  15. Using flow cytometry for counting natural planktonic bacteria and understanding the structure of planktonic bacterial communities

    Directory of Open Access Journals (Sweden)

    Josep M. Gasol

    2000-06-01

    Full Text Available Flow cytometry is rapidly becoming a routine methodology in aquatic microbial ecology. The combination of simple to use bench-top flow cytometers and highly fluorescent nucleic acid stains allows fast and easy determination of microbe abundance in the plankton of lakes and oceans. The different dyes and protocols used to stain and count planktonic bacteria as well as the equipment in use are reviewed, with special attention to some of the problems encountered in daily routine practice such as fixation, staining and absolute counting. One of the main advantages of flow cytometry over epifluorescence microscopy is the ability to obtain cell-specific measurements in large numbers of cells with limited effort. We discuss how this characteristic has been used for differentiating photosynthetic from non-photosynthetic prokaryotes, for measuring bacterial cell size and nucleic acid content, and for estimating the relative activity and physiological state of each cell. We also describe how some of the flow cytometrically obtained data can be used to characterize the role of microbes on carbon cycling in the aquatic environment and we prospect the likely avenues of progress in the study of planktonic prokaryotes through the use of flow cytometry.

  16. Antimicrobial potencial of Schinus terebenthifolius on bacterial colonies collected by pressure ulcers.

    Directory of Open Access Journals (Sweden)

    Marcileide da Silva Santos

    2012-01-01

    Full Text Available The aim of this study is investigate the antimicrobial potential of plant species Schinus terebenthifolius, aroeira-red, on bacterial colonies of the exudate from pressure ulcers. Clinical samples were collectedfrom pressure ulcers of 6 patients of ADEFAL, plated on blood agar and after incubation an aliquot of suspension (in the range of 0.5 Mac Farland was sown in Mueller-Hinton. The plant extracts were ground and standardized with the aid of sieves of 150 and 75 micrometers. The resulting powder was mixed with distilled water (10% m.v-1. To evaluate the antimicrobial activity, the disks were sterile filter paper with 10g of each extract. saturatresults referring to antibacterial activity of Schinus terebenthifolius (leaf indicate an average inhibition zone of bacterial growth of 10.8 mm. Regarding Schinus terebenthifolius (stem this study reveals the inefficiency of 10% of the extract as antimicrobial agent. This fact legitimizes the literature findings which show antimicrobial activity of plant extract Schinus terebenthifolius (stem, only when tested at a concentration above 10. The efficiency of the leaves of Schinus terebenthifolius supports the use of this product to minimize bacterial colonization and future infections. However, the results that showed antibacterial inactivity of Schinus terebenthifolius (stem makes impracticable use this part of plant to treat pressure ulcers use of the extract of this plant a concentration of 10%.

  17. Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species.

    Science.gov (United States)

    Luo, Chengwei; Walk, Seth T; Gordon, David M; Feldgarden, Michael; Tiedje, James M; Konstantinidis, Konstantinos T

    2011-04-26

    Defining bacterial species remains a challenging problem even for the model bacterium Escherichia coli and has major practical consequences for reliable diagnosis of infectious disease agents and regulations for transport and possession of organisms of economic importance. E. coli traditionally is thought to live within the gastrointestinal tract of humans and other warm-blooded animals and not to survive for extended periods outside its host; this understanding is the basis for its widespread use as a fecal contamination indicator. Here, we report the genome sequences of nine environmentally adapted strains that are phenotypically and taxonomically indistinguishable from typical E. coli (commensal or pathogenic). We find, however, that the commensal genomes encode for more functions that are important for fitness in the human gut, do not exchange genetic material with their environmental counterparts, and hence do not evolve according to the recently proposed fragmented speciation model. These findings are consistent with a more stringent and ecologic definition for bacterial species than the current definition and provide means to start replacing traditional approaches of defining distinctive phenotypes for new species with omics-based procedures. They also have important implications for reliable diagnosis and regulation of pathogenic E. coli and for the coliform cell-counting test.

  18. Understanding anti-tuberculosis drug efficacy: rethinking bacterial populations and how we model them

    Directory of Open Access Journals (Sweden)

    Dimitrios Evangelopoulos

    2015-03-01

    Full Text Available Tuberculosis still remains a global health emergency, claiming 1.5 million lives in 2013. The bacterium responsible for this disease, Mycobacterium tuberculosis (M.tb, has successfully survived within hostile host environments, adapting to immune defence mechanisms, for centuries. This has resulted in a disease that is challenging to treat, requiring lengthy chemotherapy with multi-drug regimens. One explanation for this difficulty in eliminating M.tb bacilli in vivo is the disparate action of antimicrobials on heterogeneous populations of M.tb, where mycobacterial physiological state may influence drug efficacy. In order to develop improved drug combinations that effectively target diverse mycobacterial phenotypes, it is important to understand how such subpopulations of M.tb are formed during human infection. We review here the in vitro and in vivo systems used to model M.tb subpopulations that may persist during drug therapy, and offer aspirations for future research in this field.

  19. Bacterial endosymbionts in field-collected samples of Trialeurodes sp. nr. abutiloneus (Hemiptera: Aleyrodidae).

    Science.gov (United States)

    Cass, Bodil N; Mozes-Daube, Netta; Iasur-Kruh, Lilach; Bondy, Elizabeth C; Kelly, Suzanne E; Hunter, Martha S; Zchori-Fein, Einat

    2014-01-01

    Facultative bacterial endosymbionts are common, influential associates of arthropods, yet their movement among host species has not been well documented. Plant-mediated transmission of Rickettsia has been shown for the whitefly Bemisia tabaci. Bemisia tabaci in USA cotton fields harbors the secondary symbionts Rickettsia and Hamiltonella, and co-occurs with Trialeurodes sp. nr. abutiloneus whiteflies. To determine whether symbionts may be shared, the microbial diversity of these whiteflies on cotton across the USA was analyzed. Trialeurodes sp. nr. abutiloneus bore Portiera, Pseudomonas, Serratia, Arsenophonus and Wolbachia. No Rickettsia or Hamiltonella were detected. These results provide no evidence for horizontal transmission of symbionts between these whitefly genera. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  20. Behaviour as a Lever of Ecological Transition? Understanding and Acting on Individual Behaviour and Collective Dynamics

    International Nuclear Information System (INIS)

    Martin, Solange; Gaspard, Albane

    2017-01-01

    Beyond broad policy declarations, the implementation of ecological transition - which consists mainly in curbing consumption of energy and raw materials in our societies - requires substantial behavioural change at the collective, but also, quite obviously, the individual level. Yet, though there is general consensus around the principle of embarking on the path to transition, things get more complicated when it comes to changing our practices and habits. Can we act on individual behaviour and collective dynamics in respect of this particular aim of ecological transition, and, if so, how are we to go about it? Solange Martin and Albane Gaspard have examined this question for the French Environment and Energy Management Agency (ADEME) and offer us the fruit of their labours here. They show, for example, how the social and human sciences help to understand behaviour both at the individual level and in its collective dimensions, and they outline different possible lines of action to modify it. But, given the entanglement between various levels, it is essential, if we are to act effectively on behaviour, to combine approaches, tools and actors, and to analyse and understand social practices thoroughly before implementing political projects or measures

  1. The Role of Antibiotic Prophylaxis in Reducing Bacterial Contamination of Autologous Bone Graft Collected from Implant Site

    Directory of Open Access Journals (Sweden)

    Rodolfo Mauceri

    2017-01-01

    Full Text Available The aim of this study was to evaluate if antibiotic prophylaxis reduces the bacterial contamination of bone particles collected directly from the burs used for implant site preparation. Thirty-four patients underwent the surgical procedures for a total of 34 implant sites. One 1 gr. tablet of amoxicillin + clavulanic acid was given to the test group 12 hours and 1 hour before the surgery. The control group did not take antibiotic prophylaxis. Bone particles were collected and centrifuged. The suspensions were subjected to serial dilutions and each dilution was examined twice using a spatulation technique in Trypticase Soy Agar (TSA, in Sabouraud Dextrose Agar, and in Mitis Salivarius Agar (MSA. The number of colonies was calculated and the identification of various microorganisms was made. The most represented species, in both groups of patients, belonged to the “oral Streptococci.” For TSA, the test and control groups differed significantly (p = 0.018. Conversely, there was no significant difference for MSA (p = 0.201 and for the number of bacterial species isolated in the samples of the two groups of patients (p = 0.898. The antibiotic prophylaxis reduced, but did not cancel, the risk of infection of the autogenous particulate bone graft. This trial is registered with IRCT2017102537002N1.

  2. The Role of Antibiotic Prophylaxis in Reducing Bacterial Contamination of Autologous Bone Graft Collected from Implant Site.

    Science.gov (United States)

    Mauceri, Rodolfo; Campisi, Giuseppina; Matranga, Domenica; Mauceri, Nicola; Pizzo, Giuseppe; Melilli, Dario

    2017-01-01

    The aim of this study was to evaluate if antibiotic prophylaxis reduces the bacterial contamination of bone particles collected directly from the burs used for implant site preparation. Thirty-four patients underwent the surgical procedures for a total of 34 implant sites. One 1 gr. tablet of amoxicillin + clavulanic acid was given to the test group 12 hours and 1 hour before the surgery. The control group did not take antibiotic prophylaxis. Bone particles were collected and centrifuged. The suspensions were subjected to serial dilutions and each dilution was examined twice using a spatulation technique in Trypticase Soy Agar (TSA), in Sabouraud Dextrose Agar, and in Mitis Salivarius Agar (MSA). The number of colonies was calculated and the identification of various microorganisms was made. The most represented species, in both groups of patients, belonged to the "oral Streptococci." For TSA, the test and control groups differed significantly ( p = 0.018). Conversely, there was no significant difference for MSA ( p = 0.201) and for the number of bacterial species isolated in the samples of the two groups of patients ( p = 0.898). The antibiotic prophylaxis reduced, but did not cancel, the risk of infection of the autogenous particulate bone graft. This trial is registered with IRCT2017102537002N1.

  3. The ARTT motif and a unified structural understanding of substraterecognition in ADP ribosylating bacterial toxins and eukaryotic ADPribosyltransferases

    Energy Technology Data Exchange (ETDEWEB)

    Han, S.; Tainer, J.A.

    2001-08-01

    ADP-ribosylation is a widely occurring and biologically critical covalent chemical modification process in pathogenic mechanisms, intracellular signaling systems, DNA repair, and cell division. The reaction is catalyzed by ADP-ribosyltransferases, which transfer the ADP-ribose moiety of NAD to a target protein with nicotinamide release. A family of bacterial toxins and eukaryotic enzymes has been termed the mono-ADP-ribosyltransferases, in distinction to the poly-ADP-ribosyltransferases, which catalyze the addition of multiple ADP-ribose groups to the carboxyl terminus of eukaryotic nucleoproteins. Despite the limited primary sequence homology among the different ADP-ribosyltransferases, a central cleft bearing NAD-binding pocket formed by the two perpendicular b-sheet core has been remarkably conserved between bacterial toxins and eukaryotic mono- and poly-ADP-ribosyltransferases. The majority of bacterial toxins and eukaryotic mono-ADP-ribosyltransferases are characterized by conserved His and catalytic Glu residues. In contrast, Diphtheria toxin, Pseudomonas exotoxin A, and eukaryotic poly-ADP-ribosyltransferases are characterized by conserved Arg and catalytic Glu residues. The NAD-binding core of a binary toxin and a C3-like toxin family identified an ARTT motif (ADP-ribosylating turn-turn motif) that is implicated in substrate specificity and recognition by structural and mutagenic studies. Here we apply structure-based sequence alignment and comparative structural analyses of all known structures of ADP-ribosyltransfeases to suggest that this ARTT motif is functionally important in many ADP-ribosylating enzymes that bear a NAD binding cleft as characterized by conserved Arg and catalytic Glu residues. Overall, structure-based sequence analysis reveals common core structures and conserved active sites of ADP-ribosyltransferases to support similar NAD binding mechanisms but differing mechanisms of target protein binding via sequence variations within the ARTT

  4. Mapping quorum sensing onto neural networks to understand collective decision making in heterogeneous microbial communities

    Science.gov (United States)

    Yusufaly, Tahir I.; Boedicker, James Q.

    2017-08-01

    Microbial communities frequently communicate via quorum sensing (QS), where cells produce, secrete, and respond to a threshold level of an autoinducer (AI) molecule, thereby modulating gene expression. However, the biology of QS remains incompletely understood in heterogeneous communities, where variant bacterial strains possess distinct QS systems that produce chemically unique AIs. AI molecules bind to ‘cognate’ receptors, but also to ‘non-cognate’ receptors found in other strains, resulting in inter-strain crosstalk. Understanding these interactions is a prerequisite for deciphering the consequences of crosstalk in real ecosystems, where multiple AIs are regularly present in the same environment. As a step towards this goal, we map crosstalk in a heterogeneous community of variant QS strains onto an artificial neural network model. This formulation allows us to systematically analyze how crosstalk regulates the community’s capacity for flexible decision making, as quantified by the Boltzmann entropy of all QS gene expression states of the system. In a mean-field limit of complete cross-inhibition between variant strains, the model is exactly solvable, allowing for an analytical formula for the number of variants that maximize capacity as a function of signal kinetics and activation parameters. An analysis of previous experimental results on the Staphylococcus aureus two-component Agr system indicates that the observed combination of variant numbers, gene expression rates and threshold concentrations lies near this critical regime of parameter space where capacity peaks. The results are suggestive of a potential evolutionary driving force for diversification in certain QS systems.

  5. Understanding the impact of water distribution system conditions on the biodegradation of haloacetic acids and expression of bacterial dehalogenase genes.

    Science.gov (United States)

    Behbahani, Mohsen; Lin, Boren; Phares, Tamara L; Seo, Youngwoo

    2018-06-05

    The objective of this study is to evaluate the influence of water distribution system conditions (pH, total organic carbon, residual chlorine, and phosphate) on haloacetic acids (HAAs) biodegradation. A series of batch microcosm tests were conducted to determine biodegradation kinetics and collected biomass was used for real time quantitative reverse transcription polymerase chain reaction analyses to monitor how these drinking water distribution system conditions affect the relative expression of bacterial dehalogenase genes. It was observed that tested water distribution system conditions affected HAA biodegradation with different removal efficiencies (0-100%). HAA biodegradation was improved in tested samples with TOC (3 mg/L) and pH 8.5 compared to those of TOC (0 mg/L) and pH 7, respectively. However, slight improvement was observed with the increased PO 4 concentration (3.5 mg/L), and the presence of residual chlorine even at low concentration prohibited biodegradation of HAAs. The observed trend in the relative expression of dehII genes was compatible with the HAA biodegradation trend. Overall relative expression ratio of dehII genes was lower at pH 7, phosphate (0.5 mg/L), and TOC (0 mg/L) in comparison with pH 8.5, phosphate (3.5 mg/L), and TOC (3 mg/L) in the same experimental conditions. Copyright © 2018 Elsevier B.V. All rights reserved.

  6. The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

    DEFF Research Database (Denmark)

    Lagkouvardos, Ilias; Pukall, Rüdiger; Abt, Birte

    2016-01-01

    BC), a public repository of bacterial strains and associated genomes from the mouse gut, and studied host-specificity of colonization and sequence-based relevance of the resource. The collection includes several strains representing novel species, genera and even one family. Genomic analyses showed that certain...... of intestinal microbiomes and their interactions with diet and host. It is thus important to study in detail the diversity and functions of gut microbiota members, including those colonizing the mouse intestine. To address these issues, we aimed at establishing the Mouse Intestinal Bacterial Collection (mi...... and molecular studies. The resource is available at www.dsmz.de/miBC....

  7. Understanding institutional stakeholders’ perspectives on multidrug-resistant bacterial organism at the end of life: a qualitative study

    Science.gov (United States)

    Heckel, Maria; Herbst, Franziska A; Adelhardt, Thomas; Tiedtke, Johanna M; Sturm, Alexander; Stiel, Stephanie; Ostgathe, Christoph

    2017-01-01

    Background Information lacks about institutional stakeholders’ perspectives on management approaches of multidrug-resistant bacterial organism in end-of-life situations. The term “institutional stakeholder” includes persons in leading positions with responsibility in hospitals’ multidrug-resistant bacterial organism management. They have great influence on how strategies on multidrug-resistant bacterial organism management approaches in institutions of the public health system are designed. This study targeted institutional stakeholders’ individual perspectives on multidrug-resistant bacterial organism colonization or infection and isolation measures at the end of life. Methods Between March and December 2014, institutional stakeholders of two study centers, a German palliative care unit and a geriatric ward, were queried in semistructured interviews. Interviews were audiotaped, transcribed verbatim, and analyzed qualitatively with the aid of the software MAXQDA for qualitative data analysis using principles of Grounded Theory. In addition, two external stakeholders were interviewed to enrich data. Results Key issues addressed by institutional stakeholders (N=18) were the relevance of multidrug-resistant bacterial organism in palliative and geriatric care, contradictions between hygiene principles and patients’ and family caregivers’ needs and divergence from standards, frame conditions, and reflections on standardization of multidrug-resistant bacterial organism end-of-life care procedures. Results show that institutional stakeholders face a dilemma between their responsibility in protecting third persons and ensuring patients’ quality of life. Until further empirical evidence establishes a clear multidrug-resistant bacterial organism management approach in end-of-life care, stakeholders suggest a case-based approach. Conclusion The institutional stakeholders’ perspectives and their suggestion of a case-based approach advance the development

  8. Understanding institutional stakeholders' perspectives on multidrug-resistant bacterial organism at the end of life: a qualitative study.

    Science.gov (United States)

    Heckel, Maria; Herbst, Franziska A; Adelhardt, Thomas; Tiedtke, Johanna M; Sturm, Alexander; Stiel, Stephanie; Ostgathe, Christoph

    2017-01-01

    Information lacks about institutional stakeholders' perspectives on management approaches of multidrug-resistant bacterial organism in end-of-life situations. The term "institutional stakeholder" includes persons in leading positions with responsibility in hospitals' multidrug-resistant bacterial organism management. They have great influence on how strategies on multidrug-resistant bacterial organism management approaches in institutions of the public health system are designed. This study targeted institutional stakeholders' individual perspectives on multidrug-resistant bacterial organism colonization or infection and isolation measures at the end of life. Between March and December 2014, institutional stakeholders of two study centers, a German palliative care unit and a geriatric ward, were queried in semistructured interviews. Interviews were audiotaped, transcribed verbatim, and analyzed qualitatively with the aid of the software MAXQDA for qualitative data analysis using principles of Grounded Theory. In addition, two external stakeholders were interviewed to enrich data. Key issues addressed by institutional stakeholders (N=18) were the relevance of multidrug-resistant bacterial organism in palliative and geriatric care, contradictions between hygiene principles and patients' and family caregivers' needs and divergence from standards, frame conditions, and reflections on standardization of multidrug-resistant bacterial organism end-of-life care procedures. Results show that institutional stakeholders face a dilemma between their responsibility in protecting third persons and ensuring patients' quality of life. Until further empirical evidence establishes a clear multidrug-resistant bacterial organism management approach in end-of-life care, stakeholders suggest a case-based approach. The institutional stakeholders' perspectives and their suggestion of a case-based approach advance the development process of a patient-, family-, staff-, and institutional

  9. Bacterial Proteasomes.

    Science.gov (United States)

    Jastrab, Jordan B; Darwin, K Heran

    2015-01-01

    Interest in bacterial proteasomes was sparked by the discovery that proteasomal degradation is required for the pathogenesis of Mycobacterium tuberculosis, one of the world's deadliest pathogens. Although bacterial proteasomes are structurally similar to their eukaryotic and archaeal homologs, there are key differences in their mechanisms of assembly, activation, and substrate targeting for degradation. In this article, we compare and contrast bacterial proteasomes with their archaeal and eukaryotic counterparts, and we discuss recent advances in our understanding of how bacterial proteasomes function to influence microbial physiology.

  10. Theoretical-methodological approach to social imaginary and collective representations: Notes for a sociological understanding of image

    Directory of Open Access Journals (Sweden)

    Jorge Eliécer Martínez Posada

    2009-01-01

    Full Text Available The study of social imaginaries and collective representations from a sociological perspective involves agencying interpretative exercises of image reconstruction, whether mental or pictorial images. Thus, the theoretical path followed in this text points to the understanding of social imaginaries and collective representations, as knowledge tradition socially constructed, and social images, which become historically symbolic points of reference of social action.

  11. The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

    DEFF Research Database (Denmark)

    Lagkouvardos, Ilias; Pukall, Rüdiger; Abt, Birte

    2016-01-01

    BC), a public repository of bacterial strains and associated genomes from the mouse gut, and studied host-specificity of colonization and sequence-based relevance of the resource. The collection includes several strains representing novel species, genera and even one family. Genomic analyses showed that certain...

  12. “Streptomyces massilialgeriensis” sp. nov., a new bacterial species isolated from an extremely saline soil collected from the dry lake of Ank el Djamel in Algeria

    Directory of Open Access Journals (Sweden)

    C.E. Djaballah

    2018-01-01

    Full Text Available We report here the main characteristics of “Streptomyces massilialgeriensis” strain S35T (CSUR = P3927, a new bacterial species within the Streptomyces genus, isolated from an extremely saline soil sample collected from the site of Garaet Ank Djemel in the Wilaya of Oum El Bouaghi, Algeria.

  13. Rhizosphere bacterial carbon turnover is higher in nucleic acids than membrane lipids: implications for understanding soil carbon cycling

    Directory of Open Access Journals (Sweden)

    Ashish A. Malik

    2015-04-01

    Full Text Available Using a pulse-chase 13CO2 plant labeling experiment we compared the flow of plant carbon into macromolecular fractions of root-associated soil microorganisms. Time dependent 13C dilution patterns in microbial cellular fractions were used to calculate their turnover time. The turnover times of microbial biomolecules were found to vary: microbial RNA (19 h and DNA (30 h turned over fastest followed by chloroform fumigation extraction-derived soluble cell lysis products (14 d, while phospholipid fatty acids (PLFAs had the slowest turnover (42 d. PLFA/NLFA 13C analyses suggest that both mutualistic arbuscular mycorrhizal and saprophytic fungi are dominant in initial plant carbon uptake. In contrast, high initial 13C enrichment in RNA hints at bacterial importance in initial C uptake due to the dominance of bacterial derived RNA in total extracts of soil RNA. To explain this discrepancy, we observed low renewal rate of bacterial lipids, which may therefore bias lipid fatty acid based interpretations of the role of bacteria in soil microbial food webs. Based on our findings, we question current assumptions regarding plant-microbe carbon flux and suggest that the rhizosphere bacterial contribution to plant assimilate uptake could be higher. This highlights the need for more detailed quantitative investigations with nucleic acid biomarkers to further validate these findings.

  14. Understanding institutional stakeholders’ perspectives on multidrug-resistant bacterial organism at the end of life: a qualitative study

    Directory of Open Access Journals (Sweden)

    Heckel M

    2017-10-01

    Full Text Available Maria Heckel,1 Franziska A Herbst,2 Thomas Adelhardt,3 Johanna M Tiedtke,4 Alexander Sturm,5 Stephanie Stiel,2 Christoph Ostgathe1 1Department of Palliative Medicine, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU, Universitätsklinikum Erlangen, Bavaria, Germany; 2Institute for General Practice, Hannover Medical School, Hannover, Germany; 3Division of Health Management, School of Business and Economics, Institute of Management (IFM, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU, Bavaria, Germany; 4Institute of Psychogerontology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU, Bavaria, Germany; 5Department of General Internal and Geriatric Medicine, Institute for Biomedicine of Aging, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU, Hospital of the Order of St John of God Regensburg, Bavaria, Germany Background: Information lacks about institutional stakeholders’ perspectives on management approaches of multidrug-resistant bacterial organism in end-of-life situations. The term “institutional stakeholder” includes persons in leading positions with responsibility in hospitals’ multidrug-resistant bacterial organism management. They have great influence on how strategies on multidrug-resistant bacterial organism management approaches in institutions of the public health system are designed. This study targeted institutional stakeholders’ individual perspectives on multidrug-resistant bacterial organism colonization or infection and isolation measures at the end of life. Methods: Between March and December 2014, institutional stakeholders of two study centers, a German palliative care unit and a geriatric ward, were queried in semistructured interviews. Interviews were audiotaped, transcribed verbatim, and analyzed qualitatively with the aid of the software MAXQDA for qualitative data analysis using principles of Grounded Theory. In addition, two external

  15. Understanding mixed forms of refuse collection, privatisation and its reverse in the Netherlands

    NARCIS (Netherlands)

    Gradus, R.H.J.M.; Dijkgraaf, E.; Wassenaar, M.C.

    2014-01-01

    Based on panel data for almost all Dutch municipalities, we analyze changes in the mode of service production for refuse collection between 1998 and 2010. We distinguish execution by private enterprises, municipal enterprises, municipal cooperation, outsourcing to neighboring municipalities, and

  16. The Cryogenic Dark Matter Search: First 5-Tower Data and Improved Understanding of Ionization Collection

    Energy Technology Data Exchange (ETDEWEB)

    Bailey, Catherine N. [Case Western Reserve Univ., Cleveland, OH (United States)

    2010-01-01

    The Cryogenic Dark Matter Search (CDMS) is searching for Weakly Interacting Massive Particles (WIMPs) with cryogenic particle detectors. These detectors have the ability to discriminate between nuclear recoil candidate and electron recoil background events by collecting both phonon and ionization energy from recoils in the detector crystals. The CDMS-II experiment has completed analysis of the first data runs with 30 semiconductor detectors at the Soudan Underground Laboratory, resulting in a world leading WIMP-nucleon spin-independent cross section limit for WIMP masses above 44 GeV/c2. As CDMS aims to achieve greater WIMP sensitivity, it is necessary to increase the detector mass and discrimination between signal and background events. Incomplete ionization collection results in the largest background in the CDMS detectors as this causes electron recoil background interactions to appear as false candidate events. Two primary causes of incomplete ionization collection are surface and bulk trapping. Recent work has been focused on reducing surface trapping through the modification of fabrication methods for future detectors. Analyzing data taken with test devices has shown that hydrogen passivation of the amorphous silicon blocking layer worsens surface trapping. Additional data has shown that the iron-ion implantation used to lower the critical temperature of the tungsten transition-edge sensors causes a degradation of the ionization collection. Using selective implantation on future detectors may improve ionization collection for events near the phonon side detector surface. Bulk trapping is minimized by neutralizing ionized lattice impurities. Detector investigations at testing facilities and in situ at the experimental site have provided methods to optimize the neutralization process and monitor running conditions to maintain full ionization collection. This work details my contribution to the 5-tower data taking, monitoring, and analysis effort as

  17. Evaluating bacterial community structures in oil collected from the sea surface and sediment in the northern Gulf of Mexico after the Deepwater Horizon oil spill

    OpenAIRE

    Liu, Zhanfei; Liu, Jiqing

    2013-01-01

    Bacterial community structures were evaluated in oil samples using culture-independent pyrosequencing, including oil mousses collected on sea surface and salt marshes during the Deepwater Horizon oil spill, and oil deposited in sediments adjacent to the wellhead 1 year after the spill. Phylogenetic analysis suggested that Erythrobacter, Rhodovulum, Stappia, and Thalassospira of Alphaproteobacteria were the prevailing groups in the oil mousses, which may relate to high temperatures and strong ...

  18. Treasures in Archived Histopathology Collections: Preserving the Past for Future Understanding (Histologic)

    Science.gov (United States)

    Extensive collections of histopathology materials from studies of marine and freshwater fish, mollusks, crustaceans, echinoderms, and other organisms are archived at the Registry of Tumors in Lower Animals (RTLA), the U.S. Environmental Protection Agency (EPA), NOAA’s National Ma...

  19. Treasures in Archived Histopathology Collections: Preserving the Past for Future Understanding.(SETAC)

    Science.gov (United States)

    Extensive collections of histopathology materials from studies of marine and freshwater mollusks, crustaceans, echinoderms, and other organisms are archived in the Registry of Tumors in Lower Animals (RTLA), the U.S. Environmental Protection Agency, NOAA’s National Marine Fisheri...

  20. Treasures in Archived Histopathology Collections: Preserving the Past for Future Understanding (IMCC09)

    Science.gov (United States)

    Extensive collections of histopathology materials from studies of marine and freshwater fish, mollusks, crustaceans, echinoderms, and other organisms are archived in the Registry of Tumors in Lower Animals (RTLA), the U.S. Environmental Protection Agency, NOAA’s National Marine...

  1. Treasures in Archived Histolopathology Collections: Preserving the Past for Future Understanding

    Science.gov (United States)

    Extensive collections of histopathology materials from studies of marine and freshwater mollusks, crustaceans, echinoderms, and other organisms are archived in the Registry of Tumors in Lower Animals (RTLA), the U.S. Environmental Protection Agency, NOAA’s National Marine Fishe...

  2. Treasures in Archived Histopathology Collections: Preserving the Past for Future Understanding (ISAAH-6)

    Science.gov (United States)

    Extensive collections of histopathology materials from studies of marine and freshwater fish, mollusks, crustaceans, echinoderms, and other organisms are archived in the Registry of Tumors in Lower Animals (RTLA), the U.S. Environmental Protection Agency, NOAA’s National Marine F...

  3. Treasures in Archived Histopathology Collections: Preserving the Past for Future Understanding (NACSETAC)

    Science.gov (United States)

    Extensive collections of histopathology materials from studies of marine and freshwater mollusks, crustaceans, echinoderms, and other organisms are archived in the Registry of Tumors in Lower Animals (RTLA), the U.S. Environmental Protection Agency, NOAA’s National Marine Fishe...

  4. Genome-wide association analysis identifies resistance loci for bacterial blight in a diverse collection of indica rice germplasm.

    Science.gov (United States)

    Zhang, Fan; Wu, Zhi-Chao; Wang, Ming-Ming; Zhang, Fan; Dingkuhn, Michael; Xu, Jian-Long; Zhou, Yong-Li; Li, Zhi-Kang

    2017-01-01

    Bacterial blight, which is caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating rice diseases worldwide. The development and use of disease-resistant cultivars have been the most effective strategy to control bacterial blight. Identifying the genes mediating bacterial blight resistance is a prerequisite for breeding cultivars with broad-spectrum and durable resistance. We herein describe a genome-wide association study involving 172 diverse Oryza sativa ssp. indica accessions to identify loci influencing the resistance to representative strains of six Xoo races. Twelve resistance loci containing 121 significantly associated signals were identified using 317,894 single nucleotide polymorphisms, which explained 13.3-59.9% of the variability in lesion length caused by Xoo races P1, P6, and P9a. Two hotspot regions (L11 and L12) were located within or nearby two cloned R genes (xa25 and Xa26) and one fine-mapped R gene (Xa4). Our results confirmed the relatively high resolution of genome-wide association studies. Moreover, we detected novel significant associations on chromosomes 2, 3, and 6-10. Haplotype analyses of xa25, the Xa26 paralog (MRKc; LOC_Os11g47290), and a Xa4 candidate gene (LOC_11g46870) revealed differences in bacterial blight resistance among indica subgroups. These differences were responsible for the observed variations in lesion lengths resulting from infections by Xoo races P1 and P9a. Our findings may be relevant for future studies involving bacterial blight resistance gene cloning, and provide insights into the genetic basis for bacterial blight resistance in indica rice, which may be useful for knowledge-based crop improvement.

  5. Genome-wide association analysis identifies resistance loci for bacterial blight in a diverse collection of indica rice germplasm

    Science.gov (United States)

    Wang, Ming-Ming; Zhang, Fan; Dingkuhn, Michael; Xu, Jian-Long; Zhou, Yong-Li; Li, Zhi-Kang

    2017-01-01

    Bacterial blight, which is caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating rice diseases worldwide. The development and use of disease-resistant cultivars have been the most effective strategy to control bacterial blight. Identifying the genes mediating bacterial blight resistance is a prerequisite for breeding cultivars with broad-spectrum and durable resistance. We herein describe a genome-wide association study involving 172 diverse Oryza sativa ssp. indica accessions to identify loci influencing the resistance to representative strains of six Xoo races. Twelve resistance loci containing 121 significantly associated signals were identified using 317,894 single nucleotide polymorphisms, which explained 13.3–59.9% of the variability in lesion length caused by Xoo races P1, P6, and P9a. Two hotspot regions (L11 and L12) were located within or nearby two cloned R genes (xa25 and Xa26) and one fine-mapped R gene (Xa4). Our results confirmed the relatively high resolution of genome-wide association studies. Moreover, we detected novel significant associations on chromosomes 2, 3, and 6–10. Haplotype analyses of xa25, the Xa26 paralog (MRKc; LOC_Os11g47290), and a Xa4 candidate gene (LOC_11g46870) revealed differences in bacterial blight resistance among indica subgroups. These differences were responsible for the observed variations in lesion lengths resulting from infections by Xoo races P1 and P9a. Our findings may be relevant for future studies involving bacterial blight resistance gene cloning, and provide insights into the genetic basis for bacterial blight resistance in indica rice, which may be useful for knowledge-based crop improvement. PMID:28355306

  6. Contributions of Latin American female academics to understand the collective actions of women

    Directory of Open Access Journals (Sweden)

    María Eugenia Ibarra Melo

    2015-04-01

    Full Text Available This article presents a review of academic work on the political participation of women in collective action promoted by social organizations, networks, and the movement of women and feminist in Latin America and Colombia, published in the period from 1990 to 2014. This approach gives priority to the analysis of the content of the texts, it focuses on the way as their authors build objects of research, and on the theoretical references and contributions to the knowledge of the relationship gender and collective action. The different national and regional experiences reported by these studies provide a wealth of descriptive and analytical material. However, based on these findings, the article concludes that it is necessary to enlarge the interpretations about the importance that gender changes have in political culture.

  7. Evaluating bacterial community structures in oil collected from the sea surface and sediment in the northern Gulf of Mexico after the Deepwater Horizon oil spill.

    Science.gov (United States)

    Liu, Zhanfei; Liu, Jiqing

    2013-06-01

    Bacterial community structures were evaluated in oil samples using culture-independent pyrosequencing, including oil mousses collected on sea surface and salt marshes during the Deepwater Horizon oil spill, and oil deposited in sediments adjacent to the wellhead 1 year after the spill. Phylogenetic analysis suggested that Erythrobacter, Rhodovulum, Stappia, and Thalassospira of Alphaproteobacteria were the prevailing groups in the oil mousses, which may relate to high temperatures and strong irradiance in surface Gulf waters. In the mousse collected from the leaves of Spartina alterniflora, Vibrio of Gammaproteobacteria represented 57% of the total operational taxonomic units, suggesting that this indigenous genus is particularly responsive to the oil contamination in salt marshes. The bacterial communities in oil-contaminated sediments were highly diversified. The relatively high abundance of the Methylococcus, Methylobacter, Actinobacteria, Firmicutes, and Chlorofexi bacteria resembles those found in certain cold-seep sediments with gas hydrates. Bacterial communities in the overlying water of the oil-contaminated sediment were dominated by Ralstonia of Betaproteobacteria, which can degrade small aromatics, and Saccharophagus degradans of Gammaproteobacteria, a cellulose degrader, suggesting that overlying water was affected by the oil-contaminated sediments, possibly due to the dissolution of small aromatics and biosurfactants produced during biodegradation. Overall, these results provided key information needed to evaluate oil degradation in the region and develop future bioremediation strategies. © 2013 The Authors. Microbiology Open published by John Wiley & Sons Ltd.

  8. Understanding and Defining sociohydrological spaces and their boundaries: an interdisciplinary perspective from collective fieldwork

    Science.gov (United States)

    Riaux, Jeanne; Leduc, Christian; Ben Aïssa, Nadhira; Burte, Julien; Calvez, Roger; habaieb, Hamadi; Ogilvie, Andrew; Massuel, Sylvain; Rochette, Romain

    2014-05-01

    Focussing on the interactions between water and society, researchers from various scientific disciplines have worked together on a common case study, the Merguellil catchment in Central Tunisia. The aim was to foster interactions between wide-ranging disciplines and their associated approaches, as the segmented analysis of water resources, uses and management is known to limit the comprehensive understanding of water issues. One of the major difficulties in developing a interdisciplinary approach is defining a suitable common observation space or "territory". Research in social sciences notably showed that hydrological catchments, suited to integrated water resource management, are rarely relevant to socio-political issues (water transfers, management of interfluves, etc.). Likewise, hydrological research regularly highlights the mismatch between surface and ground water processes and boundaries. Hydrological, hydrogeological and sociological boundaries also fluctuate when considering different time frames, socio-political organisations and processes. Finally, a suitable observation space must also be coherent to the variety of local stakeholders involved in the research. The present paper addressed the question of what is a common multidisciplinary observation space? What approach can help define and identify boundaries that make sense to hydrologists, agronomists, anthropologists and local stakeholders? How do we reconcile physical limits and territories? In the first instance, we focus on the value and importance of fieldwork, crucial in anthropology, but equally important for hydrologists and agronomists. Through a mutual process of defining the limits and characteristics of our research object, relevant socio-hydrological spaces were able to emerge These were circumscribed through the physical characteristics (based upon hydrological boundaries and processes) and the human particularities (political organisation, productive activities) of the study area. The

  9. Streamlining Safety Data Collection in Hospital-Acquired Bacterial Pneumonia and Ventilator-Associated Bacterial Pneumonia Trials: Recommendations of the Clinical Trials Transformation Initiative Antibacterial Drug Development Project Team.

    Science.gov (United States)

    Donnelly, Helen; Alemayehu, Demissie; Botgros, Radu; Comic-Savic, Sabrina; Eisenstein, Barry; Lorenz, Benjamin; Merchant, Kunal; Pelfrene, Eric; Reith, Christina; Santiago, Jonas; Tiernan, Rosemary; Wunderink, Richard; Tenaerts, Pamela; Knirsch, Charles

    2016-08-15

    Resistant bacteria are one of the leading causes of hospital-acquired/ventilator-associated bacterial pneumonia (HABP/VABP). HABP/VABP trials are complex and difficult to conduct due to the large number of medical procedures, adverse events, and concomitant medications involved. Differences in the legislative frameworks between different regions of the world may also lead to excessive data collection. The Clinical Trials Transformation Initiative (CTTI) seeks to advance antibacterial drug development (ABDD) by streamlining clinical trials to improve efficiency and feasibility while maintaining ethical rigor, patient safety, information value, and scientific validity. In 2013, CTTI engaged a multidisciplinary group of experts to discuss challenges impeding the conduct of HABP/VABP trials. Separate workstreams identified challenges associated with current data collection processes. Experts defined "data collection" as the act of capturing and reporting certain data on the case report form as opposed to recording of data as part of routine clinical care. The ABDD Project Team developed strategies for streamlining safety data collection in HABP/VABP trials using a Quality by Design approach. Current safety data collection processes in HABP/VABP trials often include extraneous information. More targeted strategies for safety data collection in HABP/VABP trials will rely on optimal protocol design and prespecification of which safety data are essential to satisfy regulatory reporting requirements. A consensus and a cultural change in clinical trial design and conduct, which involve recognition of the need for more efficient data collection, are urgently needed to advance ABDD and to improve HABP/VABP trials in particular. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

  10. Hormone-dependent bacterial growth, persistence and biofilm formation--a pilot study investigating human follicular fluid collected during IVF cycles.

    Directory of Open Access Journals (Sweden)

    Elise S Pelzer

    Full Text Available Human follicular fluid, considered sterile, is aspirated as part of an in vitro fertilization (IVF cycle. However, it is easily contaminated by the trans-vaginal collection route and little information exists in its potential to support the growth of microorganisms. The objectives of this study were to determine whether human follicular fluid can support bacterial growth over time, whether the steroid hormones estradiol and progesterone (present at high levels within follicular fluid contribute to the in vitro growth of bacterial species, and whether species isolated from follicular fluid form biofilms. We found that bacteria in follicular fluid could persist for at least 28 weeks in vitro and that the steroid hormones stimulated the growth of some bacterial species, specifically Lactobacillus spp., Bifidobacterium spp. Streptococcus spp. and E. coli. Several species, Lactobacillus spp., Propionibacterium spp., and Streptococcus spp., formed biofilms when incubated in native follicular fluids in vitro (18/24, 75%. We conclude that bacteria aspirated along with follicular fluid during IVF cycles demonstrate a persistent pattern of growth. This discovery is important since it can offer a new avenue for investigation in infertile couples.

  11. The impact of recent improvements in cryo-electron microscopy technology on the understanding of bacterial ribosome assembly.

    Science.gov (United States)

    Razi, Aida; Britton, Robert A; Ortega, Joaquin

    2017-02-17

    Cryo-electron microscopy (cryo-EM) had played a central role in the study of ribosome structure and the process of translation in bacteria since the development of this technique in the mid 1980s. Until recently cryo-EM structures were limited to ∼10 Å in the best cases. However, the recent advent of direct electron detectors has greatly improved the resolution of cryo-EM structures to the point where atomic resolution is now achievable. This improved resolution will allow cryo-EM to make groundbreaking contributions in essential aspects of ribosome biology, including the assembly process. In this review, we summarize important insights that cryo-EM, in combination with chemical and genetic approaches, has already brought to our current understanding of the ribosomal assembly process in bacteria using previous detector technology. More importantly, we discuss how the higher resolution structures now attainable with direct electron detectors can be leveraged to propose precise testable models regarding this process. These structures will provide an effective platform to develop new antibiotics that target this fundamental cellular process.

  12. Recent Advances and Understanding of Using Probiotic-Based Interventions to Restore Homeostasis of the Microbiome for the Prevention/Therapy of Bacterial Diseases.

    Science.gov (United States)

    Suchodolski, Jan S; Jergens, Albert E

    2016-04-01

    The importance of the microbiome in health and disease has galvanized interest in using manipulations of the gastrointestinal ecosystem to prevent and/or combat gut bacterial infections and to restore mucosal homeostasis in patients with generalized microbial imbalances (i.e., dysbiosis), including the human inflammatory bowel diseases, Crohn's disease, and ulcerative colitis. Probiotics, prebiotics, or their combination use (i.e., synbiotics) are one mechanism for modifying the microbiota and exerting direct and indirect effects on the host immune responses and metabolomics profiles. These beneficial effects are transferred through various pathways, including the production of antimicrobial peptides, promoting the growth of beneficial microbes and enhancing immunomodulatory functions via various metabolites. While probiotic therapy has been used empirically for decades with mixed success, the recent advances in molecular and mass spectrophotometric techniques for the characterization of the complexity and diversity of the intestinal microbiome has aided in better understanding of host-microbe interactions. It is important to better understand the functional properties of the microbiome, because it is now clear that the microbiota secretes many metabolites that have a direct impact on host immune responses. This information will improve selection of the most appropriate probiotic strains that selectively target intestinal disease processes.

  13. Bacterial communities in urban aerosols collected with wetted-wall cyclonic samplers and seasonal fluctuations of live and culturable airborne bacteria.

    Science.gov (United States)

    Ravva, Subbarao V; Hernlem, Bradley J; Sarreal, Chester Z; Mandrell, Robert E

    2012-02-01

    Airborne transmission of bacterial pathogens from point sources (e.g., ranches, dairy waste treatment facilities) to areas of food production (farms) has been suspected. Determining the incidence, transport and viability of extremely low levels of pathogens require collection of high volumes of air and characterization of live bacteria from aerosols. We monitored the numbers of culturable bacteria in urban aerosols on 21 separate days during a 9 month period using high volume cyclonic samplers at an elevation of 6 m above ground level. Culturable bacteria in aerosols fluctuated from 3 CFU to 6 million CFU/L of air per hour and correlated significantly with changes in seasonal temperatures, but not with humidity or wind speed. Concentrations of viable bacteria determined by fluorescence staining and flow cytometry correlated significantly with culturable bacteria. Members of the phylum Proteobacteria constituted 98% of the bacterial community, which was characterized using 16S rRNA gene sequencing using DNA from aerosols. Aquabacterium sp., previously characterized from aquatic environments, represented 63% of all clones and the second most common were Burkholderia sp; these are ubiquitous in nature and some are potential human pathogens. Whole genome amplification prior to sequencing resulted in a substantial decrease in species diversity compared to characterizing culturable bacteria sorted by flow cytometry based on scatter signals. Although 27 isolated colonies were characterized, we were able to culture 38% of bacteria characterized by sequencing. The whole genome amplification method amplified DNA preferentially from Phyllobacterium myrsinacearum, a minor member of the bacterial communities, whereas Variovorax paradoxus dominated the cultured organisms.

  14. Strain Library Imaging Protocol for high-throughput, automated single-cell microscopy of large bacterial collections arrayed on multiwell plates.

    Science.gov (United States)

    Shi, Handuo; Colavin, Alexandre; Lee, Timothy K; Huang, Kerwyn Casey

    2017-02-01

    Single-cell microscopy is a powerful tool for studying gene functions using strain libraries, but it suffers from throughput limitations. Here we describe the Strain Library Imaging Protocol (SLIP), which is a high-throughput, automated microscopy workflow for large strain collections that requires minimal user involvement. SLIP involves transferring arrayed bacterial cultures from multiwell plates onto large agar pads using inexpensive replicator pins and automatically imaging the resulting single cells. The acquired images are subsequently reviewed and analyzed by custom MATLAB scripts that segment single-cell contours and extract quantitative metrics. SLIP yields rich data sets on cell morphology and gene expression that illustrate the function of certain genes and the connections among strains in a library. For a library arrayed on 96-well plates, image acquisition can be completed within 4 min per plate.

  15. Selection for bacterial leaf-blight (Xanthomonas oryzae) and sheath-blight (Rhizoctonia oryzae) resistant mutants in a collection of early rice mutants

    International Nuclear Information System (INIS)

    Ismachin Kartoprawiro, M.; Mugiono

    1977-01-01

    Two of the most important and common rice diseases in Indonesia are bacterial leaf blight (BLB) and sheath blight (SB). The best rice yielding varieties in Indonesia, Pelita I/1 and IR5, were treated with gamma radiation and EMS. All the early maturing mutants which were selected from M 2 and M 3 generations, and afterwards in the M 8 generation we tested for their reaction to bacterial leaf blight and sheath blight. Pelita I/1 is moderately resistant to BLB and moderately susceptible to SB, but IR5 is susceptible to BLB or SB. At 30 and 60 days after transplanting, 107 early maturing mutants were inoculated with BLB. The bacteria were isolated from three different rice fields, and grown into Wakimoto media. Inoculation was done by the cutting method with suspension of 10 -7 -10 -8 cell/cm 3 . The virulence of bacteria isolated from the three fields was different. Resistant mutants were only observed in the Pelita I/1 early mutant collection; however, moderate resistance was found in the IR5 early mutants collection. At late growth stage the plant seems relatively more resistant to BLB. Early mutants of Pelita I/1 were inoculated with fungus SB following the procedure of the International Rice Sheath Blight Nursery (IRSHBN). Of 96 mutants, 55 were susceptible and 41 were moderately susceptible. Pelita I/1 was moderately susceptible with 48% damage and, compared with this, 9 mutant lines showed less than 40% damage. Selection was also carried out by natural infection; however, owing to ecoclimatic conditions the result was not convincing. (author)

  16. Damage assessment in Braunsbach 2016: data collection and analysis for an improved understanding of damaging processes during flash floods

    Science.gov (United States)

    Laudan, Jonas; Rözer, Viktor; Sieg, Tobias; Vogel, Kristin; Thieken, Annegret H.

    2017-12-01

    Flash floods are caused by intense rainfall events and represent an insufficiently understood phenomenon in Germany. As a result of higher precipitation intensities, flash floods might occur more frequently in future. In combination with changing land use patterns and urbanisation, damage mitigation, insurance and risk management in flash-flood-prone regions are becoming increasingly important. However, a better understanding of damage caused by flash floods requires ex post collection of relevant but yet sparsely available information for research. At the end of May 2016, very high and concentrated rainfall intensities led to severe flash floods in several southern German municipalities. The small town of Braunsbach stood as a prime example of the devastating potential of such events. Eight to ten days after the flash flood event, damage assessment and data collection were conducted in Braunsbach by investigating all affected buildings and their surroundings. To record and store the data on site, the open-source software bundle KoBoCollect was used as an efficient and easy way to gather information. Since the damage driving factors of flash floods are expected to differ from those of riverine flooding, a post-hoc data analysis was performed, aiming to identify the influence of flood processes and building attributes on damage grades, which reflect the extent of structural damage. Data analyses include the application of random forest, a random general linear model and multinomial logistic regression as well as the construction of a local impact map to reveal influences on the damage grades. Further, a Spearman's Rho correlation matrix was calculated. The results reveal that the damage driving factors of flash floods differ from those of riverine floods to a certain extent. The exposition of a building in flow direction shows an especially strong correlation with the damage grade and has a high predictive power within the constructed damage models. Additionally

  17. Bacterial Prostatitis: Bacterial Virulence, Clinical Outcomes, and New Directions.

    Science.gov (United States)

    Krieger, John N; Thumbikat, Praveen

    2016-02-01

    Four prostatitis syndromes are recognized clinically: acute bacterial prostatitis, chronic bacterial prostatitis, chronic prostatitis/chronic pelvic pain syndrome, and asymptomatic prostatitis. Because Escherichia coli represents the most common cause of bacterial prostatitis, we investigated the importance of bacterial virulence factors and antimicrobial resistance in E. coli strains causing prostatitis and the potential association of these characteristics with clinical outcomes. A structured literature review revealed that we have limited understanding of the virulence-associated characteristics of E. coli causing acute prostatitis. Therefore, we completed a comprehensive microbiological and molecular investigation of a unique strain collection isolated from healthy young men. We also considered new data from an animal model system suggesting certain E. coli might prove important in the etiology of chronic prostatitis/chronic pelvic pain syndrome. Our human data suggest that E. coli needs multiple pathogenicity-associated traits to overcome anatomic and immune responses in healthy young men without urological risk factors. The phylogenetic background and accumulation of an exceptional repertoire of extraintestinal pathogenic virulence-associated genes indicate that these E. coli strains belong to a highly virulent subset of uropathogenic variants. In contrast, antibiotic resistance confers little added advantage to E. coli strains in these healthy outpatients. Our animal model data also suggest that certain pathogenic E. coli may be important in the etiology of chronic prostatitis/chronic pelvic pain syndrome through mechanisms that are dependent on the host genetic background and the virulence of the bacterial strain.

  18. Bacterial Keratitis

    Science.gov (United States)

    ... Español Eye Health / Eye Health A-Z Bacterial Keratitis Sections What Is Bacterial Keratitis? Bacterial Keratitis Symptoms ... Lens Care Bacterial Keratitis Treatment What Is Bacterial Keratitis? Leer en Español: ¿Qué Es la Queratitis Bacteriana? ...

  19. The effect of dissolved organic carbon on bacterial adhesion to conditioning films adsorbed on glass from natural seawater collected during different seasons

    NARCIS (Netherlands)

    Bakker, DP; Klijnstra, JW; Busscher, HJ; van der Mei, HC

    2003-01-01

    Adhesion of three marine bacterial strains, i.e. Marinobacter hydrocarbonoclasticus , Psychrobacter sp. and Halomonas pacifica with different cell surface hydrophobicities was measured on glass in a stagnation point flow chamber. Prior to bacterial adhesion, the glass surface was conditioned for 1 h

  20. The effect of dissolved organic carbon on bacterial adhesion to conditioning films adsorbed on glass from natural seawater collected during different seasons

    NARCIS (Netherlands)

    Bakker, D.P.; Klijnstra, J.W.; Busscher, H.J.; Mei, H.C. van der

    2003-01-01

    Adhesion of three marine bacterial strains, i.e. Marinobacter hydrocarbonoclasticus, Psychrobacter sp. and Halomonas pacifica with different cell surface hydrophobicities was measured on glass in a stagnation point flow chamber. Prior to bacterial adhesion, the glass surface was conditioned for 1 h

  1. Practical benefits of knowing the enemy: modern molecular tools for diagnosing the etiology of bacterial diseases and understanding the taxonomy and diversity of plant-pathogenic bacteria.

    Science.gov (United States)

    Bull, Carolee T; Koike, Steven T

    2015-01-01

    Knowing the identity of bacterial plant pathogens is essential to strategic and sustainable disease management in agricultural systems. This knowledge is critical for growers, diagnosticians, extension agents, and others dealing with crops. However, such identifications are linked to bacterial taxonomy, a complicated and changing discipline that depends on methods and information that are often not used by those who are diagnosing field problems. Modern molecular tools for fingerprinting and sequencing allow for pathogen identification in the absence of distinguishing or conveniently tested phenotypic characteristics. These methods are also useful in studying the etiology and epidemiology of phytopathogenic bacteria from epidemics, as was done in numerous studies conducted in California's Salinas Valley. Multilocus and whole-genome sequence analyses are becoming the cornerstones of studies of microbial diversity and bacterial taxonomy. Whole-genome sequence analysis needs to become adequately accessible, automated, and affordable in order to be used routinely for identification and epidemiology. The power of molecular tools in accurately identifying bacterial pathogenesis is therefore of value to the farmer, diagnostician, phytobacteriologist, and taxonomist.

  2. Understanding the Mechanisms of Collective Decision Making in Ecological Restoration: An Agent-Based Model of Actors and Organizations

    OpenAIRE

    Cristy Watkins; Dean Massey; Jeremy Brooks; Kristen Ross; Moira L. Zellner

    2013-01-01

    Ecological restoration, particularly in urban contexts, is a complex collective decision-making process that involves a diversity of stakeholders and experts, each with their own perceptions and preferences about what landscapes should and can look like, how to get them to the desired state, and on what timeline. We investigate how structural and behavioral factors may influence collective decision making in the context of ecological restoration, with the purpose of establishing general relat...

  3. The meaning of collective terrorist threat : Understanding the subjective causes of terrorism reduces its negative psychological impact

    NARCIS (Netherlands)

    Fischer, Peter; Postmes, Tom; Koeppl, Julia; Conway, Lianne; Fredriksson, Tom

    This article hypothesized that the possibility to construct intellectual meaning of a terrorist attack (i.e., whether participants can cognitively understand why the perpetrators did their crime) reduces the negative psychological consequences typically associated with increased terrorist threat.

  4. Diversity of the bacterial and fungal microflora from the midgut and cuticle of phlebotomine sand flies collected in North-Western Iran.

    Directory of Open Access Journals (Sweden)

    Mohammad Akhoundi

    Full Text Available BACKGROUND: Phlebotomine sand flies are the vectors of the leishmaniases, parasitic diseases caused by Leishmania spp. Little is known about the prevalence and diversity of sand fly microflora colonizing the midgut or the cuticle. Particularly, there is little information on the fungal diversity. This information is important for development of vector control strategies. METHODOLOGY/PRINCIPAL FINDINGS: FIVE SAND FLY SPECIES: Phlebotomus papatasi, P. sergenti, P. kandelakii, P. perfiliewi and P. halepensis were caught in Bileh Savar and Kaleybar in North-Western Iran that are located in endemic foci of visceral leishmaniasis. A total of 35 specimens were processed. Bacterial and fungal strains were identified by routine microbiological methods. We characterized 39 fungal isolates from the cuticle and/or the midgut. They belong to six different genera including Penicillium (17 isolates, Aspergillus (14, Acremonium (5, Fusarium (1, Geotrichum (1 and Candida (1. We identified 33 Gram-negative bacteria: Serratia marcescens (9 isolates, Enterobacter cloacae (6, Pseudomonas fluorescens (6, Klebsiella ozaenae (4, Acinetobacter sp. (3, Escherichia coli (3, Asaia sp. (1 and Pantoea sp. (1 as well as Gram-positive bacteria Bacillus subtilis (5 and Micrococcus luteus (5 in 10 isolates. CONCLUSION/SIGNIFICANCE: Our study provides new data on the microbiotic diversity of field-collected sand flies and for the first time, evidence of the presence of Asaia sp. in sand flies. We have also found a link between physiological stages (unfed, fresh fed, semi gravid and gravid of sand flies and number of bacteria that they carry. Interestingly Pantoea sp. and Klebsiella ozaenae have been isolated in Old World sand fly species. The presence of latter species on sand fly cuticle and in the female midgut suggests a role for this arthropod in dissemination of these pathogenic bacteria in endemic areas. Further experiments are required to clearly delineate the vectorial

  5. Diversity of the bacterial and fungal microflora from the midgut and cuticle of phlebotomine sand flies collected in North-Western Iran.

    Science.gov (United States)

    Akhoundi, Mohammad; Bakhtiari, Rounak; Guillard, Thomas; Baghaei, Ahmad; Tolouei, Reza; Sereno, Denis; Toubas, Dominique; Depaquit, Jérôme; Abyaneh, Mehdi Razzaghi

    2012-01-01

    Phlebotomine sand flies are the vectors of the leishmaniases, parasitic diseases caused by Leishmania spp. Little is known about the prevalence and diversity of sand fly microflora colonizing the midgut or the cuticle. Particularly, there is little information on the fungal diversity. This information is important for development of vector control strategies. FIVE SAND FLY SPECIES: Phlebotomus papatasi, P. sergenti, P. kandelakii, P. perfiliewi and P. halepensis were caught in Bileh Savar and Kaleybar in North-Western Iran that are located in endemic foci of visceral leishmaniasis. A total of 35 specimens were processed. Bacterial and fungal strains were identified by routine microbiological methods. We characterized 39 fungal isolates from the cuticle and/or the midgut. They belong to six different genera including Penicillium (17 isolates), Aspergillus (14), Acremonium (5), Fusarium (1), Geotrichum (1) and Candida (1). We identified 33 Gram-negative bacteria: Serratia marcescens (9 isolates), Enterobacter cloacae (6), Pseudomonas fluorescens (6), Klebsiella ozaenae (4), Acinetobacter sp. (3), Escherichia coli (3), Asaia sp. (1) and Pantoea sp. (1) as well as Gram-positive bacteria Bacillus subtilis (5) and Micrococcus luteus (5) in 10 isolates. Our study provides new data on the microbiotic diversity of field-collected sand flies and for the first time, evidence of the presence of Asaia sp. in sand flies. We have also found a link between physiological stages (unfed, fresh fed, semi gravid and gravid) of sand flies and number of bacteria that they carry. Interestingly Pantoea sp. and Klebsiella ozaenae have been isolated in Old World sand fly species. The presence of latter species on sand fly cuticle and in the female midgut suggests a role for this arthropod in dissemination of these pathogenic bacteria in endemic areas. Further experiments are required to clearly delineate the vectorial role (passive or active) of sand flies.

  6. The Use of Mobile Devices as Means of Data Collection in Supporting Elementary School Students' Conceptual Understanding about Plants

    Science.gov (United States)

    Zacharia, Zacharias C.; Lazaridou, Charalambia; Avraamidou, Lucy

    2016-01-01

    The purpose of this study was to examine the impact of mobile learning among young learners. Specifically, we investigated whether the use of mobile devices for data collection during field trips outside the classroom could enhance fourth graders' learning about the parts of the flower and their functions, flower pollinators and the process of…

  7. The use of mobile devices as means of data collection in supporting elementary school students' conceptual understanding about plants

    NARCIS (Netherlands)

    Zacharia, Zacharias C.; Lazaridou, Charalambia; Avraamidou, Lucy

    2016-01-01

    The purpose of this study was to examine the impact of mobile learning among young learners. Specifically, we investigated whether the use of mobile devices for data collection during field trips outside the classroom could enhance fourth graders' learning about the parts of the flower and their

  8. Strengthening understanding and perceptions of mineral fertilizer use among smallholder farmers: evidence from collective trials in western Kenya

    NARCIS (Netherlands)

    Misiko, M.; Tittonell, P.A.; Giller, K.E.; Richards, P.

    2011-01-01

    It is widely recognized that mineral fertilizers must play an important part in improving agricultural productivity in western Kenyan farming systems. This paper suggests that for this goal to be realized, farmers’ knowledge must be strengthened to improve their understanding of fertilizers and

  9. Understanding the Mechanisms of Collective Decision Making in Ecological Restoration: An Agent-Based Model of Actors and Organizations

    Directory of Open Access Journals (Sweden)

    Cristy Watkins

    2013-06-01

    Full Text Available Ecological restoration, particularly in urban contexts, is a complex collective decision-making process that involves a diversity of stakeholders and experts, each with their own perceptions and preferences about what landscapes should and can look like, how to get them to the desired state, and on what timeline. We investigate how structural and behavioral factors may influence collective decision making in the context of ecological restoration, with the purpose of establishing general relationships between management styles (defined by structural and behavioral factors of the organization and decision outcomes. Informed by existing literature on collective decision making and by empirical data from the Chicago Wilderness region, we present a stylized agent-based model that maps out and simulates the processes by which individuals within restoration organizations communicate, discuss, and ultimately make a decision. Our study examines how structural and behavioral characteristics - including: (a the number of actors and groups involved in decision making, (b the frequency and type of interactions among actors, (c the initial setup of positions and respect, (d outside information, and (e entrenchment and cost of dissent - lead to or prohibit group convergence in terms of collective position, variation in position across actors, and final decision strategies. We found that formal meetings and group leaders are important facilitators of convergence, especially when multiple groups are present, new information is introduced in the process, and participants are polarized around an issue. Also, intergroup interactions are particularly important for overall convergence. Position entrenchment slows the convergence process and increases the need for decision strategies involving outside intervention. Cost of dissent can reinforce these effects. Our study formalizes collective decision-making processes within the context of ecological restoration

  10. Bacterial meningitis

    NARCIS (Netherlands)

    Roos, Karen L.; van de Beek, Diederik

    2010-01-01

    Bacterial meningitis is a neurological emergency. Empiric antimicrobial and adjunctive therapy should be initiated as soon as a single set of blood cultures has been obtained. Clinical signs suggestive of bacterial meningitis include fever, headache, meningismus, vomiting, photophobia, and an

  11. Bacterial Networks in Cells and Communities.

    Science.gov (United States)

    Sourjik, Victor; Vorholt, Julia A

    2015-11-20

    Research on the bacterial regulatory networks is currently experiencing a true revival, driven by advances in methodology and by emergence of novel concepts. The biannual conference Bacterial Networks (BacNet15) held in May 2015, in Sant Feliu de Guíxols, Spain, covered progress in the studies of regulatory networks that control bacterial physiology, cell biology, stress responses, metabolism, collective behavior and evolution. It demonstrated how interdisciplinary approaches that combine molecular biology and biochemistry with the latest microscopy developments, whole cell (-omics) approaches and mathematical modeling can help understand design principles relevant in microbiology. It further showed how current biotechnology and medical microbiology could profit from our knowledge of and ability to engineer regulatory networks of bacteria. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Now You See It… Now You Don’t: Understanding Airborne Mapping LiDAR Collection and Data Product Generation for Archaeological Research in Mesoamerica

    Directory of Open Access Journals (Sweden)

    Juan Carlos Fernandez-Diaz

    2014-10-01

    Full Text Available In this paper we provide a description of airborne mapping LiDAR, also known as airborne laser scanning (ALS, technology and its workflow from mission planning to final data product generation, with a specific emphasis on archaeological research. ALS observations are highly customizable, and can be tailored to meet specific research needs. Thus it is important for an archaeologist to fully understand the options available during planning, collection and data product generation before commissioning an ALS survey, to ensure the intended research questions can be answered with the resultant data products. Also this knowledge is of great use for the researcher trying to understand the quality and limitations of existing datasets collected for other purposes. Throughout the paper we use examples from archeological ALS projects to illustrate the key concepts of importance for the archaeology researcher.

  13. Empirical study of Kanji as archetypal images: understanding the collective unconscious as part of the Japanese language.

    Science.gov (United States)

    Sotirova-Kohli, Milena; Rosen, David H; Smith, Steven M; Henderson, Patti; Taki-Reece, Sachiko

    2011-02-01

    Chinese characters originated as a semiotic system independent from spoken language and in the Japanese language they function non-phonetically with speakers exhibiting right-hemispheric advantage in their processing. We tested the hypothesis that Chinese characters are archetypal images and therefore part of our collective unconscious memory. Our study builds on the first empirical study of archetypal memory of Rosen et al. (1991) which demonstrated that archetypal symbols presented matched with their correct meaning were better learned and recalled. In a series of three experiments we used 40 Chinese characters instead of the archetypal symbols used by Rosen, et al. (1991). The results provided empirical evidence that Chinese characters matched with their correct meaning were significantly better recalled than the ones that were mismatched. Thus, we demonstrated that there appears to be unconscious knowledge of the meaning of the Chinese characters which was triggered as a result of priming when the characters were correctly matched with their meaning. On this basis, we suggest that Chinese characters exhibit the same cognitive qualities as archetypal symbols. Thus, in the Japanese language an archetypal image is integrated non-phonetically into the system of language and signifies the concept independent from the phonetic signifier and is equal to it. © 2011, The Society of Analytical Psychology.

  14. Visual Soccer Analytics: Understanding the Characteristics of Collective Team Movement Based on Feature-Driven Analysis and Abstraction

    Directory of Open Access Journals (Sweden)

    Manuel Stein

    2015-10-01

    Full Text Available With recent advances in sensor technologies, large amounts of movement data have become available in many application areas. A novel, promising application is the data-driven analysis of team sport. Specifically, soccer matches comprise rich, multivariate movement data at high temporal and geospatial resolution. Capturing and analyzing complex movement patterns and interdependencies between the players with respect to various characteristics is challenging. So far, soccer experts manually post-analyze game situations and depict certain patterns with respect to their experience. We propose a visual analysis system for interactive identification of soccer patterns and situations being of interest to the analyst. Our approach builds on a preliminary system, which is enhanced by semantic features defined together with a soccer domain expert. The system includes a range of useful visualizations to show the ranking of features over time and plots the change of game play situations, both helping the analyst to interpret complex game situations. A novel workflow includes improving the analysis process by a learning stage, taking into account user feedback. We evaluate our approach by analyzing real-world soccer matches, illustrate several use cases and collect additional expert feedback. The resulting findings are discussed with subject matter experts.

  15. The meaning of collective terrorist threat: understanding the subjective causes of terrorism reduces its negative psychological impact.

    Science.gov (United States)

    Fischer, Peter; Postmes, Tom; Koeppl, Julia; Conway, Lianne; Fredriksson, Tom

    2011-05-01

    This article hypothesized that the possibility to construct intellectual meaning of a terrorist attack (i.e., whether participants can cognitively understand why the perpetrators did their crime) reduces the negative psychological consequences typically associated with increased terrorist threat. Concretely, the authors investigated the effect of intellectual meaning (induced by providing additional information about potential economic, cultural, and historical reasons for the terrorist attack) on perceived terrorist threat and associated emotional well-being. Study 1 revealed that pictures of terrorist attacks elicited less experienced terrorist threat when they were presented with background information about the terrorists' motives (meaning provided) rather than without additional background information (no meaning provided). Study 2 replicated this effect with a different manipulation of terrorist threat (i.e., newspaper article) and clarified the underlying psychological process: Participants in the high terror salience condition with meaning provided experienced less terrorist threat and thus more emotional well-being in the face of crisis than participants in the high terror salience condition without meaning provided. Theoretical and practical implications in the context of psychological health and mass media effects are discussed.

  16. Bacterial adhesion

    NARCIS (Netherlands)

    Loosdrecht, van M.C.M.

    1988-01-01

    As mentioned in the introduction of this thesis bacterial adhesion has been studied from a variety of (mostly practice oriented) starting points. This has resulted in a range of widely divergent approaches. In order to elucidate general principles in bacterial adhesion phenomena, we felt it

  17. Impact of the freeze-drying process on product appearance, residual moisture content, viability, and batch uniformity of freeze-dried bacterial cultures safeguarded at culture collections.

    Science.gov (United States)

    Peiren, Jindrich; Hellemans, Ann; De Vos, Paul

    2016-07-01

    In this study, causes of collapsed bacterial cultures in glass ampoules observed after freeze-drying were investigated as well as the influence of collapse on residual moisture content (RMC) and viability. Also, the effect of heat radiation and post freeze-drying treatments on the RMC was studied. Cake morphologies of 21 bacterial strains obtained after freeze-drying with one standard protocol could be classified visually into four major types: no collapse, porous, partial collapse, and collapse. The more pronounced the collapse, the higher residual moisture content of the freeze-dried product, ranging from 1.53 % for non-collapsed products to 3.62 % for collapsed products. The most important cause of collapse was the mass of the inserted cotton plug in the ampoule. Default cotton plugs with a mass between 21 and 30 mg inside the ampoule did not affect the viability of freeze-dried Aliivibrio fischeri LMG 4414(T) compared to ampoules without cotton plugs. Cotton plugs with a mass higher than 65 mg inside the ampoule induced a full collapsed product with rubbery look (melt-back) and decreasing viability during storage. Heat radiation effects in the freeze-drying chamber and post freeze-drying treatments such as exposure time to air after freeze-drying and manifold drying time prior to heat sealing of ampoules influenced the RMC of freeze-dried products. To produce uniform batches of freeze-dried bacterial strains with intact cake structures and highest viabilities, inserted cotton plugs should not exceed 21 mg per ampoule. Furthermore, heat radiation effects should be calculated in the design of the primary drying phase and manifold drying time before heat sealing should be determined as a function of exposure time to air.

  18. [Diagnosis of bacterial vaginosis].

    Science.gov (United States)

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

    2013-01-01

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

  19. Bacterial Vaginosis

    Science.gov (United States)

    ... Archive STDs Home Page Bacterial Vaginosis (BV) Chlamydia Gonorrhea Genital Herpes Hepatitis HIV/AIDS & STDs Human Papillomavirus ( ... of getting other STDs, such as chlamydia and gonorrhea . These bacteria can sometimes cause pelvic inflammatory disease ( ...

  20. From bacterial avirulence genes to effector functions via the hrp delivery system: an overview of 25 years of progress in our understanding of plant innate immunity.

    Science.gov (United States)

    Mansfield, John W

    2009-11-01

    Cloning the first avirulence (avr) gene has led not only to a deeper understanding of gene-for-gene interactions in plant disease, but also to fundamental insights into the suppression of basal defences against microbial attack. This article (focusing on Pseudomonas syringae) charts the development of ideas and research progress over the 25 years following the breakthrough achieved by Staskawicz and coworkers. Advances in gene cloning technology underpinned the identification of both avr and hrp genes, the latter being required for the activation of the defensive hypersensitive reaction (HR) and pathogenicity. The delivery of Avr proteins through the type III secretion machinery encoded by hrp gene clusters was demonstrated, and the activity of the proteins inside plant cells as elicitors of the HR was confirmed. Key roles for avr genes in pathogenic fitness have now been established. The rebranding of Avr proteins as effectors, proteins that suppress the HR and cell wall-based defences, has led to the ongoing search for their targets, and is generating new insights into the co-ordination of plant resistance against diverse microbes. Bioinformatics-led analysis of effector gene distribution in genomes has provided a remarkable view of the interchange of effectors and also their functional domains, as the arms race of attack and defence drives the evolution of microbial pathogenicity. The application of our accrued knowledge for the development of disease control strategies is considered.

  1. Bacterial blight of cotton

    Directory of Open Access Journals (Sweden)

    Aïda JALLOUL

    2015-04-01

    Full Text Available Bacterial blight of cotton (Gossypium ssp., caused by Xanthomonas citri pathovar malvacearum, is a severe disease occurring in all cotton-growing areas. The interactions between host plants and the bacteria are based on the gene-for-gene concept, representing a complex resistance gene/avr gene system. In light of the recent data, this review focuses on the understanding of these interactions with emphasis on (1 the genetic basis for plant resistance and bacterial virulence, (2 physiological mechanisms involved in the hypersensitive response to the pathogen, including hormonal signaling, the oxylipin pathway, synthesis of antimicrobial molecules and alteration of host cell structures, and (3 control of the disease.

  2. Molecular approaches for bacterial azoreductases

    Directory of Open Access Journals (Sweden)

    Montira Leelakriangsak

    2013-12-01

    Full Text Available Azo dyes are the dominant types of synthetic dyes, widely used in textiles, foods, leather, printing, tattooing, cosmetics, and pharmaceutical industries. Many microorganisms are able to decolorize azo dyes, and there is increasing interest in biological waste treatment methods. Bacterial azoreductases can cleave azo linkages (-N=N- in azo dyes, forming aromatic amines. This review mainly focuses on employing molecular approaches, including gene manipulation and recombinant strains, to study bacterial azoreductases. The construction of the recombinant protein by cloning and the overexpression of azoreductase is described. The mechanisms and function of bacterial azoreductases can be studied by other molecular techniques discussed in this review, such as RT-PCR, southern blot analysis, western blot analysis, zymography, and muta-genesis in order to understand bacterial azoreductase properties, function and application. In addition, understanding the regulation of azoreductase gene expression will lead to the systematic use of gene manipulation in bacterial strains for new strategies in future waste remediation technologies.

  3. Urban greenness influences airborne bacterial community composition.

    Science.gov (United States)

    Mhuireach, Gwynne; Johnson, Bart R; Altrichter, Adam E; Ladau, Joshua; Meadow, James F; Pollard, Katherine S; Green, Jessica L

    2016-11-15

    Urban green space provides health benefits for city dwellers, and new evidence suggests that microorganisms associated with soil and vegetation could play a role. While airborne microorganisms are ubiquitous in urban areas, the influence of nearby vegetation on airborne microbial communities remains poorly understood. We examined airborne microbial communities in parks and parking lots in Eugene, Oregon, using high-throughput sequencing of the bacterial 16S rRNA gene on the Illumina MiSeq platform to identify bacterial taxa, and GIS to measure vegetation cover in buffer zones of different diameters. Our goal was to explore variation among highly vegetated (parks) versus non-vegetated (parking lots) urban environments. A secondary objective was to evaluate passive versus active collection methods for outdoor airborne microbial sampling. Airborne bacterial communities from five parks were different from those of five parking lots (p=0.023), although alpha diversity was similar. Direct gradient analysis showed that the proportion of vegetated area within a 50m radius of the sampling station explained 15% of the variation in bacterial community composition. A number of key taxa, including several Acidobacteriaceae were substantially more abundant in parks, while parking lots had higher relative abundance of Acetobacteraceae. Parks had greater beta diversity than parking lots, i.e. individual parks were characterized by unique bacterial signatures, whereas parking lot communities tended to be similar to each other. Although parks and parking lots were selected to form pairs of nearby sites, spatial proximity did not appear to affect compositional similarity. Our results also showed that passive and active collection methods gave comparable results, indicating the "settling dish" method is effective for outdoor airborne sampling. This work sets a foundation for understanding how urban vegetation may impact microbial communities, with potential implications for designing

  4. Investigation of the Efficiencies of Bioaerosol Samplers for Collecting Aerosolized Bacteria Using a Fluorescent Tracer. I: Effects of Non-sampling Processes on Bacterial Culturability

    NARCIS (Netherlands)

    Zhao, Y.; Aarnink, A.J.A.; Doornenbal, P.; Huynh, T.T.T.; Groot Koerkamp, P.W.G.; Jong, de M.C.M.; Landman, W.J.M.

    2011-01-01

    By sampling aerosolized microorganisms, the efficiency of a bioaerosol sampler can be calculated depending on its ability both to collect microorganisms and to preserve their culturability during a sampling process. However, those culturability losses in the non-sampling processes should not be

  5. BACTERIAL CONSORTIUM

    Directory of Open Access Journals (Sweden)

    Payel Sarkar

    2013-01-01

    Full Text Available Petroleum aromatic hydrocarbons like benzen e, toluene, ethyl benzene and xylene, together known as BTEX, has almost the same chemical structure. These aromatic hydrocarbons are released as pollutants in th e environment. This work was taken up to develop a solvent tolerant bacterial cons ortium that could degrade BTEX compounds as they all share a common chemical structure. We have isolated almost 60 different types of bacterial strains from different petroleum contaminated sites. Of these 60 bacterial strains almost 20 microorganisms were screene d on the basis of capability to tolerate high concentration of BTEX. Ten differe nt consortia were prepared and the compatibility of the bacterial strains within the consortia was checked by gram staining and BTEX tolerance level. Four successful mi crobial consortia were selected in which all the bacterial strains concomitantly grew in presence of high concentration of BTEX (10% of toluene, 10% of benzene 5% ethyl benzene and 1% xylene. Consortium #2 showed the highest growth rate in pr esence of BTEX. Degradation of BTEX by consortium #2 was monitored for 5 days by gradual decrease in the volume of the solvents. The maximum reduction observed wa s 85% in 5 days. Gas chromatography results also reveal that could completely degrade benzene and ethyl benzene within 48 hours. Almost 90% degradation of toluene and xylene in 48 hours was exhibited by consortium #2. It could also tolerate and degrade many industrial solvents such as chloroform, DMSO, acetonitrile having a wide range of log P values (0.03–3.1. Degradation of aromatic hydrocarbon like BTEX by a solvent tolerant bacterial consortium is greatly significant as it could degrade high concentration of pollutants compared to a bacterium and also reduces the time span of degradation.

  6. Bacterial Ecology

    DEFF Research Database (Denmark)

    Fenchel, Tom

    2011-01-01

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

  7. Bacterial meningitis

    NARCIS (Netherlands)

    Heckenberg, Sebastiaan G. B.; Brouwer, Matthijs C.; van de Beek, Diederik

    2014-01-01

    Bacterial meningitis is a neurologic emergency. Vaccination against common pathogens has decreased the burden of disease. Early diagnosis and rapid initiation of empiric antimicrobial and adjunctive therapy are vital. Therapy should be initiated as soon as blood cultures have been obtained,

  8. Bacterial lipases

    NARCIS (Netherlands)

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

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

  9. Bacterial Ecology

    DEFF Research Database (Denmark)

    Fenchel, Tom

    2011-01-01

    , the production and oxidation of methane, nitrate reduction and fixation of atmospheric nitrogen are exclusively carried out by different groups of bacteria. Some bacterial species – ‘extremophiles’ – thrive in extreme environments in which no eukaryotic organisms can survive with respect to temperature, salinity...

  10. Bacterial Vaginosis

    Science.gov (United States)

    ... that coats the walls of the vagina Vaginal discharge with an unpleasant or fishlike odor Vaginal pain or itching Burning during urination Doctors are unsure of the incubation period for bacterial vaginosis. How Is the Diagnosis Made? Your child’s pediatrician can make the diagnosis ...

  11. Bacterial stress

    Indian Academy of Sciences (India)

    First page Back Continue Last page Graphics. Bacterial stress. Physicochemical and chemical parameters: temperature, pressure, pH, salt concentration, oxygen, irradiation. Nutritional depravation: nutrient starvation, water shortage. Toxic compounds: Antibiotics, heavy metals, toxins, mutagens. Interactions with other cells: ...

  12. Understanding Pediatric Bacterial Preseptal and Orbital Cellulitis

    Science.gov (United States)

    Gonzalez, Mithra O.; Durairaj, Vikram D.

    2010-01-01

    Pediatric preseptal and orbital cellulitis are infectious disorders that result in periorbital inflammation. Preseptal cellulitis is often associated with breaches in the skin barrier whereas orbital cellulitis is commonly associated with paranasal sinusitis. Orbital cellulitis may be associated with subperiosteal abscess. It is important to distinguish between preseptal from orbital cellulitis. Clinical examination and diagnostic imaging are useful in determining appropriate management. Patients are usually treated with broad spectrum antibiotics and surgery when indicated. PMID:20616919

  13. Understanding Pediatric Bacterial Preseptal and Orbital Cellulitis

    OpenAIRE

    Gonzalez, Mithra O.; Durairaj, Vikram D.

    2010-01-01

    Pediatric preseptal and orbital cellulitis are infectious disorders that result in periorbital inflammation. Preseptal cellulitis is often associated with breaches in the skin barrier whereas orbital cellulitis is commonly associated with paranasal sinusitis. Orbital cellulitis may be associated with subperiosteal abscess. It is important to distinguish between preseptal from orbital cellulitis. Clinical examination and diagnostic imaging are useful in determining appropriate management. Pati...

  14. Bacterial Adhesion & Blocking Bacterial Adhesion

    DEFF Research Database (Denmark)

    Vejborg, Rebecca Munk

    2008-01-01

    reduce or delay bacterial biofilm formation of a range of urinary tract infectious E.coli and Klebsiella isolates. Several other proteinaceous coatings were also found to display anti-adhesive properties, possibly providing a measure for controlling the colonization of implant materials. Several other...... components. These substances may both mediate and stabilize the bacterial biofilm. Finally, several adhesive structures were examined, and a novel physiological biofilm phenotype in E.coli biofilms was characterized, namely cell chain formation. The autotransporter protein, antigen 43, was implicated...

  15. Diagnosis of bacterial vaginosis

    Directory of Open Access Journals (Sweden)

    Đukić Slobodanka

    2013-01-01

    Full Text Available Bacterial vaginosis is a common, complex clinical syndrome characterized by alterations in the normal vaginal flora. When symptomatic, it is associated with a malodorous vaginal discharge and on occasion vaginal burning or itching. Under normal conditions, lactobacilli constitute 95% of the bacteria in the vagina. Bacterial vaginosis is associated with severe reduction or absence of the normal H2O2­producing lactobacilli and overgrowth of anaerobic bacteria and Gardnerella vaginalis, Atopobium vaginae, Mycoplasma hominis and Mobiluncus species. Most types of infectious disease are diagnosed by culture, by isolating an antigen or RNA/DNA from the microbe, or by serodiagnosis to determine the presence of antibodies to the microbe. Therefore, demonstration of the presence of an infectious agent is often a necessary criterion for the diagnosis of the disease. This is not the case for bacterial vaginosis, since the ultimate cause of the disease is not yet known. There are a variety of methods for the diagnosis of bacterial vaginosis but no method can at present be regarded as the best. Diagnosing bacterial vaginosis has long been based on the clinical criteria of Amsel, whereby three of four defined criteria must be satisfied. Nugent’s scoring system has been further developed and includes validation of the categories of observable bacteria structures. Up­to­date molecular tests are introduced, and better understanding of vaginal microbiome, a clear definition for bacterial vaginosis, and short­term and long­term fluctuations in vaginal microflora will help to better define molecular tests within the broader clinical context.

  16. bacterial flora and antibiotic sensitivity

    African Journals Online (AJOL)

    Purulent pelvic collections are common pathologies observed in contemporary gynaecological practice. They may originate from chronic pelvic inflammatory disease, from abortions or following normal deliveries. This study was designed to compare the bacterial flora in purulent pelvic collections obtained from HIV infected ...

  17. Bacterial lipases

    OpenAIRE

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

    1994-01-01

    Many different bacterial species produce lipases which hydrolyze esters of glycerol with preferably long-chain fatty acids. They act at the interface generated by a hydrophobic lipid substrate in a hydrophilic aqueous medium. A characteristic property of lipases is called interfacial activation, meaning a sharp increase in lipase activity observed when the substrate starts to form an emulsion, thereby presenting to the enzyme an interfacial area. As a consequence, the kinetics of a lipase rea...

  18. Data collected in the Southern California Bight in order to understand the coastal waters ecological systems, 1977 - 1999 (NODC Accession 0001162)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Chemistry, fish species, atmospheric pollutants, and temperature profile were collected using CTD casts and other collection methods in the Southern California Bight...

  19. Bacterial mitosis

    DEFF Research Database (Denmark)

    Møller-Jensen, Jakob; Borch, Jonas; Dam, Mette

    2003-01-01

    Bacterial DNA segregation takes place in an active and ordered fashion. In the case of Escherichia coli plasmid R1, the partitioning system (par) separates paired plasmid copies and moves them to opposite cell poles. Here we address the mechanism by which the three components of the R1 par system...... movement is powered by insertional polymerization of ParM. Consistently, we find that segregating plasmids are positioned at the ends of extending ParM filaments. Thus, the process of R1 plasmid segregation in E. coli appears to be mechanistically analogous to the actin-based motility operating...

  20. Spatial variation in the bacterial and denitrifying bacterial community in a biofilter treating subsurface agricultural drainage.

    Science.gov (United States)

    Andrus, J Malia; Porter, Matthew D; Rodríguez, Luis F; Kuehlhorn, Timothy; Cooke, Richard A C; Zhang, Yuanhui; Kent, Angela D; Zilles, Julie L

    2014-02-01

    Denitrifying biofilters can remove agricultural nitrates from subsurface drainage, reducing nitrate pollution that contributes to coastal hypoxic zones. The performance and reliability of natural and engineered systems dependent upon microbially mediated processes, such as the denitrifying biofilters, can be affected by the spatial structure of their microbial communities. Furthermore, our understanding of the relationship between microbial community composition and function is influenced by the spatial distribution of samples.In this study we characterized the spatial structure of bacterial communities in a denitrifying biofilter in central Illinois. Bacterial communities were assessed using automated ribosomal intergenic spacer analysis for bacteria and terminal restriction fragment length polymorphism of nosZ for denitrifying bacteria.Non-metric multidimensional scaling and analysis of similarity (ANOSIM) analyses indicated that bacteria showed statistically significant spatial structure by depth and transect,while denitrifying bacteria did not exhibit significant spatial structure. For determination of spatial patterns, we developed a package of automated functions for the R statistical environment that allows directional analysis of microbial community composition data using either ANOSIM or Mantel statistics.Applying this package to the biofilter data, the flow path correlation range for the bacterial community was 6.4 m at the shallower, periodically in undated depth and 10.7 m at the deeper, continually submerged depth. These spatial structures suggest a strong influence of hydrology on the microbial community composition in these denitrifying biofilters. Understanding such spatial structure can also guide optimal sample collection strategies for microbial community analyses.

  1. Enhancing captive breeding in giant pandas (Ailuropoda melanoleuca): maintaining lactation when cubs are rejected, and understanding variation in milk collection and associated factors.

    Science.gov (United States)

    Wei, Rongping; Zhang, Guiquan; Yin, Feng; Zhang, Hemin; Liu, Dingzhen

    2009-07-01

    From 1997 to 2002, a female giant panda (Ailuropoda melanoleuca) was artificially stimulated and lactation was maintained, after her neonates were removed due to the female's inability to provide maternal care. Milk samples were collected and the amount of milk collected was quantified. The lactation curve of this animal was estimated based on the Gamma function: Y(t)=at(b)e(-ct). The amount of milk collected showed significant, positive relationships with the number of days after parturition both in 1999 and in the whole study period from 1998 to 2002. This female's lactation curves fit the type I pattern of a typical mammalian lactation curve. Daily milk collection (g) during the first 30 days after parturition, and from 31 to 60 days after parturition, showed a consistent pattern with one peak at around 8:00 hr. More milk was collected during the latter period than during the former period. The amount of milk (g) collected on mucus excretion days was significantly less than that on days after mucus excretion had ended, yet no significant difference was found between milk collected one day before mucus days and on mucus days, or between milk collected one day before and one day after mucus days. Mucus excretion from the gastrointestinal tract significantly impacted the amount of milk collected. The results from this study may aid the captive propagation and conservation of giant pandas and other endangered and rare captive mammal species.

  2. Teaching Teaching & Understanding Understanding

    DEFF Research Database (Denmark)

    2006-01-01

    "Teaching Teaching & Understanding Understanding" is a 19-minute award-winning short-film about teaching at university and higher-level educational institutions. It is based on the "Constructive Alignment" theory developed by Prof. John Biggs. The film delivers a foundation for understanding what...

  3. Bacterial Communities: Interactions to Scale

    Directory of Open Access Journals (Sweden)

    Reed M. Stubbendieck

    2016-08-01

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

  4. Bacterial flora of sturgeon fingerling

    International Nuclear Information System (INIS)

    Arani, A.S.; Mosahab, R.

    2008-01-01

    The study on microbial populations is a suitable tool to understand and apply control methods to improve the sanitary level of production in fish breeding and rearing centers, ensure health of sturgeon fingerlings at the time of their release into the rivers and also in the conversation and restoration of these valuable stocks in the Caspian Sea, Iran. A laboratory research based on Austin methods (Austin, B., Austin, D.A. 1993) was conducted for bacterial study on 3 sturgeon species naming A. persicus, A. stellatus and A. nudiventris during different growth stages. Bacterial flora of Acinetobacter, Moraxella, Aeromonas, Vibrio, Edwardsiella, Staphylococcus, Proteus, Yersinia, Pseudomonas and Plesiomonas were determined. The factors which may induce changes in bacterial populations during different stages of fife are the followings: quality of water in rearing ponds, different conditions for growth stages, suitable time for colonization of bacterial flora in rearing pond, water temperature increase in fingerlings size and feeding condition. (author)

  5. Right Here Right Now: Developing an understanding of responses to smoking policy developments using online data collection in near to real time

    Directory of Open Access Journals (Sweden)

    Gillian Fergie

    2015-10-01

    Full Text Available Background: Health policymakers require timely evidence to inform decision-making, however, rapid social change often outpaces the capacity of traditional approaches to research to produce meaningful insights. The pervasion of mobile technologies and internet access offers opportunities for capturing context specific and near real-time data on people’s perceptions, behaviours and everyday experiences that could usefully inform decision-making. The Right Here Right Now pilot study was established to provide insights into public responses to, and lived experiences of, contemporary social and health issues. From May to October 2015, a cohort of 180 adults living in Glasgow were asked weekly questions. These questions were developed with decision-makers working in health and social policy or in response to topical newsworthy public health issues that arose. The questions were delivered through an online system and allowed participants to answer directly by website, SMS or post. Aim: An issue that was of high public health policy interest and debate during this period was the need for further tobacco and nicotine control. The aim of this study was to explore the potential of using an online data collection system with a cohort of Glasgow residents to provide rapid insights into public opinion on such policy developments. Method: Three smoking/vaping related questions were sent out to Right Here Right Now participants over the course of the study. The questions were in four parts, first a multiple choice question and then three qualitative follow-up questions based on participants’ responses to part one. The questions were developed with stakeholders working in health advocacy and policy development. They focused on: perceptions of the pervasion of e-cigarettes; legislation on smoking in cars carrying children; and reflections on ten years of the ‘smoking ban’ in enclosed public places. Results: The response rate ranged from 45% to 55% (65

  6. Analysis of hindgut bacterial phyla frequency and diversity in subterranean termites exposed to chitosan-treated wood

    Science.gov (United States)

    Olanrewaju Raji; Juliet D. Tang; Telmah Telmadarrehei; Dragica Jeremic

    2017-01-01

    The termite hindgut contains a microbial community that symbiotically aids in digestion of lignocellulosic materials. For better understanding of the dynamics of the bacteria-termite relationship, a species survey of bacterial hindgut microbes in subterranean termites (Reticulitermes flavipes: Kollar) collected from Louisville, Mississippi was...

  7. BACTERIAL PLASMIDS

    Directory of Open Access Journals (Sweden)

    Marina Dinic

    2007-12-01

    Full Text Available Plasmids, extrachromosomal DNA, were identified in bacteria pertaining to family of Enterobacteriacae for the very first time. After that, they were discovered in almost every single observed strain. The structure of plasmids is made of circular double chain DNA molecules which are replicated autonomously in a host cell. Their length may vary from few up to several hundred kilobase (kb. Among the bacteria, plasmids are mostly transferred horizontally by conjugation process. Plasmid replication process can be divided into three stages: initiation, elongation, and termination. The process involves DNA helicase I, DNA gyrase, DNA polymerase III, endonuclease, and ligase.Plasmids contain genes essential for plasmid function and their preservation in a host cell (the beginning and the control of replication. Some of them possess genes whichcontrol plasmid stability. There is a common opinion that plasmids are unnecessary fora growth of bacterial population and their vital functions; thus, in many cases they can be taken up or kicked out with no lethal effects to a plasmid host cell. However,there are numerous biological functions of bacteria related to plasmids. Plasmids identification and classification are based upon their genetic features which are presented permanently in all of them, and these are: abilities to preserve themselves in a host cell and to control a replication process. In this way, plasmids classification among incompatibility groups is performed. The method of replicon typing, which is based on genotype and not on phenotype characteristics, has the same results as in compatibility grouping.

  8. Collective antibiotic tolerance: mechanisms, dynamics and intervention.

    Science.gov (United States)

    Meredith, Hannah R; Srimani, Jaydeep K; Lee, Anna J; Lopatkin, Allison J; You, Lingchong

    2015-03-01

    Bacteria have developed resistance against every antibiotic at a rate that is alarming considering the timescale at which new antibiotics are developed. Thus, there is a critical need to use antibiotics more effectively, extend the shelf life of existing antibiotics and minimize their side effects. This requires understanding the mechanisms underlying bacterial drug responses. Past studies have focused on survival in the presence of antibiotics by individual cells, as genetic mutants or persisters. Also important, however, is the fact that a population of bacterial cells can collectively survive antibiotic treatments lethal to individual cells. This tolerance can arise by diverse mechanisms, including resistance-conferring enzyme production, titration-mediated bistable growth inhibition, swarming and interpopulation interactions. These strategies can enable rapid population recovery after antibiotic treatment and provide a time window during which otherwise susceptible bacteria can acquire inheritable genetic resistance. Here, we emphasize the potential for targeting collective antibiotic tolerance behaviors as an antibacterial treatment strategy.

  9. Joshua Lederberg's Legacy to Bacterial Genetics

    Indian Academy of Sciences (India)

    Srimath

    team which developed the artificial intelligence software program DENDRAL. ... to clear up all the uncertainties and lay the firm foundations of modern bacterial genetics. In order to understand and appreciate. As far as bacterial genetics is concerned, even the very existence ... Do they exist before exposure to the selective.

  10. Metagenomics-enabled understanding of the functions and activities of microbial communities at ERSP field research

    Energy Technology Data Exchange (ETDEWEB)

    Tiedje, James M. [Michigan State Univ., East Lansing, MI (United States)

    2014-01-08

    The focus of our work is to better understand the bioremediation of uranium in the subsurface. To evaluate the natural occurring uranium-immobilizing bacterial populations, we have anaerobically enriched uranium contaminated soil sediments (FW107, FW102-2, and FW102-3) collected from ORNL iFRC site (S3 area).

  11. In Situ Hydrocarbon Degradation by Indigenous Nearshore Bacterial Populations

    International Nuclear Information System (INIS)

    Cherrier, J.

    2005-01-01

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

  12. Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host–Microbe Model System

    Science.gov (United States)

    Bhatnagar, Srijak; Eisen, Jonathan A.; Kopp, Artyom

    2011-01-01

    Drosophila melanogaster is emerging as an important model of non-pathogenic host–microbe interactions. The genetic and experimental tractability of Drosophila has led to significant gains in our understanding of animal–microbial symbiosis. However, the full implications of these results cannot be appreciated without the knowledge of the microbial communities associated with natural Drosophila populations. In particular, it is not clear whether laboratory cultures can serve as an accurate model of host–microbe interactions that occur in the wild, or those that have occurred over evolutionary time. To fill this gap, we characterized natural bacterial communities associated with 14 species of Drosophila and related genera collected from distant geographic locations. To represent the ecological diversity of Drosophilids, examined species included fruit-, flower-, mushroom-, and cactus-feeders. In parallel, wild host populations were compared to laboratory strains, and controlled experiments were performed to assess the importance of host species and diet in shaping bacterial microbiome composition. We find that Drosophilid flies have taxonomically restricted bacterial communities, with 85% of the natural bacterial microbiome composed of only four bacterial families. The dominant bacterial taxa are widespread and found in many different host species despite the taxonomic, ecological, and geographic diversity of their hosts. Both natural surveys and laboratory experiments indicate that host diet plays a major role in shaping the Drosophila bacterial microbiome. Despite this, the internal bacterial microbiome represents only a highly reduced subset of the external bacterial communities, suggesting that the host exercises some level of control over the bacteria that inhabit its digestive tract. Finally, we show that laboratory strains provide only a limited model of natural host–microbe interactions. Bacterial taxa used in experimental studies are rare or absent in

  13. pH affects bacterial community composition in soils across the Huashan Watershed, China.

    Science.gov (United States)

    Huang, Rui; Zhao, Dayong; Zeng, Jin; Shen, Feng; Cao, Xinyi; Jiang, Cuiling; Huang, Feng; Feng, Jingwei; Yu, Zhongbo; Wu, Qinglong L

    2016-09-01

    To investigate soil bacterial richness and diversity and to determine the correlations between bacterial communities and soil properties, 8 soil samples were collected from the Huashan watershed in Anhui, China. Subsequently, 454 high-throughput pyrosequencing and bioinformatics analyses were performed to examine the soil bacterial community compositions. The operational taxonomic unit richness of the bacterial community ranged from 3664 to 5899, and the diversity indices, including Chao1, Shannon-Wiener, and Faith's phylogenetic diversity ranged from 7751 to 15 204, 7.386 to 8.327, and 415.77 to 679.11, respectively. The 2 most dominant phyla in the soil samples were Actinobacteria and Proteobacteria. The richness and diversity of the bacterial community were positively correlated with soil pH. The Mantel test revealed that the soil pH was the dominant factor influencing the bacterial community. The positive modular structure of co-occurrence patterns at the genus level was discovered by network analysis. The results obtained in this study provide useful information that enhances our understanding of the effects of soil properties on the bacterial communities.

  14. Current knowledge of bacterial vaginosis

    Directory of Open Access Journals (Sweden)

    Đukić Slobodanka

    2011-01-01

    Full Text Available Bacterial vaginosis, earlier termed nonspecific vaginitis (anaerobic vaginosis because of the absence of recognized pathogens, is most common vaginal syndrome of women of childbearing age affecting 15-30%. This syndrome, whose aetiology and pathogenesis remains unknown, is characterized by significant changes in the vaginal ecosystem. These changes consist of a decrease in the number of lactobacilli and a large increase in the number of anaerobic organisms. The bacteria adhere to desquamated epithelial cells with a distinctive appearance of clue cells The main complaints of women with symptomatic bacterial vaginosis include vaginal discharge and odour. However, a significant number of all women who have bacterial vaginosis deny symptoms. Bacterial vaginosis is associated with a number of gynaecologic and obstetric complications including cervicitis, cervical neoplasia, pelvic inflammatory disease, postoperative infections, and preterm labour. The diagnosis is most frequently made based on vaginal smear stained according to Gram (Nugent scoring method. Metronidazole and clindamycin are the drugs of choice for treatment of women with bacterial vaginosis. Which women should undergo treatment? According to the prevailing attitude, it should include women with symptoms. Symptomatic women with frequent relapses of bacterial vaginosisas, as a rule, have poor response to the applied therapy. To achieve better efficiency in the treatment of such women, it is necessary to have more extensive understanding of all factors in the pathogenesis of the syndrome.

  15. Hispanic Association of Colleges and Universities (HACU) Hispanic Higher Education Research Collective (H3ERC) Research Agenda: Impacting Education and Changing Lives through Understanding

    Science.gov (United States)

    Hispanic Association of Colleges and Universities, 2011

    2011-01-01

    With support from the Lumina Foundation, the Hispanic Association of Colleges and Universities (HACU) has launched HACU's Hispanic Higher Education Research Collective (H3ERC). The first major task of this virtual gathering of researchers and practitioners in Hispanic higher education has been to assess the state of our knowledge of the key issues…

  16. Characterization of the bacterial communities of life stages of free living lone star ticks (Amblyomma americanum.

    Directory of Open Access Journals (Sweden)

    Amanda Jo Williams-Newkirk

    Full Text Available The lone star tick (Amblyomma americanum is an abundant and aggressive biter of humans, domestic animals, and wildlife in the southeastern-central USA and an important vector of several known and suspected zoonotic bacterial pathogens. However, the biological drivers of bacterial community variation in this tick are still poorly defined. Knowing the community context in which tick-borne bacterial pathogens exist and evolve is required to fully understand the ecology and immunobiology of the ticks and to design effective public health and veterinary interventions. We performed a metagenomic survey of the bacterial communities of questing A. americanum and tested 131 individuals (66 nymphs, 24 males, and 41 females from five sites in three states. Pyrosequencing was performed with barcoded eubacterial primers targeting variable 16S rRNA gene regions 5-3. The bacterial communities were dominated by Rickettsia (likely R. amblyommii and an obligate Coxiella symbiont, together accounting for 6.7-100% of sequences per tick. DNAs from Midichloria, Borrelia, Wolbachia, Ehrlichia, Pseudomonas, or unidentified Bacillales, Enterobacteriaceae, or Rhizobiales groups were also detected frequently. Wolbachia and Midichloria significantly co-occurred in Georgia (p<0.00001, but not in other states. The significance of the Midichloria-Wolbachia co-occurrence is unknown. Among ticks collected in Georgia, nymphs differed from adults in both the composition (p = 0.002 and structure (p = 0.002 of their bacterial communities. Adults differed only in their community structure (p = 0.002 with males containing more Rickettsia and females containing more Coxiella. Comparisons among adult ticks collected in New York and North Carolina supported the findings from the Georgia collection despite differences in geography, collection date, and sample handling, implying that the differences detected are consistent attributes. The data also suggest that some members of

  17. Collective stories and well-being: using a dialogical narrative approach to understand peer relationships among combat veterans experiencing post-traumatic stress disorder.

    Science.gov (United States)

    Caddick, Nick; Phoenix, Cassandra; Smith, Brett

    2015-03-01

    Using a dialogical narrative approach, this original research explored how combat veterans experiencing post-traumatic stress disorder made sense of peer relationships with other veterans and what effects these relationships had on their well-being. Interviews and participant observations were conducted with 15 male combat veterans (aged 27-60 years) and one member of the civilian emergency services, the majority of whom were diagnosed with post-traumatic stress disorder following traumatic exposure in a range of armed conflicts. All participants were part of a surfing charity for veterans experiencing post-traumatic stress disorder. Data were rigorously analysed using a dialogical narrative analysis (DNA). Findings revealed the collective story that veterans used to make sense of peer relationships within the group. This collective story worked for the veterans to shape their experiences of well-being by fostering camaraderie, stimulating deeper connections and countering the negative effects of post-traumatic stress disorder. Potential therapeutic effects of the collective story were also identified. This article extends previous knowledge on combat veterans and social relationships and advances the field of narrative health psychology through the empirical application of a sophisticated dialogical narrative approach. © The Author(s) 2015.

  18. Phenotypic signatures arising from unbalanced bacterial growth.

    Science.gov (United States)

    Tan, Cheemeng; Smith, Robert Phillip; Tsai, Ming-Chi; Schwartz, Russell; You, Lingchong

    2014-08-01

    Fluctuations in the growth rate of a bacterial culture during unbalanced growth are generally considered undesirable in quantitative studies of bacterial physiology. Under well-controlled experimental conditions, however, these fluctuations are not random but instead reflect the interplay between intra-cellular networks underlying bacterial growth and the growth environment. Therefore, these fluctuations could be considered quantitative phenotypes of the bacteria under a specific growth condition. Here, we present a method to identify "phenotypic signatures" by time-frequency analysis of unbalanced growth curves measured with high temporal resolution. The signatures are then applied to differentiate amongst different bacterial strains or the same strain under different growth conditions, and to identify the essential architecture of the gene network underlying the observed growth dynamics. Our method has implications for both basic understanding of bacterial physiology and for the classification of bacterial strains.

  19. Understanding Cancer Prognosis

    Medline Plus

    Full Text Available ... our information on Coping With Cancer helpful. Understanding Statistics About Survival Doctors estimate prognosis by using statistics that researchers have collected over many years about ...

  20. Aerotaxis in Bacterial Turbulence

    Science.gov (United States)

    Fernandez, Vicente; Bisson, Antoine; Bitton, Cindy; Waisbord, Nicolas; Smriga, Steven; Rusconi, Roberto; Stocker, Roman

    2012-11-01

    Concentrated suspensions of motile bacteria exhibit correlated dynamics on spatial scales much larger than an individual bacterium. The resulting flows, visually similar to turbulence, can increase mixing and decrease viscosity. However, it remains unclear to what degree the collective dynamics depend on the motile behavior of bacteria at the individual level. Using a new microfluidic device to create controlled horizontal oxygen gradients, we studied the two dimensional behavior of dense suspensions of Bacillus subtilis. This system makes it possible to assess the interplay between the coherent large-scale motions of the suspension, oxygen transport, and the directional response of cells to oxygen gradients (aerotaxis). At the same time, this device has enabled us to examine the onset of bacterial turbulence and its influence on the propagation of the diffusing oxygen front, as the bacteria begin in a dormant state and transition to swimming when exposed to oxygen.

  1. Bacterial community structure and soil properties of a subarctic tundra soil in Council, Alaska.

    Science.gov (United States)

    Kim, Hye Min; Jung, Ji Young; Yergeau, Etienne; Hwang, Chung Yeon; Hinzman, Larry; Nam, Sungjin; Hong, Soon Gyu; Kim, Ok-Sun; Chun, Jongsik; Lee, Yoo Kyung

    2014-08-01

    The subarctic region is highly responsive and vulnerable to climate change. Understanding the structure of subarctic soil microbial communities is essential for predicting the response of the subarctic soil environment to climate change. To determine the composition of the bacterial community and its relationship with soil properties, we investigated the bacterial community structure and properties of surface soil from the moist acidic tussock tundra in Council, Alaska. We collected 70 soil samples with 25-m intervals between sampling points from 0-10 cm to 10-20 cm depths. The bacterial community was analyzed by pyrosequencing of 16S rRNA genes, and the following soil properties were analyzed: soil moisture content (MC), pH, total carbon (TC), total nitrogen (TN), and inorganic nitrogen (NH4+ and NO3-). The community compositions of the two different depths showed that Alphaproteobacteria decreased with soil depth. Among the soil properties measured, soil pH was the most significant factor correlating with bacterial community in both upper and lower-layer soils. Bacterial community similarity based on jackknifed unweighted unifrac distance showed greater similarity across horizontal layers than through the vertical depth. This study showed that soil depth and pH were the most important soil properties determining bacterial community structure of the subarctic tundra soil in Council, Alaska. © 2014 The Authors. FEMS Microbiology Ecology published by John Wiley & Sons Ltd on behalf of the Federation of European Microbiological Societies.

  2. Illumina sequencing of bacterial 16S rDNA and 16S rRNA reveals seasonal and species-specific variation in bacterial communities in four moss species.

    Science.gov (United States)

    Ma, Jing; Tang, Jing Yan; Wang, Su; Chen, Zhi Ling; Li, Xue Dong; Li, Yan Hong

    2017-09-01

    In order to better understand the factors that influence bacterial diversity and community composition in moss-associated bacteria, a study of bacterial communities in four moss species collected in three seasons was carried out via high-throughput sequencing of 16S rDNA and 16S rRNA. Moss species included Cratoneuron filicinum, Pylaisiella polyantha, Campyliadelphus polygamum, and Grimmia pilifera, with samples collected in May, July, and October 2015 from rocks at Beijing Songshan National Nature Reserve. In total, the bacterial richness and diversity were high regardless of moss species, sampling season, or data source (DNA vs. RNA). Bacterial sequences were assigned to a total of 558 OTUs and 279 genera in 16 phyla. Proteobacteria and Actinobacteria were the two most abundant phyla, and Cellvibrio, Lapillicoccus, Jatrophihabitans, Friedmanniella, Oligoflexus, and Bosea the most common genera in the samples. A clustering algorithm and principal coordinate analysis revealed that C. filicinum and C. polygamum had similar bacterial communities, as did P. polyantha and G. pilifera. Metabolically active bacteria showed the same pattern in addition to seasonal variation: bacterial communities were most similar in summer and autumn, looking at each moss species separately. In contrast, DNA profiles lacked obvious seasonal dynamics. A partial least squares discriminant analysis identified three groups of samples that correlated with differences in moss species resources. Although bacterial community composition did vary with the sampling season and data source, these were not the most important factors influencing bacterial communities. Previous reports exhibited that mosses have been widely used in biomonitoring of air pollution by enriching some substances or elements in the moss-tag technique and the abundant moss associated bacteria might also be important components involved in the related biological processes. Thus, this survey not only enhanced our understanding

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

    Science.gov (United States)

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

    2014-12-01

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

  4. Comparison of bacterial communities in leachate from decomposing bovine carcasses

    Directory of Open Access Journals (Sweden)

    Seung Hak Yang

    2017-11-01

    Full Text Available Objective Burial is associated with environmental effects such as the contamination of ground or surface water with biological materials generated during the decomposition process. Therefore, bacterial communities in leachates originating from the decomposing bovine carcasses were investigated. Methods To understand the process of bovine (Hanwoo carcass decomposition, we simulated burial using a lab-scale reactor with a volume of 5.15 m3. Leachate samples from 3 carcasses were collected using a peristaltic pump once a month for a period of 5 months, and bacterial communities in samples were identified by pyrosequencing of the 16S rRNA gene. Results We obtained a total of 110,442 reads from the triplicate samples of various sampling time points (total of 15 samples, and found that the phylum Firmicutes was dominant at most sampling times. Differences in the bacterial communities at the various time points were observed among the triplicate samples. The bacterial communities sampled at 4 months showed the most different compositions. The genera Pseudomonas and Psychrobacter in the phylum Proteobacteria were dominant in all of the samples obtained after 3 months. Bacillaceae, Clostridium, and Clostridiales were found to be predominant after 4 months in the leachate from one carcass, whereas Planococcaceae was found to be a dominant in samples obtained at the first and second months from the other two carcasses. The results showed that potentially pathogenic microbes such as Clostridium derived from bovine leachate could dominate the soil environment of a burial site. Conclusion Our results indicated that the composition of bacterial communities in leachates of a decomposing bovine shifted continuously during the experimental period, with significant changes detected after 4 months of burial.

  5. Bacterial diversity in the oral cavity of ten healthy individuals

    Science.gov (United States)

    Bik, Elisabeth M.; Long, Clara Davis; Armitage, Gary C.; Loomer, Peter; Emerson, Joanne; Mongodin, Emmanuel F.; Nelson, Karen E.; Gill, Steven R.; Fraser-Liggett, Claire M.; Relman, David A.

    2010-01-01

    The composition of the oral microbiota from 10 individuals with healthy oral tissues was determined using culture-independent techniques. From each individual, 26 specimens, each from different oral sites at a single point in time, were collected and pooled. An eleventh pool was constructed using portions of the subgingival specimens from all 10 individuals. The 16S rRNA gene was amplified using broad-range bacterial primers, and clone libraries from the individual and subgingival pools were constructed. From a total of 11 368 high-quality, non-chimeric, near full-length sequences, 247 species-level phylotypes (using a 99% sequence identity threshold) and 9 bacteria phyla were identified. At least 15 bacterial genera were conserved among all 10 individuals, with significant interindividual differences at the species and strain level. Comparisons of these oral bacterial sequences to near full-length sequences found previously in the large intestines and feces of other healthy individuals suggest that the mouth and intestinal tract harbor distinct sets of bacteria. Co-occurrence analysis demonstrated significant segregation of taxa when community membership was examined at the level of genus, but not at the level of species, suggesting that ecologically-significant, competitive interactions are more apparent at a broader taxonomic level than species. This study is one of the more comprehensive, high-resolution analyses of bacterial diversity within the healthy human mouth to date, and highlights the value of tools from macroecology for enhancing our understanding of bacterial ecology in human health. PMID:20336157

  6. Prevention of bacterial adhesion

    DEFF Research Database (Denmark)

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

    2010-01-01

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

  7. Building a Collective Understanding of Prisons

    Science.gov (United States)

    Pahomov, Larissa

    2013-01-01

    Larissa Pahomov teaches students English and Journalism at Science Leadership Academy in Philadelphia, Pennsylvania. The school opened its doors to students just seven years ago and was designed to encourage both inquiry and critical pedagogy. To those ends, there is a thematic curriculum for each grade level--for sophomores, it's…

  8. Understanding the degradation of Congo red and bacterial diversity in an air-cathode microbial fuel cell being evaluated for simultaneous azo dye removal from wastewater and bioelectricity generation.

    Science.gov (United States)

    Sun, Jian; Li, Youming; Hu, Yongyou; Hou, Bin; Zhang, Yaping; Li, Sizhe

    2013-04-01

    We investigated the mechanism of Congo red degradation and bacterial diversity in a single-chambered microbial fuel cell (MFC) incorporating a microfiltration membrane and air-cathode. The MFC was operated continuously for more than 4 months using a mixture of Congo red and glucose as fuel. We demonstrated that the Congo red azo bonds were reduced at the anode to form aromatic amines. This is consistent with the known mechanism of anaerobic biodegradation of azo dyes. The MFC developed a less dense biofilm at the anode in the presence of Congo red compared to its absence indicating that Congo red degradation negatively affected biofilm formation. Denaturing gradient gel electrophoresis and direct 16S ribosomal DNA gene nucleotide sequencing revealed that the microbial communities differed depending on whether Congo red was present in the MFC. Geobacter-like species known to generate electricity were detected in the presence or absence of Congo red. In contrast, Azospirillum, Methylobacterium, Rhodobacter, Desulfovibrio, Trichococcus, and Bacteroides species were only detected in its presence. These species were most likely responsible for degrading Congo red.

  9. Microbial culture collection for enhancement of microbial biotechnology

    International Nuclear Information System (INIS)

    Jong Bor Chyan; Pauline Liew Woan Ying; Goh Chee Meng; Mat Rasol Awang

    2007-01-01

    A bacterial culture collection was established in Agrotechnology and Biosciences Division since 2004. The culture collection was named MINT Bacterial Culture Collection (MBCC). The main objective is to preserve the indigenous bacterial cultures isolated from various environments. Later, the collection was extended to commercially available plasmids, recombinant clones and selected PCR products. This paper describes the importance of culture collection, the experience and the difficulties encountered. (Author)

  10. Oral bacterial DNA findings in pericardial fluid

    Directory of Open Access Journals (Sweden)

    Anne-Mari Louhelainen

    2014-11-01

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

  11. Bacterial colonization and gut development in preterm neonates

    DEFF Research Database (Denmark)

    Cilieborg, Malene S.; Boye, Mette; Sangild, Per Torp

    2012-01-01

    Necrotizing enterocolitis (NEC) develops in 5–10% of preterm infants in association with enteral feeding and bacterial colonization. It remains unclear how diet and bacteria interact to protect or provoke the immature gastrointestinal tract. Understanding the factors that control bacterial...... colonization may provide the clue to prevent NEC, and studies in infants must be combined with animal models to understand the mechanisms of the microbiota–epithelium interactions. Analyses of infant fecal samples show that the density and distribution of bacterial species are highly variable......, such as mother's colostrum or milk, that help the immature intestinal immune system to respond appropriately to the highly variable bacterial colonization....

  12. Characterization of the cervical bacterial community in dairy cows with metritis and during different physiological phases.

    Science.gov (United States)

    Wang, Yu; Wang, Jifang; Li, Huatao; Fu, Kaiqiang; Pang, Binbin; Yang, Yan; Liu, Yuan; Tian, Wenru; Cao, Rongfeng

    2018-03-01

    For the development of disease prevention and intervention strategies, a better understanding of the dynamics and interactions within cervical bacterial communities in both healthy cows and cows with metritis is required. Understanding the complexity and ecology of microorganisms in the vagina of dairy cows with metritis and during different physiological phases is critical for developing strategies to balance microorganism content. To gain deeper insight into fluctuations within the cervical microbiota, swab samples were collected from 40 Holstein dairy cows, and16S rDNA amplicon sequencing was used to analyze cervical bacterial diversity. Meanwhile, vaginal bacterial composition was analyzed during different physiological phases, including the formative (CF), gestational (CG), and postpartum (CP) stages, and in cows with metritis (CM). The results revealed a complex profile with extensive differences in the cervical bacterial composition. A total of 678,043clean 16S rDNA V4-V6 reads were gained, and 1877 Operational Taxonomic Units (OTUs) were observed after calculation. At both the phylum and genus levels, the top 10 bacteria by percentage were the same when comparing the CF, CG, and CP groups of cows, with some variation in abundance. At the phylum level, the cervical microbial community in the CF, CG, and CP groups included mainly Firmicutes, which accounted for 39.3%, 48.3%, and 49.6% of the total microbial composition of each group, respectively. However, the cervical bacterial community in the CM group consisted of mostly Bacteroidetes, which accounted for 72.6% of the total microbial composition. The second major bacterial community in the CF and CG groups of cows was Proteobacteria, which accounted for 28.3%and 30.1% of the total microbial compositions of these groups, respectively, while the second major bacterial community in the CP group was Bacteroidetes (23.5%). However, in the CM group, the second major bacterial community was Fusobacteria, which

  13. Studying bacterial multispecies biofilms

    DEFF Research Database (Denmark)

    Røder, Henriette Lyng; Sørensen, Søren Johannes; Burmølle, Mette

    2016-01-01

    , but the identity and significance of interspecies bacterial interactions is neglected in these analyses. There is therefore an urgent need for bridging the gap between metagenomic analysis and in vitro models suitable for studies of bacterial interactions.Bacterial interactions and coadaptation are important......The high prevalence and significance of multispecies biofilms have now been demonstrated in various bacterial habitats with medical, industrial, and ecological relevance. It is highly evident that several species of bacteria coexist and interact in biofilms, which highlights the need for evaluating...

  14. Choanal and cloacal aerobic bacterial flora in captive green iguanas: a comparative analysis

    Directory of Open Access Journals (Sweden)

    Silvia Barazorda Romero

    2015-01-01

    Full Text Available The aims of this study were to characterize the choanal and cloacal aerobic bacterial flora in healthy captive green iguanas and to compare it with the bacterial flora of the biofilm present in the water container of each terrarium. Samples were collected from the choana and the cloaca of 20 healthy captive adult green iguanas and from the biofilm of 15 water containers. The final identification of aerobic bacteria was performed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Salmonella positive samples were serotyped. The most common strains observed at each test location were from 1 choanae: Staphylococcus spp., Enterobacter cloacae and Comamonas testosteroni; 2 cloacae: Citrobacter spp., Salmonella spp. and Corynebacterium spp.; and 3 biofilms: Pseudomonas spp., Salmonella spp. and Acidovorax spp. We showed that apart from Salmonella spp., the choanal and cloacal bacterial flora differed from the microorganisms present in the biofilm of the animal’s water container. These data revealed that healthy captive adult green iguanas harbored several aerobic bacterial strains that in immunosuppressed reptiles may act as opportunistic pathogens. Also, several of the aerobic bacteria identified in samples are potential zoonotic agents. Characterization of the normal background flora in captive reptiles and their environment can contribute to an understanding of the spread of bacterial contamination and the risk of potential zoonotic diseases for people in contact with these animals.

  15. Plant growth-promoting bacterial endophytes.

    Science.gov (United States)

    Santoyo, Gustavo; Moreno-Hagelsieb, Gabriel; Orozco-Mosqueda, Ma del Carmen; Glick, Bernard R

    2016-02-01

    Bacterial endophytes ubiquitously colonize the internal tissues of plants, being found in nearly every plant worldwide. Some endophytes are able to promote the growth of plants. For those strains the mechanisms of plant growth-promotion known to be employed by bacterial endophytes are similar to the mechanisms used by rhizospheric bacteria, e.g., the acquisition of resources needed for plant growth and modulation of plant growth and development. Similar to rhizospheric plant growth-promoting bacteria, endophytic plant growth-promoting bacteria can act to facilitate plant growth in agriculture, horticulture and silviculture as well as in strategies for environmental cleanup (i.e., phytoremediation). Genome comparisons between bacterial endophytes and the genomes of rhizospheric plant growth-promoting bacteria are starting to unveil potential genetic factors involved in an endophytic lifestyle, which should facilitate a better understanding of the functioning of bacterial endophytes. Copyright © 2015 Elsevier GmbH. All rights reserved.

  16. Bacterial strategies of resistance to antimicrobial peptides.

    Science.gov (United States)

    Joo, Hwang-Soo; Fu, Chih-Iung; Otto, Michael

    2016-05-26

    Antimicrobial peptides (AMPs) are a key component of the host's innate immune system, targeting invasive and colonizing bacteria. For successful survival and colonization of the host, bacteria have a series of mechanisms to interfere with AMP activity, and AMP resistance is intimately connected with the virulence potential of bacterial pathogens. In particular, because AMPs are considered as potential novel antimicrobial drugs, it is vital to understand bacterial AMP resistance mechanisms. This review gives a comparative overview of Gram-positive and Gram-negative bacterial strategies of resistance to various AMPs, such as repulsion or sequestration by bacterial surface structures, alteration of membrane charge or fluidity, degradation and removal by efflux pumps.This article is part of the themed issue 'Evolutionary ecology of arthropod antimicrobial peptides'. © 2016 The Author(s).

  17. Procoagulant and fibrinolytic activity in cerebrospinal fluid from adults with bacterial meningitis

    NARCIS (Netherlands)

    Weisfelt, Martijn; Determann, Rogier M.; de Gans, Jan; van der Ende, Arie; Levi, Marcel; van de Beek, Diederik; Schultz, Marcus J.

    2007-01-01

    OBJECTIVES: This study investigated levels of coagulation and fibrinolysis factors in cerebrospinal fluid (CSF) from adults with bacterial meningitis in relation to development of brain infarction. METHODS: CSF was collected from 92 adults with community-acquired bacterial meningitis, who

  18. Bacterial growth efficiency in a tropical estuary: Seasonal variability subsidized by allochthonous carbon

    Digital Repository Service at National Institute of Oceanography (India)

    Ram, A.S.P.; Nair, S.; Chandramohan, D.

    Bacterial growth efficiency (BGE) is a key factor in understanding bacterial influence on carbon flow in aquatic ecosystems. Intra-annual variability in BGE, and bacteria-mediated carbon flow in the tropical Mandovi and Zuari estuaries (southwest...

  19. Bacterial biofilm and associated infections

    Directory of Open Access Journals (Sweden)

    Muhsin Jamal

    2018-01-01

    Full Text Available Microscopic entities, microorganisms that drastically affect human health need to be thoroughly investigated. A biofilm is an architectural colony of microorganisms, within a matrix of extracellular polymeric substance that they produce. Biofilm contains microbial cells adherent to one-another and to a static surface (living or non-living. Bacterial biofilms are usually pathogenic in nature and can cause nosocomial infections. The National Institutes of Health (NIH revealed that among all microbial and chronic infections, 65% and 80%, respectively, are associated with biofilm formation. The process of biofilm formation consists of many steps, starting with attachment to a living or non-living surface that will lead to formation of micro-colony, giving rise to three-dimensional structures and ending up, after maturation, with detachment. During formation of biofilm several species of bacteria communicate with one another, employing quorum sensing. In general, bacterial biofilms show resistance against human immune system, as well as against antibiotics. Health related concerns speak loud due to the biofilm potential to cause diseases, utilizing both device-related and non-device-related infections. In summary, the understanding of bacterial biofilm is important to manage and/or to eradicate biofilm-related diseases. The current review is, therefore, an effort to encompass the current concepts in biofilm formation and its implications in human health and disease.

  20. Understanding Carbohydrates

    Science.gov (United States)

    ... Size: A A A Listen En Español Understanding Carbohydrates How much and what type of carbohydrate foods ... glucose levels in your target range. Explore: Understanding Carbohydrates Glycemic Index and Diabetes Learn about the glycemic ...

  1. Cerebrospinal Fluid Cathelicidin Correlates With the Bacterial Load and Outcomes in Childhood Bacterial Meningitis.

    Science.gov (United States)

    Savonius, Okko; Helve, Otto; Roine, Irmeli; Andersson, Sture; Saukkoriipi, Annika; González Mata, Antonio; Peltola, Heikki; Pelkonen, Tuula

    2018-02-01

    Large cerebrospinal fluid (CSF) bacterial load in bacterial meningitis (BM) relates to poor outcome. However, the antimicrobial peptide cathelicidin seems important to host defense. We studied how cathelicidin concentrations and bacterial load in CSF relate in childhood BM and to what extent they may predict the disease outcome. The patient data originated from a large prospective clinical trial in Latin America in 1996-2003 in which the CSF samples were collected on admission (CSF1) and 12-24 hours later (CSF2). The cathelicidin concentrations were measured by enzyme-linked immunosorbent assay and the CSF bacterial load by real-time polymerase chain reaction. This analysis comprised 76 children with meningitis caused by Haemophilus influenzae type b (n = 44), Streptococcus pneumoniae (n = 28) or Neisseria meningitidis (n = 4). The cathelicidin concentration correlated with the bacterial genome count in both samples (CSF1: ρ = 0.531, P < 0.001; CSF2: ρ = 0.553, P < 0.001). A high CSF1 ratio of cathelicidin to the bacterial genome count was associated with fewer audiologic sequelae (odds ratio: 0.11, 95% confidence interval: 0.02-0.61, P = 0.01) and more favorable neurologic outcomes (odds ratio: 3.95, 95% confidence interval: 1.22-12.8, P = 0.02), but not with better survival. In conclusion, CSF cathelicidin and the bacterial load were closely related in childhood BM. A high initial cathelicidin-to-bacterial genome count ratio predicted better outcomes in survivors.

  2. Southern leaf blight disease severity is correlated with decreased maize leaf epiphytic bacterial species richness and the phyllosphere bacterial diversity decline is enhanced by nitrogen fertilization

    Directory of Open Access Journals (Sweden)

    Heather eManching

    2014-08-01

    Full Text Available Plant leaves are inhabited by a diverse group of microorganisms that are important contributors to optimal growth. Biotic and abiotic effects on plant growth are usually studied in controlled settings examining response to variation in single factors and in field settings with large numbers of variables. Multi-factor experiments with combinations of stresses bridge this gap, increasing our understanding of the genotype-environment-phenotype functional map for the host plant and the affiliated epiphytic community. The maize inbred B73 was exposed to single and combination abiotic and the biotic stress treatments: low nitrogen fertilizer and high levels of infection with southern leaf blight (causal agent Cochliobolus heterostrophus. Microbial epiphyte samples were collected at the vegetative early-season phase and species composition was determined using 16S ribosomal intergenic spacer analysis. Plant traits and level of southern leaf blight disease were measured late-season. Bacterial diversity was different among stress treatment groups (P< 0.001. Lower species richness—alpha diversity--was correlated with increased severity of southern leaf blight disease when disease pressure was high. Nitrogen fertilization intensified the decline in bacterial alpha diversity. While no single bacterial ribotype was consistently associated with disease severity, small sets of ribotypes were good predictors of disease levels. Difference in leaf bacterial-epiphyte diversity early in the season were correlated with plant disease severity, supporting further tests of microbial epiphyte-disease correlations for use in predicting disease progression.

  3. [Spontaneous bacterial peritonitis].

    Science.gov (United States)

    Strauss, Edna; Caly, Wanda Regina

    2003-01-01

    Spontaneous bacterial peritonitis occurs in 30% of patients with ascites due to cirrhosis leading to high morbidity and mortality rates. The pathogenesis of spontaneous bacterial peritonitis is related to altered host defenses observed in end-stage liver disease, overgrowth of microorganisms, and bacterial translocation from the intestinal lumen to mesenteric lymph nodes. Clinical manifestations vary from severe to slight or absent, demanding analysis of the ascitic fluid. The diagnosis is confirmed by a number of neutrophils over 250/mm3 associated or not to bacterial growth in culture of an ascites sample. Enterobacteriae prevail and Escherichia coli has been the most frequent bacterium reported. Mortality rates decreased markedly in the last two decades due to early diagnosis and prompt antibiotic treatment. Third generation intravenous cephalosporins are effective in 70% to 95% of the cases. Recurrence of spontaneous bacterial peritonitis is common and can be prevented by the continuous use of oral norfloxacin. The development of bacterial resistance demands the search for new options in the prophylaxis of spontaneous bacterial peritonitis; probiotics are a promising new approach, but deserve further evaluation. Short-term antibiotic prophylaxis is recommended for patients with cirrhosis and ascites shortly after an acute episode of gastrointestinal bleeding.

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

    Science.gov (United States)

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

    2017-01-01

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

  5. Bacterial Agents Associated with Seasonal Meningitis in Ebonyi ...

    African Journals Online (AJOL)

    Seasonal bacterial meningitis has been a regular occurrence in Ebonyi State, Nigeria. In a prospective study of 45 children of both sexes, aged 0 to 17yr (mean 12.5 + 1.5yr), infected with bacterial meningitis, in whom appropriate specimens were collected, examined and analyzed in order to identify the predominant ...

  6. Prevalence of antibacterial resistant bacterial contaminants from ...

    African Journals Online (AJOL)

    Mobile phones contaminated with bacteria may act as fomites. Antibiotic resistant bacterial contamination of mobile phones of inpatients was studied. One hundred and six samples were collected from mobile phones of patients admitted in various hospitals in Jazan province of Saudi Arabia. Eighty-nine (83.9%) out of 106 ...

  7. Microbial minimalism: genome reduction in bacterial pathogens.

    Science.gov (United States)

    Moran, Nancy A

    2002-03-08

    When bacterial lineages make the transition from free-living or facultatively parasitic life cycles to permanent associations with hosts, they undergo a major loss of genes and DNA. Complete genome sequences are providing an understanding of how extreme genome reduction affects evolutionary directions and metabolic capabilities of obligate pathogens and symbionts.

  8. Interfering with bacterial gossip

    DEFF Research Database (Denmark)

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

    2011-01-01

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

  9. The epidemiology of bacterial meningitis in Kosovo.

    Science.gov (United States)

    Namani, Sadie A; Koci, Remzie A; Qehaja-Buçaj, Emine; Ajazaj-Berisha, Lindita; Mehmeti, Murat

    2014-07-14

    The purpose of this study was to present the epidemiologic features of bacterial meningitis in the developing country of Kosovo. Data were collected from active surveillance of bacterial meningitis cases treated at the University Clinical Center of Kosovo in the years 2000 (first post-war year) and 2010. Meningitis cases in 2000 compared with 2010 showed a 35.5% decline in incidence (from 4.8 to 3.1 cases per 100,000 population) and a decrease in the case fatality rate from 10% to 5%. In children, there was a lower mortality rate (5% versus 2%) and a lower incidence of neurological complications (13% versus 16%) as compared to adults (32% versus 10% and 16% versus 35%, respectively). Neisseria meningitidis was the most common pathogen of bacterial meningitis in both study periods. Bacterial meningitis was most prevalent in the pediatric population, and showed an increase in the median age, from three years in 2000 to seven years in 2010. A steady number of bacterial meningitis cases in adults throughout last decade (around 20 cases per year) was recorded. During the last decade, gradual changes have been observed in the epidemiology of bacterial meningitis that are unrelated to the introduction of new vaccines, but are partly due to the improvement of living conditions.

  10. Role of quorum sensing in bacterial infections

    Science.gov (United States)

    Castillo-Juárez, Israel; Maeda, Toshinari; Mandujano-Tinoco, Edna Ayerim; Tomás, María; Pérez-Eretza, Berenice; García-Contreras, Silvia Julieta; Wood, Thomas K; García-Contreras, Rodolfo

    2015-01-01

    Quorum sensing (QS) is cell communication that is widely used by bacterial pathogens to coordinate the expression of several collective traits, including the production of multiple virulence factors, biofilm formation, and swarming motility once a population threshold is reached. Several lines of evidence indicate that QS enhances virulence of bacterial pathogens in animal models as well as in human infections; however, its relative importance for bacterial pathogenesis is still incomplete. In this review, we discuss the present evidence from in vitro and in vivo experiments in animal models, as well as from clinical studies, that link QS systems with human infections. We focus on two major QS bacterial models, the opportunistic Gram negative bacteria Pseudomonas aeruginosa and the Gram positive Staphylococcus aureus, which are also two of the main agents responsible of nosocomial and wound infections. In addition, QS communication systems in other bacterial, eukaryotic pathogens, and even immune and cancer cells are also reviewed, and finally, the new approaches proposed to combat bacterial infections by the attenuation of their QS communication systems and virulence are also discussed. PMID:26244150

  11. Presence of pathogenic Escherichia coli is correlated with bacterial community diversity and composition on pre-harvest cattle hides.

    Science.gov (United States)

    Chopyk, Jessica; Moore, Ryan M; DiSpirito, Zachary; Stromberg, Zachary R; Lewis, Gentry L; Renter, David G; Cernicchiaro, Natalia; Moxley, Rodney A; Wommack, K Eric

    2016-03-22

    Since 1982, specific serotypes of Shiga toxin-producing Escherichia coli (STEC) have been recognized as significant foodborne pathogens acquired from contaminated beef and, more recently, other food products. Cattle are the major reservoir hosts of these organisms, and while there have been advancements in food safety practices and industry standards, STEC still remains prevalent within beef cattle operations with cattle hides implicated as major sources of carcass contamination. To investigate whether the composition of hide-specific microbial communities are associated with STEC prevalence, 16S ribosomal RNA (rRNA) bacterial community profiles were obtained from hide and fecal samples collected from a large commercial feedlot over a 3-month period. These community data were examined amidst an extensive collection of prevalence data on a subgroup of STEC that cause illness in humans, referred to as enterohemorrhagic E. coli (EHEC). Fecal 16S rRNA gene OTUs (operational taxonomic units) were subtracted from the OTUs found within each hide 16S rRNA amplicon library to identify hide-specific bacterial populations. Comparative analysis of alpha diversity revealed a significant correlation between low bacterial diversity and samples positive for the presence of E. coli O157:H7 and/or the non-O157 groups: O26, O111, O103, O121, O45, and O145. This trend occurred regardless of diversity metric or fecal OTU presence. The number of EHEC serogroups present in the samples had a compounding effect on the inverse relationship between pathogen presence and bacterial diversity. Beta diversity data showed differences in bacterial community composition between samples containing O157 and non-O157 populations, with certain OTUs demonstrating significant changes in relative abundance. The cumulative prevalence of the targeted EHEC serogroups was correlated with low bacterial community diversity on pre-harvest cattle hides. Understanding the relationship between indigenous hide

  12. Immunity to bacterial infection in the chicken.

    Science.gov (United States)

    Wigley, Paul

    2013-11-01

    Bacterial infections remain important to the poultry industry both in terms of animal and public health, the latter due to the importance of poultry as a source of foodborne bacterial zoonoses such as Salmonella and Campylobacter. As such, much focus of research to the immune response to bacterial infection has been to Salmonella. In this review we will focus on how research on avian salmonellosis has developed our understanding of immunity to bacteria in the chicken from understanding the role of TLRs in recognition of bacterial pathogens, through the role of heterophils, macrophages and γδ lymphocytes in innate immunity and activation of adaptive responses to the role of cellular and humoral immunity in immune clearance and protection. What is known of the immune response to other bacterial infections and in particular infections that have emerged recently as major problems in poultry production including Campylobacter jejuni, Avian Pathogenic Escherichia coli, Ornithobacterium rhinotracheale and Clostridium perfringens are discussed. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. Bacterial surface adaptation

    Science.gov (United States)

    Utada, Andrew

    2014-03-01

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

  14. Bacterial Meningitis in Infants

    Directory of Open Access Journals (Sweden)

    J Gordon Millichap

    2004-04-01

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

  15. Factitious Bacterial Meningitis Revisited

    Science.gov (United States)

    Peterson, E.; Thrupp, L.; Uchiyama, N.; Hawkins, B.; Wolvin, B.; Greene, G.

    1982-01-01

    Nonviable gram-negative bacilli were seen in smears of cerebrospinal fluid from eight infants in whom bacterial meningitis was ruled out. Tubes from commercial kits were the source of the factitious organisms. PMID:7153328

  16. Vimentin in Bacterial Infections

    DEFF Research Database (Denmark)

    Mak, Tim N; Brüggemann, Holger

    2016-01-01

    filaments (IFs). IFs have not only roles in maintaining the structural integrity of the cell, but they are also involved in many cellular processes including cell adhesion, immune signaling, and autophagy, processes that are important in the context of bacterial infections. Here, we summarize the knowledge...... about the role of IFs in bacterial infections, focusing on the type III IF protein vimentin. Recent studies have revealed the involvement of vimentin in host cell defenses, acting as ligand for several pattern recognition receptors of the innate immune system. Two main aspects of bacteria......-vimentin interactions are presented in this review: the role of vimentin in pathogen-binding on the cell surface and subsequent bacterial invasion and the interaction of cytosolic vimentin and intracellular pathogens with regards to innate immune signaling. Mechanistic insight is presented involving distinct bacterial...

  17. Investigation of multimodal forward scatter phenotyping from bacterial colonies

    Science.gov (United States)

    Kim, Huisung

    A rapid, label-free, and elastic light scattering (ELS) based bacterial colony phenotyping technology, bacterial rapid detection using optical scattering technology (BARDOT) provides a successful classification of several bacterial genus and species. For a thorough understanding of the phenomena and overcoming the limitations of the previous design, five additional modalities from a bacterial colony: 3D morphology, spatial optical density (OD) distribution, spectral forward scattering pattern, spectral OD, and surface backward reflection pattern are proposed to enhance the classification/identification ratio, and the feasibilities of each modality are verified. For the verification, three different instruments: integrated colony morphology analyzer (ICMA), multi-spectral BARDOT (MS-BARDOT) , and multi-modal BARDOT (MM-BARDOT) are proposed and developed. The ICMA can measure 3D morphology and spatial OD distribution of the colony simultaneously. A commercialized confocal displacement meter is used to measure the profiles of the bacterial colonies, together with a custom built optical density measurement unit to interrogate the biophysics behind the collective behavior of a bacterial colony. The system delivers essential information related to the quantitative growth dynamics (height, diameter, aspect ratio, optical density) of the bacterial colony, as well as, a relationship in between the morphological characteristics of the bacterial colony and its forward scattering pattern. Two different genera: Escherichia coli O157:H7 EDL933, and Staphylococcus aureus ATCC 25923 are selected for the analysis of the spatially resolved growth dynamics, while, Bacillus spp. such as B. subtilis ATCC 6633, B. cereus ATCC 14579, B. thuringiensis DUP6044, B. polymyxa B719W, and B. megaterium DSP 81319, are interrogated since some of the Bacillus spp. provides strikingly different characteristics of ELS patterns, and the origin of the speckle patterns are successfully correlated with

  18. Volatiles in Inter-Specific Bacterial Interactions.

    Science.gov (United States)

    Tyc, Olaf; Zweers, Hans; de Boer, Wietse; Garbeva, Paolina

    2015-01-01

    The importance of volatile organic compounds for functioning of microbes is receiving increased research attention. However, to date very little is known on how inter-specific bacterial interactions effect volatiles production as most studies have been focused on volatiles produced by monocultures of well-described bacterial genera. In this study we aimed to understand how inter-specific bacterial interactions affect the composition, production and activity of volatiles. Four phylogenetically different bacterial species namely: Chryseobacterium, Dyella, Janthinobacterium, and Tsukamurella were selected. Earlier results had shown that pairwise combinations of these bacteria induced antimicrobial activity in agar media whereas this was not the case for monocultures. In the current study, we examined if these observations were also reflected by the production of antimicrobial volatiles. Thus, the identity and antimicrobial activity of volatiles produced by the bacteria were determined in monoculture as well in pairwise combinations. Antimicrobial activity of the volatiles was assessed against fungal, oomycetal, and bacterial model organisms. Our results revealed that inter-specific bacterial interactions affected volatiles blend composition. Fungi and oomycetes showed high sensitivity to bacterial volatiles whereas the effect of volatiles on bacteria varied between no effects, growth inhibition to growth promotion depending on the volatile blend composition. In total 35 volatile compounds were detected most of which were sulfur-containing compounds. Two commonly produced sulfur-containing volatile compounds (dimethyl disulfide and dimethyl trisulfide) were tested for their effect on three target bacteria. Here, we display the importance of inter-specific interactions on bacterial volatiles production and their antimicrobial activities.

  19. Volatiles in inter-specific bacterial interactions

    Directory of Open Access Journals (Sweden)

    Olaf eTyc

    2015-12-01

    Full Text Available The importance of volatile organic compounds for functioning of microbes is receiving increased research attention. However, to date very little is known on how inter-specific bacterial interactions effect volatiles production as most studies have been focused on volatiles produced by monocultures of well described bacterial genera. In this study we aimed to understand how inter-specific bacterial interactions affect the composition, production and activity of volatiles. Four phylogenetically different bacterial species namely: Chryseobacterium, Dyella, Janthinobacterium and Tsukamurella were selected. Earlier results had shown that pairwise combinations of these bacteria induced antimicrobial activity in agar media whereas this was not the case for monocultures. In the current study, we examined if these observations were also reflected by the production of antimicrobial volatiles. Thus, the identity and antimicrobial activity of volatiles produced by the bacteria were determined in monoculture as well in pairwise combinations. Antimicrobial activity of the volatiles was assessed against fungal, oomycetal and bacterial model organisms. Our results revealed that inter-specific bacterial interactions affected volatiles blend composition. Fungi and oomycetes showed high sensitivity to bacterial volatiles whereas the effect of volatiles on bacteria varied between no effects, growth inhibition to growth promotion depending on the volatile blend composition. In total 35 volatile compounds were detected most of which were sulfur-containing compounds. Two commonly produced sulfur-containing volatile compounds (dimethyl disulfide and dimethyl trisulfide were tested for their effect on three target bacteria. Here we display the importance of inter-specific interactions on bacterial volatiles production and their antimicrobial activities.

  20. The Composition and Spatial Patterns of Bacterial Virulence Factors and Antibiotic Resistance Genes in 19 Wastewater Treatment Plants

    OpenAIRE

    Zhang, Bing; Xia, Yu; Wen, Xianghua; Wang, Xiaohui; Yang, Yunfeng; Zhou, Jizhong; Zhang, Yu

    2016-01-01

    Bacterial pathogenicity and antibiotic resistance are of concern for environmental safety and public health. Accumulating evidence suggests that wastewater treatment plants (WWTPs) are as an important sink and source of pathogens and antibiotic resistance genes (ARGs). Virulence genes (encoding virulence factors) are good indicators for bacterial pathogenic potentials. To achieve a comprehensive understanding of bacterial pathogenic potentials and antibiotic resistance in WWTPs, bacterial vir...

  1. Bacterial resistance to antimicrobial peptides: an evolving phenomenon.

    Science.gov (United States)

    Fleitas, Osmel; Agbale, Caleb M; Franco, Octavio L

    2016-06-01

    Bacterial resistance to conventional antibiotics is currently a real problem all over the world, making novel antimicrobial compounds a real research priority. Some of the most promising compounds found to date are antimicrobial peptides (AMPs). The benefits of these drugs include their broad spectrum of activity that affects several microbial processes, making the emergence of resistance less likely. However, bacterial resistance to AMPs is an evolving phenomenon that compromises the therapeutic potential of these compounds. Therefore, it is mandatory to understand bacterial mechanisms of resistance to AMPs in depth, in order to develop more powerful AMPs that overcome the bacterial resistance response.

  2. How Do Health Care Providers Diagnose Bacterial Vaginosis (BV)?

    Science.gov (United States)

    ... Share Facebook Twitter Pinterest Email Print How do health care providers diagnose Bacterial Vaginosis (BV)? Diagnosis of BV requires a vaginal exam by a qualified health care provider and the laboratory testing of fluid collected ...

  3. Rapid detection of bacterial pathogens using flourescence spectroscopy and chemometrics

    Science.gov (United States)

    This work presents the development of a method for rapid bacterial identification based on the fluorescence spectroscopy combined with multivariate analysis. Fluorescence spectra of pure three different genera of bacteria (Escherichia coli, Salmonella, and Campylobacter) were collected from 200...

  4. New Application of Hyperspectral Imaging for Bacterial Cell Classification

    Science.gov (United States)

    Hyperspectral microscopy has shown potential as a method for rapid detection of foodborne pathogenic bacteria with spectral characteristics from bacterial cells. Hyperspectral microscope images (HMIs) are collected from broiler chicken isolates of Salmonella serotypes Enteritidis, Typhimurium, Infa...

  5. (MDR) Bacterial Activity of Endophytic Fungi Isolated from the

    African Journals Online (AJOL)

    MDR) bacterial potential of culturable endophytes from A. corniculatum in Beibu Gulf, China. Methods: The plant parts were collected from healthy-looking A. corniculatum. The endophytes were isolated and identified by colonial morphology and ...

  6. Antibiotics susceptibility patterns of urine bacterial isolates in Zaria ...

    African Journals Online (AJOL)

    Methods: Urine samples collected from students of Faculty of Pharmaceutical Sciences, Ahmadu Bello University and Kaduna State Polytechnic, Zaria, Nigeria, commercial sex workers, and illiterate men and women in Zaria were cultured and bacterial isolates identified using standard microbiological procedures.

  7. Understanding classification

    NARCIS (Netherlands)

    Subianto, M.

    2009-01-01

    In practical data analysis, the understandability of models plays an important role in their acceptance. In the data mining literature, however, understandability plays is hardly ever mentioned. If it is mentioned, it is interpreted as meaning that the models have to be simple. In this thesis we

  8. Embodied understanding.

    Science.gov (United States)

    Johnson, Mark

    2015-01-01

    Western culture has inherited a view of understanding as an intellectual cognitive operation of grasping of concepts and their relations. However, cognitive science research has shown that this received intellectualist conception is substantially out of touch with how humans actually make and experience meaning. The view emerging from the mind sciences recognizes that understanding is profoundly embodied, insofar as our conceptualization and reasoning recruit sensory, motor, and affective patterns and processes to structure our understanding of, and engagement with, our world. A psychologically realistic account of understanding must begin with the patterns of ongoing interaction between an organism and its physical and cultural environments and must include both our emotional responses to changes in our body and environment, and also the actions by which we continuously transform our experience. Consequently, embodied understanding is not merely a conceptual/propositional activity of thought, but rather constitutes our most basic way of being in, and engaging with, our surroundings in a deep visceral manner.

  9. Marine Bacterial Genomics

    DEFF Research Database (Denmark)

    Machado, Henrique

    microorganisms to be used as cell factories for production. Therefore exploitation of new microbial niches and use of different strategies is an opportunity to boost discoveries. Even though scientists have started to explore several habitats other than the terrestrial ones, the marine environment stands out...... as a hitherto under-explored niche. This thesis work uses high-throughput sequencing technologies on a collection of marine bacteria established during the Galathea 3 expedition, with the purpose of unraveling new biodiversity and new bioactivities. Several tools were used for genomic analysis in order...... to better understand the potential harbored in marine bacteria. The work presented makes use of whole genome sequencing of marine bacteria to prove that the genetic repertoire for secondary metabolite production harbored in these bacteria is far larger than anticipated; to identify and develop a new...

  10. CT scan of bacterial and aseptic meningitis

    International Nuclear Information System (INIS)

    Takemoto, Kazumasa; Saiwai, Shigeo; Tamaoka, Koichi

    1983-01-01

    CT scans of the patients with aseptic and bacterial meningitis were reviewed and compared to previous reports. In aseptic meningitis, no abnormal CT findings were observed. In bacterial meningitis, CT findings were ventricular dilatation, subdural fluid collection, parenchymal low density, intracerebral hematoma and meningeal enhancement after contrast injection. Three patients among 48 suffered from status epileptics during the course of the illness. All of 3 patients developed parenchymal inhomogeneous low density and progressive ventricular dilatation which did not improve after ventricular peritoneal shunt surgery. We believe that these changes are most likely due to hypoxic hypoxemia during epileptic seizure and meningitis itself seems to play a little role. (author)

  11. Neurosonographic findings of bacterial meningitis in Infants

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Moon Chul; Lee, Sung Sik; Lee, Hong Kue; Lee, Soon Il [Sowa Children' s Hospital, Seoul (Korea, Republic of)

    1989-02-15

    44 infants under 1 year were studied retrospectively during these illness and follow up after 1 week intervals. The spectrum of sonographic features of bacterial meningitis in acute stage included normal scan (20 patients), echogenic sulci (10 patients), echogenic lining of epandymas (8 patients), Abnormal parenchymal echogenecity (6 patients). On follow up examination with 1 week intervals, variety of complications was found in 14 patients (32%) of the infants. There were ventriculomegaly in 7 patients, extraaxial fluid collection in 4 patients, brain abscess in 2 patients and poor encephalic cyst in 1 patient. We conclude that ultrasound was an effective method for evaluation of progression and complications of bacterial meningitis.

  12. CT scan of bacterial and aseptic meningitis

    Energy Technology Data Exchange (ETDEWEB)

    Takemoto, Kazumasa; Saiwai, Shigeo; Tamaoka, Koichi (Kobe Central Municipal Hospital (Japan))

    1983-01-01

    CT scans of the patients with aseptic and bacterial meningitis were reviewed and compared to previous reports. In aseptic meningitis, no abnormal CT findings were observed. In bacterial meningitis, CT findings were ventricular dilatation, subdural fluid collection, parenchymal low density, intracerebral hematoma and meningeal enhancement after contrast injection. Three patients among 48 suffered from status epileptics during the course of the illness. All of the 3 patients developed parenchymal inhomogeneous low density and progressive ventricular dilatation which did not improve after ventricular peritoneal shunt surgery. We believe that these changes are most likely due to hypoxic hypoxemia during epileptic seizure and meningitis itself seems to play a little role.

  13. Diversification of bacterial genome content through distinct mechanisms over different timescales

    Science.gov (United States)

    Croucher, Nicholas J.; Coupland, Paul G.; Stevenson, Abbie E.; Callendrello, Alanna; Bentley, Stephen D.; Hanage, William P.

    2014-01-01

    Bacterial populations often consist of multiple co-circulating lineages. Determining how such population structures arise requires understanding what drives bacterial diversification. Using 616 systematically sampled genomes, we show that Streptococcus pneumoniae lineages are typically characterized by combinations of infrequently transferred stable genomic islands: those moving primarily through transformation, along with integrative and conjugative elements and phage-related chromosomal islands. The only lineage containing extensive unique sequence corresponds to a set of atypical unencapsulated isolates that may represent a distinct species. However, prophage content is highly variable even within lineages, suggesting frequent horizontal transmission that would necessitate rapidly diversifying anti-phage mechanisms to prevent these viruses sweeping through populations. Correspondingly, two loci encoding Type I restriction-modification systems able to change their specificity over short timescales through intragenomic recombination are ubiquitous across the collection. Hence short-term pneumococcal variation is characterized by movement of phage and intragenomic rearrangements, with the slower transfer of stable loci distinguishing lineages. PMID:25407023

  14. Bioavailability of pollutants in bacterial communities of Rodrigo de Freitas Lagoon, Rio de Janeiro, Brazil

    Directory of Open Access Journals (Sweden)

    E.M. da Fonseca

    2014-09-01

    Full Text Available Processes involving heavy metals and other contaminants continue to present unsolved environmental questions. To advance the understanding of geochemical processes that involve the bioavailability of contaminants, cores where collected in the Rodrigo de Freitas lagoon, and analyzed for bacterial activity and metal concentrations. Results would suggest an extremely reducing environment where organic substances seem to be the predominant agents responsible for this geochemical process. Analytical data showed sulphate reduction to be the main agent driving this process, since this kind of bacteria was found to be active in all of the samples analyzed. Esterase enzyme production did not signal the influence of heavy metals and hydrocarbon concentrations and heavy metals were found to be unavailable for biota. However, correlation between results for bacterial biomass and the potentially mobile percentage of the total Ni concentrations would suggest a negative impact.

  15. Understanding semantics

    DEFF Research Database (Denmark)

    Thrane, Torben

    1997-01-01

    Understanding natural language is a cognitive, information-driven process. Discussing some of the consequences of this fact, the paper offers a novel look at the semantic effect of lexical nouns and the identification of reference types....

  16. Understanding Alzheimer's

    Science.gov (United States)

    ... Navigation Bar Home Current Issue Past Issues Understanding Alzheimer's Past Issues / Fall 2007 Table of Contents For ... and brain scans. No treatment so far stops Alzheimer's. However, for some in the disease's early and ...

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

    Directory of Open Access Journals (Sweden)

    Thomas E Gorochowski

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

  18. Understanding homelessness

    OpenAIRE

    Somerville, Peter

    2013-01-01

    This paper reviews the literature on understanding homelessness. It criticizes approaches that ignore, distort or diminish the humanity of homeless people, or else, add little to our understanding of that humanity. In particular, it rejects what it calls “epidemiological” approaches, which deny the possibility of agency for homeless people, insofar as those approaches view the situation of those people largely as a “social fact”, to be explained in terms of causal variables or “risk factors” ...

  19. Bacterial Cell Mechanics.

    Science.gov (United States)

    Auer, George K; Weibel, Douglas B

    2017-07-25

    Cellular mechanical properties play an integral role in bacterial survival and adaptation. Historically, the bacterial cell wall and, in particular, the layer of polymeric material called the peptidoglycan were the elements to which cell mechanics could be primarily attributed. Disrupting the biochemical machinery that assembles the peptidoglycan (e.g., using the β-lactam family of antibiotics) alters the structure of this material, leads to mechanical defects, and results in cell lysis. Decades after the discovery of peptidoglycan-synthesizing enzymes, the mechanisms that underlie their positioning and regulation are still not entirely understood. In addition, recent evidence suggests a diverse group of other biochemical elements influence bacterial cell mechanics, may be regulated by new cellular mechanisms, and may be triggered in different environmental contexts to enable cell adaptation and survival. This review summarizes the contributions that different biomolecular components of the cell wall (e.g., lipopolysaccharides, wall and lipoteichoic acids, lipid bilayers, peptidoglycan, and proteins) make to Gram-negative and Gram-positive bacterial cell mechanics. We discuss the contribution of individual proteins and macromolecular complexes in cell mechanics and the tools that make it possible to quantitatively decipher the biochemical machinery that contributes to bacterial cell mechanics. Advances in this area may provide insight into new biology and influence the development of antibacterial chemotherapies.

  20. Multiple bacterial species reside in chronic wounds

    DEFF Research Database (Denmark)

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

    2006-01-01

    The aim of the study was to investigate the bacterial profile of chronic venous leg ulcers and the importance of the profile to ulcer development. Patients with persisting venous leg ulcers were included and followed for 8 weeks. Every second week, ulcer samples were collected and the bacterial...... of P. aeruginosa in venous leg ulcers can induce ulcer enlargement and/or cause delayed healing....... species present were identified. More than one bacterial species were detected in all the ulcers. The most common bacteria found were Staphylococcus aureus (found in 93.5% of the ulcers), Enterococcus faecalis (71.7%), Pseudomonas aeruginosa (52.2%), coagulase-negative staphylococci (45.7%), Proteus...

  1. Mesoscopic modeling of bacterial flagellar microhydrodynamics.

    Science.gov (United States)

    Gebremichael, Yeshitila; Ayton, Gary S; Voth, Gregory A

    2006-11-15

    A particle-based hybrid method of elastic network model and smooth-particle hydrodynamics has been employed to describe the propulsion of bacterial flagella in a viscous hydrodynamic environment. The method explicitly models the two aspects of bacterial propulsion that involve flagellar flexibility and long-range hydrodynamic interaction of low-Reynolds-number flow. The model further incorporates the molecular organization of the flagellar filament at a coarse-grained level in terms of the 11 protofilaments. Each of these protofilaments is represented by a collection of material points that represent the flagellin proteins. A computational model of a single flexible helical segment representing the filament of a bacterial flagellum is presented. The propulsive dynamics and the flow fields generated by the motion of the model filament are examined. The nature of flagellar deformation and the influence of hydrodynamics in determining the shape of deformations are examined based on the helical filament.

  2. Influence of Physicochemical Aspects of Substratum Nanosurface on Bacterial Attachment for Bone Implant Applications

    Directory of Open Access Journals (Sweden)

    Kun Mediaswanti

    2016-01-01

    Full Text Available Biofilm formation on implant materials is responsible for periprosthetic infections. Bacterial attachment is important as the first stage in biofilm formation. It is meaningful to understand the influence of nanostructured surface on bacterial attachment. This review discusses the influence of physicochemical aspects of substratum nanosurface on bacterial attachment.

  3. Influence of Physicochemical Aspects of Substratum Nanosurface on Bacterial Attachment for Bone Implant Applications

    OpenAIRE

    Mediaswanti, Kun

    2016-01-01

    Biofilm formation on implant materials is responsible for periprosthetic infections. Bacterial attachment is important as the first stage in biofilm formation. It is meaningful to understand the influence of nanostructured surface on bacterial attachment. This review discusses the influence of physicochemical aspects of substratum nanosurface on bacterial attachment.

  4. Rhizosphere Bacterial Degradation of RDX, Understanding and Enhancement

    Science.gov (United States)

    2014-02-01

    existing probes targeting the Deltaproteobacteria (Lucker, Steger et al. 2007); but could not identify a probe targeting the entire group. Figure 32...contaminants." Environmental Science & Technology 36(7): 1579-1583. Lucker, S., D. Steger , K. U. Kjeldsen, B. J. MacGregor, M. Wagner and A. Loy (2007

  5. Bacterial meningitis in children

    International Nuclear Information System (INIS)

    Marji, S.

    2007-01-01

    To demonstrate the epidemiology, clinical manifestations and bacteriological profile of bacterial meningitis in children beyond the neonatal period in our hospital. This was a retrospective descriptive study conducted at Prince Rashid Hospital in Irbid, Jordan. The medical records of 50 children with the diagnosis of bacterial meningitis during 4 years period, were reviewed. The main cause of infection was streptococcus pneumoniae, followed by Haemophilus influenza and Niesseria meningitides. Mortality was higher in infants and meningococcal infection, while complications were more encountered in cases of streptococcus pneumoniae. Cerebrospinal fluid culture was positive in 11 cases and Latex agglutination test in 39. There is a significant reduction of the numbers of bacterial meningitis caused by Haemophilus influenza type B species. (author)

  6. Interfering with bacterial gossip

    DEFF Research Database (Denmark)

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

    2011-01-01

    Biofilm resilience poses major challenges to the development of novel antimicrobial agents. Biofilm bacteria can be considered small groups of “Special Forces” capable of infiltrating the host and destroying important components of the cellular defense system with the aim of crippling the host...... defense. Antibiotics exhibit a rather limited effect on biofilms. Furthermore, antibiotics have an ‘inherent obsolescence’ because they select for development of resistance. Bacterial infections with origin in bacterial biofilms have become a serious threat in developed countries. Pseudomonas aeruginosa...... that appropriately target bacteria in their relevant habitat with the aim of mitigating their destructive impact on patients. In this review we describe molecular mechanisms involved in “bacterial gossip” (more scientifically referred to as quorum sensing (QS) and c-di-GMP signaling), virulence, biofilm formation...

  7. Antibiotics promote aggregation within aquatic bacterial communities

    Directory of Open Access Journals (Sweden)

    Gianluca eCorno

    2014-07-01

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

  8. Bacterial genomes: habitat specificity and uncharted organisms.

    Science.gov (United States)

    Dini-Andreote, Francisco; Andreote, Fernando Dini; Araújo, Welington Luiz; Trevors, Jack T; van Elsas, Jan Dirk

    2012-07-01

    The capability and speed in generating genomic data have increased profoundly since the release of the draft human genome in 2000. Additionally, sequencing costs have continued to plummet as the next generation of highly efficient sequencing technologies (next-generation sequencing) became available and commercial facilities promote market competition. However, new challenges have emerged as researchers attempt to efficiently process the massive amounts of sequence data being generated. First, the described genome sequences are unequally distributed among the branches of bacterial life and, second, bacterial pan-genomes are often not considered when setting aims for sequencing projects. Here, we propose that scientists should be concerned with attaining an improved equal representation of most of the bacterial tree of life organisms, at the genomic level. Moreover, they should take into account the natural variation that is often observed within bacterial species and the role of the often changing surrounding environment and natural selection pressures, which is central to bacterial speciation and genome evolution. Not only will such efforts contribute to our overall understanding of the microbial diversity extant in ecosystems as well as the structuring of the extant genomes, but they will also facilitate the development of better methods for (meta)genome annotation.

  9. Adult bacterial meningitis

    DEFF Research Database (Denmark)

    Meyer, C N; Samuelsson, I S; Galle, M

    2004-01-01

    Episodes of adult bacterial meningitis (ABM) at a Danish hospital in 1991-2000 were identified from the databases of the Department of Clinical Microbiology, and compared with data from the Danish National Patient Register and the Danish National Notification System. Reduced penicillin susceptibi......Episodes of adult bacterial meningitis (ABM) at a Danish hospital in 1991-2000 were identified from the databases of the Department of Clinical Microbiology, and compared with data from the Danish National Patient Register and the Danish National Notification System. Reduced penicillin...

  10. Bacterial meningitis in infants.

    Science.gov (United States)

    Ku, Lawrence C; Boggess, Kim A; Cohen-Wolkowiez, Michael

    2015-03-01

    Neonatal bacterial meningitis is uncommon but devastating. Morbidity among survivors remains high. The types and distribution of pathogens are related to gestational age, postnatal age, and geographic region. Confirming the diagnosis is difficult. Clinical signs are often subtle, lumbar punctures are frequently deferred, and cerebrospinal fluid (CSF) cultures can be compromised by prior antibiotic exposure. Infants with bacterial meningitis can have negative blood cultures and normal CSF parameters. Promising tests such as the polymerase chain reaction require further study. Prompt treatment with antibiotics is essential. Clinical trials investigating a vaccine for preventing neonatal Group B Streptococcus infections are ongoing. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. Understanding Maple

    CERN Document Server

    Thompson, Ian

    2016-01-01

    Maple is a powerful symbolic computation system that is widely used in universities around the world. This short introduction gives readers an insight into the rules that control how the system works, and how to understand, fix, and avoid common problems. Topics covered include algebra, calculus, linear algebra, graphics, programming, and procedures. Each chapter contains numerous illustrative examples, using mathematics that does not extend beyond first-year undergraduate material. Maple worksheets containing these examples are available for download from the author's personal website. The book is suitable for new users, but where advanced topics are central to understanding Maple they are tackled head-on. Many concepts which are absent from introductory books and manuals are described in detail. With this book, students, teachers and researchers will gain a solid understanding of Maple and how to use it to solve complex mathematical problems in a simple and efficient way.

  12. Understanding physics

    CERN Document Server

    Mansfield, Michael

    2011-01-01

    Understanding Physics - Second edition is a comprehensive, yet compact, introductory physics textbook aimed at physics undergraduates and also at engineers and other scientists taking a general physics course. Written with today's students in mind, this text covers the core material required by an introductory course in a clear and refreshing way. A second colour is used throughout to enhance learning and understanding. Each topic is introduced from first principles so that the text is suitable for students without a prior background in physics. At the same time the book is designed to enable

  13. Distinct bacterial communities associated with the coral model Aiptasia in aposymbiotic and symbiotic states with Symbiodinium

    Directory of Open Access Journals (Sweden)

    Till Roethig

    2016-11-01

    Full Text Available Coral reefs are in decline. The basic functional unit of coral reefs is the coral metaorganism or holobiont consisting of the cnidarian host animal, symbiotic algae of the genus Symbiodinium, and a specific consortium of bacteria (among others, but research is slow due to the difficulty of working with corals. Aiptasia has proven a tractable model system to elucidate the intricacies of cnidarian-dinoflagellate symbioses, but characterization of the associated bacterial microbiome and the underlying genomic features relevant for bacterial selection and control is required to provide a complete and integrated understanding of holobiont function. In this work, we characterize and analyze the microbiome of aposymbiotic and symbiotic Aiptasia and show that bacterial associates are distinct in both conditions. We further show that key microbial associates can be cultured without their cnidarian host. Our results suggest that bacteria play an important role in the symbiosis of Aiptasia with Symbiodinium, a finding that underlines the power of the Aiptasia model system where cnidarian hosts can be analyzed in aposymbiotic and symbiotic states. The characterization of the native microbiome and the ability to retrieve culturable isolates contributes to the resources available for the Aiptasia model system. This provides an opportunity to comparatively analyze cnidarian metaorganisms as collective functional holobionts and as separated member species. We hope that this will accelerate research into understanding the intricacies of coral biology, which is urgently needed to develop strategies to mitigate the effects of environmental change.

  14. Development of Quorum-Based Anti-Virulence Therapeutics Targeting Gram-Negative Bacterial Pathogens

    Directory of Open Access Journals (Sweden)

    Wen Shan Yew

    2013-08-01

    Full Text Available Quorum sensing is a cell density-dependent signaling phenomenon used by bacteria for coordination of population-wide phenotypes, such as expression of virulence genes, antibiotic resistance and biofilm formation. Lately, disruption of bacterial communication has emerged as an anti-virulence strategy with enormous therapeutic potential given the increasing incidences of drug resistance in pathogenic bacteria. The quorum quenching therapeutic approach promises a lower risk of resistance development, since interference with virulence generally does not affect the growth and fitness of the bacteria and, hence, does not exert an associated selection pressure for drug-resistant strains. With better understanding of bacterial communication networks and mechanisms, many quorum quenching methods have been developed against various clinically significant bacterial pathogens. In particular, Gram-negative bacteria are an important group of pathogens, because, collectively, they are responsible for the majority of hospital-acquired infections. Here, we discuss the current understanding of existing quorum sensing mechanisms and present important inhibitory strategies that have been developed against this group of pathogenic bacteria.

  15. Understanding Energy

    Science.gov (United States)

    Menon, Deepika; Shelby, Blake; Mattingly, Christine

    2016-01-01

    "Energy" is a term often used in everyday language. Even young children associate energy with the food they eat, feeling tired after playing soccer, or when asked to turn the lights off to save light energy. However, they may not have the scientific conceptual understanding of energy at this age. Teaching energy and matter could be…

  16. Collection Mapping.

    Science.gov (United States)

    Harbour, Denise

    2002-01-01

    Explains collection mapping for library media collections. Discusses purposes for creating collection maps, including helping with selection and weeding decisions, showing how the collection supports the curriculum, and making budget decisions; and methods of data collection, including evaluating a collaboratively taught unit with the classroom…

  17. Activities of Tedizolid and Linezolid Determined by the Reference Broth Microdilution Method against 3,032 Gram-Positive Bacterial Isolates Collected in Asia-Pacific, Eastern Europe, and Latin American Countries in 2014.

    Science.gov (United States)

    Pfaller, Michael A; Flamm, Robert K; Jones, Ronald N; Farrell, David J; Mendes, Rodrigo E

    2016-09-01

    Tedizolid and linezolid in vitro activities against 3,032 Gram-positive pathogens collected in Asia-Pacific, Eastern European, and Latin American medical centers during 2014 were assessed. The isolates were tested for susceptibility by the current reference broth microdilution methods. Due to concern over the effect of MIC endpoint criteria on the results of testing the oxazolidinones tedizolid and linezolid, MIC endpoint values were read by two methods: (i) reading the MIC at the first well where the trailing began without regard for pinpoint trailing, according to CLSI M07-A10 and M100-S26 document instructions for reading linezolid (i.e., 80% inhibition of growth; these reads were designated tedizolid 80 and linezolid 80), and (ii) at 100% inhibition of growth (designated tedizolid 100 and linezolid 100). All Staphylococcus aureus, Streptococcus pyogenes, Streptococcus agalactiae, Streptococcus anginosus group, and Enterococcus faecalis isolates were inhibited at tedizolid 80 and 100 MIC values of 0.25 and 0.5, 0.25 and 0.25, 0.25 and 0.5, 0.12 and 0.25, and 0.5 and 1 μg/ml, respectively. Generally, MIC50 and MIC90 results for tedizolid 80 and linezolid 80 were one doubling dilution lower than those read at 100% inhibition. Tedizolid was 4- to 8-fold more potent than linezolid against all the isolates tested regardless of the MIC endpoint criterion used. Despite the differences in potency, >99.9% of isolates tested in this survey were susceptible to both linezolid and tedizolid using CLSI and EUCAST interpretive criteria. In conclusion, tedizolid demonstrated greater in vitro potency than linezolid against Gram-positive pathogens isolated from patients in medical centers across the Asia-Pacific region, Eastern Europe, and Latin America. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  18. Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces

    Directory of Open Access Journals (Sweden)

    Tairacan Augusto Pereira da Fonseca

    2015-10-01

    Full Text Available Currency notes have been implicated as a vehicle for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial population residing on banknotes is still unknown in Brazil. In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$ notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or “feiras” in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins. Also, our analysis revealed the presence of some potential pathogenic bacterial genera including Salmonella, Staphylococcus, and Klebsiella. The results demonstrate that there is a tremendous diversity of bacterial contamination on currency notes, including organisms known to be opportunistic pathogens. One of the factors that may contribute to the richness of bacterial diversity in currency notes is personal hygiene. Thus, our results underscore the need to increase public awareness of the importance of personal hygiene of money handlers who also handle food.

  19. Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces.

    Science.gov (United States)

    Pereira da Fonseca, Tairacan Augusto; Pessôa, Rodrigo; Sanabani, Sabri Saeed

    2015-10-22

    Currency notes have been implicated as a vehicle for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial population residing on banknotes is still unknown in Brazil. In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$) notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or "feiras" in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins. Also, our analysis revealed the presence of some potential pathogenic bacterial genera including Salmonella, Staphylococcus, and Klebsiella. The results demonstrate that there is a tremendous diversity of bacterial contamination on currency notes, including organisms known to be opportunistic pathogens. One of the factors that may contribute to the richness of bacterial diversity in currency notes is personal hygiene. Thus, our results underscore the need to increase public awareness of the importance of personal hygiene of money handlers who also handle food.

  20. The Bacterial Growth Curve.

    Science.gov (United States)

    Paulton, Richard J. L.

    1991-01-01

    A procedure that allows students to view an entire bacterial growth curve during a two- to three-hour student laboratory period is described. Observations of the lag phase, logarithmic phase, maximum stationary phase, and phase of decline are possible. A nonpathogenic, marine bacterium is used in the investigation. (KR)

  1. Bacterial fingerprints across Europe

    NARCIS (Netherlands)

    Glasner, Corinna

    2014-01-01

    Bacterial pathogens, such as Staphylococcus aureus and carbapenemase-producing Enterobacteriaceae (CPE), impose major threats to human health worldwide. Both have a ‘Jekyll & Hyde’ character, since they can be present as human commensals, but can also become harmful invasive pathogens especially

  2. [Bacterial biofilms and infection].

    Science.gov (United States)

    Lasa, I; Del Pozo, J L; Penadés, J R; Leiva, J

    2005-01-01

    In developed countries we tend to think of heart disease and the numerous forms of cancer as the main causes of mortality, but on a global scale infectious diseases come close, or may even be ahead: 14.9 million deaths in 2002 compared to cardiovascular diseases (16.9 million deaths) and cancer (7.1 million deaths) (WHO report 2004). The infectious agents responsible for human mortality have evolved as medical techniques and hygienic measures have changed. Modern-day acute infectious diseases caused by specialized bacterial pathogens such as diphtheria, tetanus, cholera, plague, which represented the main causes of death at the beginning of XX century, have been effectively controlled with antibiotics and vaccines. In their place, more than half of the infectious diseases that affect mildly immunocompromised patients involve bacterial species that are commensal with the human body; these can produce chronic infections, are resistant to antimicrobial agents and there is no effective vaccine against them. Examples of these infections are the otitis media, native valve endocarditis, chronic urinary infections, bacterial prostatitis, osteomyelitis and all the infections related to medical devices. Direct analysis of the surface of medical devices or of tissues that have been foci of chronic infections shows the presence of large numbers of bacteria surrounded by an exopolysaccharide matrix, which has been named the "biofilm". Inside the biofilm, bacteria grow protected from the action of the antibodies, phagocytic cells and antimicrobial treatments. In this article, we describe the role of bacterial biofilms in human persistent infections.

  3. EDITORIAL SPONTANEOUS BACTERIAL PERITONITIS ...

    African Journals Online (AJOL)

    hi-tech

    Spontaneous bacterial peritonitis (SBP) frequent]y occurs in patients with liver cirrhosis and ascites. It is defined as an infection of previously sterile ascitic fluid without any demonstrable intrabdominal source of infection. It is now internationally agreed that a polymorphonuclear (PMN) cell count in the ascitic fluid of over 250 ...

  4. Bacterial membrane proteomics.

    Science.gov (United States)

    Poetsch, Ansgar; Wolters, Dirk

    2008-10-01

    About one quarter to one third of all bacterial genes encode proteins of the inner or outer bacterial membrane. These proteins perform essential physiological functions, such as the import or export of metabolites, the homeostasis of metal ions, the extrusion of toxic substances or antibiotics, and the generation or conversion of energy. The last years have witnessed completion of a plethora of whole-genome sequences of bacteria important for biotechnology or medicine, which is the foundation for proteome and other functional genome analyses. In this review, we discuss the challenges in membrane proteome analysis, starting from sample preparation and leading to MS-data analysis and quantification. The current state of available proteomics technologies as well as their advantages and disadvantages will be described with a focus on shotgun proteomics. Then, we will briefly introduce the most abundant proteins and protein families present in bacterial membranes before bacterial membrane proteomics studies of the last years will be presented. It will be shown how these works enlarged our knowledge about the physiological adaptations that take place in bacteria during fine chemical production, bioremediation, protein overexpression, and during infections. Furthermore, several examples from literature demonstrate the suitability of membrane proteomics for the identification of antigens and different pathogenic strains, as well as the elucidation of membrane protein structure and function.

  5. Seizures Complicating Bacterial Meningitis

    Directory of Open Access Journals (Sweden)

    J Gordon Millichap

    2004-09-01

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

  6. Diagnosis of bacterial infection

    African Journals Online (AJOL)

    rapid and easy-to-use test for bacterial infections. Clearly, this is a very ... detect antigens or specific antibodies, e.g. group A streptococcal antigen testing can be employed to reduce antibiotic use. Culture-based tests are often ... White blood cell count 12 000 cells/mm³; or the presence of >10% ...

  7. Bacterial Meningitis Outcome

    OpenAIRE

    J Gordon Millichap

    1995-01-01

    The neurologic, psychological, and educational outcomes of bacterial meningitis in 130 children evaluated at a mean age of 8 years, and 6 years after their meningitis, are reported from the Department of Paediatrics and Clinical Epidemiology and Biostatistics Unit, University of Melbourne, and the Royal Children’s Hospital, Victoria, Australia.

  8. Corticosteroids for Bacterial Keratitis

    Science.gov (United States)

    Srinivasan, Muthiah; Mascarenhas, Jeena; Rajaraman, Revathi; Ravindran, Meenakshi; Lalitha, Prajna; Glidden, David V.; Ray, Kathryn J.; Hong, Kevin C.; Oldenburg, Catherine E.; Lee, Salena M.; Zegans, Michael E.; McLeod, Stephen D.; Lietman, Thomas M.; Acharya, Nisha R.

    2013-01-01

    Objective To determine whether there is a benefit in clinical outcomes with the use of topical corticosteroids as adjunctive therapy in the treatment of bacterial corneal ulcers. Methods Randomized, placebo-controlled, double-masked, multicenter clinical trial comparing prednisolone sodium phosphate, 1.0%, to placebo as adjunctive therapy for the treatment of bacterial corneal ulcers. Eligible patients had a culture-positive bacterial corneal ulcer and received topical moxifloxacin for at least 48 hours before randomization. Main Outcome Measures The primary outcome was best spectacle-corrected visual acuity (BSCVA) at 3 months from enrollment. Secondary outcomes included infiltrate/scar size, reepithelialization, and corneal perforation. Results Between September 1, 2006, and February 22, 2010, 1769 patients were screened for the trial and 500 patients were enrolled. No significant difference was observed in the 3-month BSCVA (−0.009 logarithm of the minimum angle of resolution [logMAR]; 95% CI, −0.085 to 0.068; P = .82), infiltrate/scar size (P = .40), time to reepithelialization (P = .44), or corneal perforation (P > .99). A significant effect of corticosteroids was observed in subgroups of baseline BSCVA (P = .03) and ulcer location (P = .04). At 3 months, patients with vision of counting fingers or worse at baseline had 0.17 logMAR better visual acuity with corticosteroids (95% CI, −0.31 to −0.02; P = .03) compared with placebo, and patients with ulcers that were completely central at baseline had 0.20 logMAR better visual acuity with corticosteroids (−0.37 to −0.04; P = .02). Conclusions We found no overall difference in 3-month BSCVA and no safety concerns with adjunctive corticosteroid therapy for bacterial corneal ulcers. Application to Clinical Practice Adjunctive topical corticosteroid use does not improve 3-month vision in patients with bacterial corneal ulcers. PMID:21987582

  9. Understanding translation

    DEFF Research Database (Denmark)

    Schjoldager, Anne Gram; Gottlieb, Henrik; Klitgård, Ida

    Understanding Translation is designed as a textbook for courses on the theory and practice of translation in general and of particular types of translation - such as interpreting, screen translation and literary translation. The aim of the book is to help you gain an in-depth understanding...... of the phenomenon of translation and to provide you with a conceptual framework for the analysis of various aspects of professional translation. Intended readers are students of translation and languages, but the book will also be relevant for others who are interested in the theory and practice of translation...... - translators, language teachers, translation users and literary, TV and film critics, for instance. Discussions focus on translation between Danish and English....

  10. Understanding Resilience

    Directory of Open Access Journals (Sweden)

    Gang eWu

    2013-02-01

    Full Text Available Resilience is the ability to adapt successfully in the face of stress and adversity. Stressful life events, trauma and chronic adversity can have a substantial impact on brain function and structure, and can result in the development of PTSD, depression and other psychiatric disorders. However, most individuals do not develop such illnesses after experiencing stressful life events, and are thus thought to be resilient. Resilience as successful adaptation relies on effective responses to environmental challenges and ultimate resistance to the deleterious effects of stress, therefore a greater understanding of the factors that promote such effects is of great relevance. This review focuses on recent findings regarding genetic, epigenetic, developmental, psychosocial and neurochemical factors that are considered essential contributors to the development of resilience. Neural circuits and pathways involved in mediating resilience are also discussed. The growing understanding of resilience factors will hopefully lead to the development of new pharmacological and psychological interventions for enhancing resilience and mitigating the untoward consequences.

  11. Understand electronics

    CERN Document Server

    Bishop, Owen

    2013-01-01

    Understand Electronics provides a readable introduction to the exciting world of electronics for the student or enthusiast with little previous knowledge. The subject is treated with the minimum of mathematics and the book is extensively illustrated.This is an essential guide for the newcomer to electronics, and replaces the author's best-selling Beginner's Guide to Electronics.The step-by-step approach makes this book ideal for introductory courses such as the Intermediate GNVQ.

  12. Understanding users

    DEFF Research Database (Denmark)

    Johannsen, Carl Gustav Viggo

    2014-01-01

    Segmentation of users can help libraries in the process of understanding user similarities and differences. Segmentation can also form the basis for selecting segments of target users and for developing tailored services for specific target segments. Several approaches and techniques have been...... segmentation project using computer-generated clusters. Compared to traditional marketing texts, this article also tries to identify user segments or images or metaphors by the library profession itself....

  13. Understanding unemployment

    OpenAIRE

    Guillaume Rocheteau

    2006-01-01

    Modern economists have built models of the labor market, which isolate the market’s key drivers and describe the way these interact to produce particular levels of unemployment. One of the most popular models used by macroeconomists today is the search-matching model of equilibrium unemployment. We explain this model, and show how it can be applied to understand the way various policies, such as unemployment benefits, taxes, or technological changes, can affect the unemployment rate.

  14. Understanding Technology?

    Directory of Open Access Journals (Sweden)

    Erik Bendtsen

    2016-11-01

    Full Text Available We are facing radical changes in our ways of living in the nearest future. Not necessarily of our own choice, but because tchnological development is moving so fast, that it will have still greater impact on many aspects of our lives. We have seen the beginnings of that change within the latest 35 years or so, but according to newest research that change will speed up immensely in the nearest years to come. The impact of that change or these changes will affect our working life immensely as a consequence of automation. How these changes are brought about and which are their consequences in a broad sense is being attempted to be understood and guessed by researchers. No one knows for sure, but specific patterns are visible. This paper will not try to guess, what will come, but will rather try to understand the deepest ”nature” of technology in order to understand the driving factors in this development: the genesis of technology in a broad sense in order to contibute to the understanding of the basis for the expected development.

  15. Dielectrophoretic assay of bacterial resistance to antibiotics

    International Nuclear Information System (INIS)

    Johari, Juliana; Huebner, Yvonne; Hull, Judith C; Dale, Jeremy W; Hughes, Michael P

    2003-01-01

    The dielectrophoretic collection spectra of antibiotic-sensitive and antibiotic-resistant strains of Staphylococcus epidermidis have been determined. These indicate that in the absence of antibiotic treatment there is a strong similarity between the dielectric properties of sensitive and resistant strains, and that there is a significant difference between the sensitive strains before and after treatment with the antibiotic streptomycin after 24 h exposure. This method offers possibilities for the assessment of bacterial resistance to antibiotics. (note)

  16. Stability of multispecies bacterial communities: signaling networks may stabilize microbiomes.

    Directory of Open Access Journals (Sweden)

    Ádám Kerényi

    Full Text Available Multispecies bacterial communities can be remarkably stable and resilient even though they consist of cells and species that compete for environmental resources. In silico models suggest that common signals released into the environment may help selected bacterial species cluster at common locations and that sharing of public goods (i.e. molecules produced and released for mutual benefit can stabilize this coexistence. In contrast, unilateral eavesdropping on signals produced by a potentially invading species may protect a community by keeping invaders away from limited resources. Shared bacterial signals, such as those found in quorum sensing systems, may thus play a key role in fine tuning competition and cooperation within multi-bacterial communities. We suggest that in addition to metabolic complementarity, signaling dynamics may be important in further understanding complex bacterial communities such as the human, animal as well as plant microbiomes.

  17. Radiometric detection of bacterial metabolism

    International Nuclear Information System (INIS)

    Camargo, E.E.; Wagner Junior, H.N.

    1979-01-01

    The measurement of 14 CO 2 produced by the bacterial oxidation of labelled compounds is discussed as a means of evaluating the bacterial metabolism. The following items are discussed:automated radiometric detection, types of graphs, clinical applications of the radiometric system and influential factors. Complementary studies on bacterial assimilation of substances are presented. (M.A.) [pt

  18. Bacterial Population Genetics in a Forensic Context

    Energy Technology Data Exchange (ETDEWEB)

    Velsko, S P

    2009-11-02

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

  19. Collection Development.

    Science.gov (United States)

    School Libraries in Canada, 2002

    2002-01-01

    Includes 21 articles that discuss collection development in Canadian school libraries. Topics include digital collections in school library media centers; print and electronic library resources; library collections; collaborative projects; print-disabled students; informing administrators of the importance of collection development; censorship;…

  20. Understanding uncertainty

    CERN Document Server

    Lindley, Dennis V

    2013-01-01

    Praise for the First Edition ""...a reference for everyone who is interested in knowing and handling uncertainty.""-Journal of Applied Statistics The critically acclaimed First Edition of Understanding Uncertainty provided a study of uncertainty addressed to scholars in all fields, showing that uncertainty could be measured by probability, and that probability obeyed three basic rules that enabled uncertainty to be handled sensibly in everyday life. These ideas were extended to embrace the scientific method and to show how decisions, containing an uncertain element, could be rationally made.

  1. Physio-chemical characteristics and bacterial diversity in copper ...

    African Journals Online (AJOL)

    The effects of seasonal change in temperature on the chemical compositions of water and bacterial diversity in copper mining wastewater reservoir (CMWR) located in Jiangxi province, China, was investigated. Wastewater samples were collected collected in December 2008 and May 2009 from different points of CMWR ...

  2. Bacterial Cell Wall Components

    Science.gov (United States)

    Ginsberg, Cynthia; Brown, Stephanie; Walker, Suzanne

    Bacterial cell-surface polysaccharides cells are surrounded by a variety of cell-surface structures that allow them to thrive in extreme environments. Components of the cell envelope and extracellular matrix are responsible for providing the cells with structural support, mediating intercellular communication, allowing the cells to move or to adhere to surfaces, protecting the cells from attack by antibiotics or the immune system, and facilitating the uptake of nutrients. Some of the most important cell wall components are polysaccharide structures. This review discusses the occurrence, structure, function, and biosynthesis of the most prevalent bacterial cell surface polysaccharides: peptidoglycan, lipopolysaccharide, arabinogalactan, and lipoarabinomannan, and capsular and extracellular polysaccharides. The roles of these polysaccharides in medicine, both as drug targets and as therapeutic agents, are also described.

  3. Understanding analysis

    CERN Document Server

    Abbott, Stephen

    2015-01-01

    This lively introductory text exposes the student to the rewards of a rigorous study of functions of a real variable. In each chapter, informal discussions of questions that give analysis its inherent fascination are followed by precise, but not overly formal, developments of the techniques needed to make sense of them. By focusing on the unifying themes of approximation and the resolution of paradoxes that arise in the transition from the finite to the infinite, the text turns what could be a daunting cascade of definitions and theorems into a coherent and engaging progression of ideas. Acutely aware of the need for rigor, the student is much better prepared to understand what constitutes a proper mathematical proof and how to write one. Fifteen years of classroom experience with the first edition of Understanding Analysis have solidified and refined the central narrative of the second edition. Roughly 150 new exercises join a selection of the best exercises from the first edition, and three more project-sty...

  4. Understanding ayurveda.

    Science.gov (United States)

    Gadgil, Vaidya Dilip

    2010-01-01

    Ayurveda needs to achieve its full potential both in India and globally. This requires imparting to its students full appreciation of Ayurveda's power and strength, particularly proper understanding of the advantages of applying it to treat chronic and acute diseases. To this end, we explain the necessity of learning Sanskrit as a medium of study, and the advantages of learning the Texts in the traditional way, rather than relying on translations with all the loss of meaning and precision, which that entails. We emphasize the use of Triskandhakosha as a means to fully understand Ayurveda fundamental concepts and technical terms, so that all their shades of meaning are fully understood, and all their usages given in different places in the texts. Only by such methods can full appreciation of Ayurvedic wisdom be achieved, and the full depth and power of its knowledge be applied. Only then will its true status among systems of medicine come to be appreciated, either in India or more widely in the world as a whole.

  5. Understanding Ayurveda

    Directory of Open Access Journals (Sweden)

    Vaidya Dilip Gadgil

    2010-01-01

    Full Text Available Ayurveda needs to achieve its full potential both in India and globally. This requires imparting to its students full appreciation of Ayurveda′s power and strength, particularly proper understanding of the advantages of applying it to treat chronic and acute diseases. To this end, we explain the necessity of learning Sanskrit as a medium of study, and the advantages of learning the Texts in the traditional way, rather than relying on translations with all the loss of meaning and precision, which that entails. We emphasize the use of Triskandhakosha as a means to fully understand Ayurveda fundamental concepts and technical terms, so that all their shades of meaning are fully understood, and all their usages given in different places in the texts. Only by such methods can full appreciation of Ayurvedic wisdom be achieved, and the full depth and power of its knowledge be applied. Only then will its true status among systems of medicine come to be appreciated, either in India or more widely in the world as a whole.

  6. Bacterial meningitis in Nottingham.

    OpenAIRE

    Ispahani, P.

    1983-01-01

    Records of 171 cases of bacterial meningitis admitted to Nottingham hospitals from January 1974 to June 1980 were reviewed. The distribution of organisms producing meningitis and the factors influencing mortality in different age groups were assessed. Neisseria meningitidis, Haemophilus influenzae and Streptococcus pneumoniae accounted for 69% of all proven cases. The overall mortality was 26% being lowest in patients with meningococcal meningitis (0%) and highest in those with pneumococcal m...

  7. Hydrocarbon pollutants shape bacterial community assembly of harbor sediments

    KAUST Repository

    Barbato, Marta

    2016-02-02

    Petroleum pollution results in co-contamination by different classes of molecules, entailing the occurrence of marine sediments difficult to remediate, as in the case of the Ancona harbor (Mediterranean Sea, Italy). Autochthonous bioaugmentation (ABA), by exploiting the indigenous microbes of the environment to be treated, could represent a successful bioremediation strategy. In this perspective we aimed to i) identify the main drivers of the bacterial communities\\' richness in the sediments, ii) establish enrichment cultures with different hydrocarbon pollutants evaluating their effects on the bacterial communities\\' composition, and iii) obtain a collection of hydrocarbon degrading bacteria potentially exploitable in ABA. The correlation between the selection of different specialized bacterial populations and the type of pollutants was demonstrated by culture-independent analyses, and by establishing a collection of bacteria with different hydrocarbon degradation traits. Our observations indicate that pollution dictates the diversity of sediment bacterial communities and shapes the ABA potential in harbor sediments.

  8. Neglected bacterial zoonoses.

    Science.gov (United States)

    Chikeka, I; Dumler, J S

    2015-05-01

    Bacterial zoonoses comprise a group of diseases in humans or animals acquired by direct contact with or by oral consumption of contaminated animal materials, or via arthropod vectors. Among neglected infections, bacterial zoonoses are among the most neglected given emerging data on incidence and prevalence as causes of acute febrile illness, even in areas where recognized neglected tropical diseases occur frequently. Although many other bacterial infections could also be considered in this neglected category, five distinct infections stand out because they are globally distributed, are acute febrile diseases, have high rates of morbidity and case fatality, and are reported as commonly as malaria, typhoid or dengue virus infections in carefully designed studies in which broad-spectrum diagnoses are actively sought. This review will focus attention on leptospirosis, relapsing fever borreliosis and rickettsioses, including scrub typhus, murine typhus and spotted fever group rickettsiosis. Of greatest interest is the lack of distinguishing clinical features among these infections when in humans, which confounds diagnosis where laboratory confirmation is lacking, and in regions where clinical diagnosis is often attributed to one of several perceived more common threats. As diseases such as malaria come under improved control, the real impact of these common and under-recognized infections will become evident, as will the requirement for the strategies and allocation of resources for their control. Copyright © 2015 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  9. Bacterial growth kinetics

    International Nuclear Information System (INIS)

    Boonkitticharoen, V.; Ehrhardt, J.C.; Kirchner, P.T.

    1989-01-01

    Quantitative measurement of bacterial growth may be made using a radioassay technique. This method measures, by scintillation counting, the 14 CO 2 derived from the bacterial metabolism of a 14 C-labeled substrate. Mathematical growth models may serve as reliable tools for estimation of the generation rate constant (or slope of the growth curve) and provide a basis for evaluating assay performance. Two models, i.e., exponential and logistic, are proposed. Both models yielded an accurate fit to the data from radioactive measurement of bacterial growth. The exponential model yielded high precision values of the generation rate constant, with an average relative standard deviation of 1.2%. Under most conditions the assay demonstrated no changes in the slopes of growth curves when the number of bacteria per inoculation was changed. However, the radiometric assay by scintillation method had a growth-inhibiting effect on a few strains of bacteria. The source of this problem was thought to be hypersensitivity to trace amounts of toluene remaining on the detector

  10. Radionuclide scintigraphy of bacterial nephritis

    Energy Technology Data Exchange (ETDEWEB)

    Conway, J.J.; Weiss, S.C.; Shkolnik, A.; Yogev, R.; Firlit, C.; Traisman, E.S.

    1984-01-01

    Pyelonephritis is a leading cause of renal failure and is expected to cost as much as three billion dollars in 1984. The diagnosis of urinary tract infection is usually not difficult. However, localization of the infection within the renal parenchyma as opposed to the collecting system is much more difficult. Flank pain, fever, bacteiuria and evidence of parenchymal involvement by intravenous urography may be absent or unrecognized particularly in the infant. Ultrasound and Nuclear Medicine are advocated as better methods to define parenchymal involvement. Such definition is important in the consideration of treatment since parenchymal involvement of the kidney carries a much more ominous potential outcome than infection restricted to within the collecting system. 38 children with a clinical diagnosis of urinary tract infection were studied. 26 of the patients demonstrated abnormal renal parenchymal findings with Gallium-67 Citrate or Tc-99m Glucoheptonate scintigraphy. Intravenous urography was notably ineffective with only 5 of the 20 interpreted as abnormal due to parenchymal disease or decreased function. 11 were entirely normal while only 5 demonstrated scars or hydronephrosis. Only 10 of 17 patients demonstrated intranvesicoureteral reflux on x-ray or nuclear cystography. Ultrasound depicted 6 of 20 patients as having parenchymal abnormalities. Seven were normal. Nonspecific findings such as dilitation of the renal pelvis or renal enlargement was noted in 11 of the 20 patients. Radionuclide Scintigraphy is the most efficacious modality to detect since acute bacterial nephritis.

  11. Antibiogram of bacterial species isolated from canine pyometra

    OpenAIRE

    Madhu Swamy; Varun Bassessar; Yamini Verma

    2013-01-01

    Aim: The aim of the present work was to ascertain the bacterial flora causing pyometra in female dogs and their antibiotic sensitivity. Materials and Methods: A study was conducted to determine the antibiogram of bacterial species isolated from 20 female dogs diagnosed with pyometra. The vaginal discharge was collected by sterile swab and streaked smoothly over Mueller Hinton medium and sensitivity towards antibiotics was determined by measuring the zone of inhibition using a Hi-media scale. ...

  12. Understanding physics

    CERN Document Server

    Cassidy, David; Rutherford, James

    2002-01-01

    Understanding Physics provides a thorough grounding in contemporary physics while placing physics into its social and historical context Based in large part on the highly respected Project Physics Course developed by two of the authors, it also integrates the results of recent pedagogical research The text thus - teaches about the basic phenomena in the physical world and the concepts developed to explain them - shows that science is a rational human endeavor with a long and continuing tradition, involving many different cultures and people - develops facility in critical thinking, reasoned argumentation, evaluation of evidence, mathematical modeling, and ethical values The treatment emphasizes not only what we know but also how we know it, why we believe it, and what effects that knowledge has - Why do we believe the Earth and planets revolve around the Sun? - Why do we believe that matter is made of atoms? - How do relativity theory and quantum mechanics alter our conception of Nature and in what ways do th...

  13. Bacterial Metabolism Shapes the Host-Pathogen Interface.

    Science.gov (United States)

    Passalacqua, Karla D; Charbonneau, Marie-Eve; O'Riordan, Mary X D

    2016-06-01

    Bacterial pathogens have evolved to exploit humans as a rich source of nutrients to support survival and replication. The pathways of bacterial metabolism that permit successful colonization are surprisingly varied and highlight remarkable metabolic flexibility. The constraints and immune pressures of distinct niches within the human body set the stage for understanding the mechanisms by which bacteria acquire critical nutrients. In this article we discuss how different bacterial pathogens carry out carbon and energy metabolism in the host and how they obtain or use key nutrients for replication and immune evasion.

  14. Bacterial metabolism shapes the host:pathogen interface

    Science.gov (United States)

    Passalacqua, Karla D.; Charbonneau, Marie-Eve; O'Riordan, Mary X.D.

    2016-01-01

    Summary Bacterial pathogens have evolved to exploit humans as a rich source of nutrients to support survival and replication. The pathways of bacterial metabolism that permit successful colonization are surprisingly varied and highlight remarkable metabolic flexibility. The constraints and immune pressures of distinct niches within the human body set the stage for understanding the mechanisms by which bacteria acquire critical nutrients. Here we discuss how different bacterial pathogens carry out carbon and energy metabolism in the host, and how they obtain or use key nutrients for replication and immune evasion. PMID:27337445

  15. [The composition of the gastrointestinal bacterial flora of mouse embryos and the placenta tissue bacterial flora].

    Science.gov (United States)

    Lei, D; Lin, Y; Jiang, X; Lan, L; Zhang, W; Wang, B X

    2017-03-02

    Objective: To explore the composition of the gastrointestinal bacterial flora of mouse embryos and the placenta tissue bacterial flora. Method: Twenty-four specimens were collected from pregnant Kunming mouse including 8 mice of early embryonic (12-13 days) gastrointestinal tissues, 8 cases of late embryonic (19-20 days)gastrointestinal tissues, 8 of late pregnancy placental tissues.The 24 samples were extracted by DNeasy Blood & Tissue kit for high-throughput DNA sequencing. Result: The level of Proteobacteria, Bacteroidetes, Actino-bacteria and Firmicutes were predominantin all specimens.The relative content of predominant bacterial phyla in each group: Proteobacteria (95.00%, 88.14%, 87.26%), Bacteroidetes(1.71%, 2.15%, 2.63%), Actino-Bacteria(1.16%, 4.10%, 3.38%), Firmicutes(0.75%, 2.62%, 2.01%). At the level of family, there were nine predominant bacterial families in which Enterobacteriaeae , Shewanel laceae and Moraxellaceae were dominant.The relative content of dominant bacterial family in eachgroup: Enterobacteriaeae (46.99%, 44.34%, 41.08%), Shewanellaceae (21.99%, 21.10%, 19.05%), Moraxellaceae (9.18%, 7.09%, 5.64%). From the species of flora, the flora from fetal gastrointestinal in early pregnancy and late pregnancy (65.44% and 62.73%) were the same as that from placenta tissue in the late pregnancy.From the abundance of bacteria, at the level of family, the same content of bacteria in three groups accounted for 78.16%, 72.53% and 65.78% respectively. Conclusion: It was proved that the gastrointestinal bacterial flora of mouse embryos and the placenta tissue bacterial flora were colonized. At the same time the bacteria are classified.

  16. How fast is a collective bacterial state established?

    Directory of Open Access Journals (Sweden)

    Mikkel Lindstrøm Sørensen

    Full Text Available Bacteria in a biofilm colony have the capacity to monitor the size and growth conditions for the colony and modify their phenotypical behaviour to optimise attacks, defence, migration, etc. The quorum sensing systems controlling this involve production and sensing of diffusive signal molecules. Frequently, quorum sensing systems carry a positive feedback loop which produces a switch at a threshold size of the colony. This all-or-none switch can be beneficial to create a sudden attack, leaving a host little time to establish a defence. The reaction-diffusion system describing a basal quorum sensing loop involves production of signal molecules, diffusion of signal molecules, and detection of signal molecules. We study the ignition process in a numerical solution for a basal quorum sensor and demonstrate that even in a large colony the ignition travels through the whole colony in a less than a minute. The ignition of the positive feedback loop was examined in different approximations. As expected, in the exact calculation the ignition was found to be delayed compared to a calculation where the binding of signal molecules was quasistatic. The buffering of signal molecules is found to have little effect on the ignition process. Contrary to expectation, we find that the ignition does not start when the threshold is reached at the center-instead it allows for the threshold to be approached in the whole colony followed by an almost simultaneous ignition of the whole biofilm aggregate.

  17. How fast is a collective bacterial state established?

    DEFF Research Database (Denmark)

    Sørensen, Mikkel Lindstrøm; Dahl, Peter; Sams, Thomas

    2017-01-01

    loop involves production of signal molecules, diffusion of signal molecules, and detection of signal molecules. We study the ignition process in a numerical solution for a basal quorum sensor and demonstrate that even in a large colony the ignition travels through the whole colony in a less than......Bacteria in a biofilm colony have the capacity to monitor the size and growth conditions for the colony and modify their phenotypical behaviour to optimise attacks, defence, migration, etc. The quorum sensing systems controlling this involve production and sensing of diffusive signal molecules....... Frequently, quorum sensing systems carry a positive feedback loop which produces a switch at a threshold size of the colony. This all-or-none switch can be beneficial to create a sudden attack, leaving a host little time to establish a defence. The reaction-diffusion system describing a basal quorum sensing...

  18. Image Understanding Research

    Science.gov (United States)

    1980-03-31

    Numerlues en Sciences Physiques et Economiques , Collection Methode Mathematiques de l’Informatique, Dunod, 1976. 47 26. P. Saint-Pierre, "Etude Theorique et...overlap since adjacent linear features are being presented. References 1. S. Rubin, "The ARGOS Image Understanding System," Ph.D. thesis, Computer Science ...Techniques," TR 480, Computer Science Center, University of Maryland, September i979. 5. Davis, Larry S. and Azriel Rosenfeld, "Hierarchical Relaxation for

  19. Effect of copper tolerant Elsholtzia splendens on bacterial community associated with Commelina communis on a copper mine spoil.

    Science.gov (United States)

    Yang, Ruyi; Guo, Fuyu; Li, Jing; Su, Nannan; Shao, Zongyuan; Zan, Shuting

    2016-08-01

    Facilitation, or positive plant-plant interaction, has received increasing concern from ecologists over the last two decades. Facilitation may occur through direct mitigation of severe environments or indirect mediation by a third participant from the same or different trophic levels. The copper (Cu) tolerant species Elsholtzia splendens facilitates the establishment and growth of co-occurring Commelina communis through indirect enrichment of microbial activity. However, whether and how E. splendens impacts the microbial community that is associated with C. communis is less known. We characterized the soil bacterial community in the rhizosphere of C. communis in the absence and presence of E. splendens using PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) and sequencing. The result showed that the richness of the bacterial community increased, but diversity and evenness remained similar, in the presence of E. splendens. Chloroflexi, Acidobacteria and Proteobacteria were the most dominant bacteria. The relative abundance of dominant and minor bacterial groups showed distinctly different responses to E. splendens. Principal component analysis and redundancy analysis indicated that variation of the bacterial community was determined by multiple factors and might be driven by the tested soil parameters collectively, or alternatively changed through plant root exudates or other microorganisms. Our results enhance the understanding of how the bacterial community associated with a beneficiary plant responds to a benefactor plant and suggests that the changes of bacterial community composition may have far-reaching influence on plant-soil feedback and the aboveground plant community in the long run. Copyright © 2016. Published by Elsevier B.V.

  20. Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function

    Directory of Open Access Journals (Sweden)

    Baneshwar Singh

    2018-01-01

    Full Text Available As vertebrate carrion decomposes, there is a release of nutrient-rich fluids into the underlying soil, which can impact associated biological community structure and function. How these changes alter soil biogeochemical cycles is relatively unknown and may prove useful in the identification of carrion decomposition islands that have long lasting, focal ecological effects. This study investigated the spatial (0, 1, and 5 m and temporal (3–732 days dynamics of human cadaver decomposition on soil bacterial and arthropod community structure and microbial function. We observed strong evidence of a predictable response to cadaver decomposition that varies over space for soil bacterial and arthropod community structure, carbon (C mineralization and microbial substrate utilization patterns. In the presence of a cadaver (i.e., 0 m samples, the relative abundance of Bacteroidetes and Firmicutes was greater, while the relative abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Verrucomicrobia was lower when compared to samples at 1 and 5 m. Micro-arthropods were more abundant (15 to 17-fold in soils collected at 0 m compared to either 1 or 5 m, but overall, micro-arthropod community composition was unrelated to either bacterial community composition or function. Bacterial community structure and microbial function also exhibited temporal relationships, whereas arthropod community structure did not. Cumulative precipitation was more effective in predicting temporal variations in bacterial abundance and microbial activity than accumulated degree days. In the presence of the cadaver (i.e., 0 m samples, the relative abundance of Actinobacteria increased significantly with cumulative precipitation. Furthermore, soil bacterial communities and C mineralization were sensitive to the introduction of human cadavers as they diverged from baseline levels and did not recover completely in approximately 2 years. These data are valuable for understanding

  1. Potential Environmental Factors Affecting Oil-Degrading Bacterial Populations in Deep and Surface Waters of the Northern Gulf of Mexico.

    Science.gov (United States)

    Liu, Jiqing; Bacosa, Hernando P; Liu, Zhanfei

    2016-01-01

    Understanding bacterial community dynamics as a result of an oil spill is important for predicting the fate of oil released to the environment and developing bioremediation strategies in the Gulf of Mexico. In this study, we aimed to elucidate the roles of temperature, water chemistry (nutrients), and initial bacterial community in selecting oil degraders through a series of incubation experiments. Surface (2 m) and bottom (1537 m) waters, collected near the Deepwater Horizon site, were amended with 200 ppm light Louisiana sweet crude oil and bacterial inoculums from surface or bottom water, and incubated at 4 or 24°C for 50 days. Bacterial community and residual oil were analyzed by pyrosequencing and gas chromatography-mass spectrometry (GC-MS), respectively. The results showed that temperature played a key role in selecting oil-degrading bacteria. Incubation at 4°C favored the development of Cycloclasticus, Pseudoalteromonas , Sulfitobacter , and Reinekea , while 24°C incubations enhanced Oleibacter, Thalassobius, Phaeobacter, and Roseobacter. Water chemistry and the initial community also had potential roles in the development of hydrocarbon-degrading bacterial communities. Pseudoalteromonas , Oleibacter , and Winogradskyella developed well in the nutrient-enriched bottom water, while Reinekea and Thalassobius were favored by low-nutrient surface water. We revealed that the combination of 4°C, crude oil and bottom inoculum was a key factor for the growth of Cycloclasticus , while the combination of surface inoculum and bottom water chemistry was important for the growth of Pseudoalteromonas . Moreover, regardless of the source of inoculum, bottom water at 24°C was a favorable condition for Oleibacter. Redundancy analysis further showed that temperature and initial community explained 57 and 19% of the variation observed, while oil and water chemistry contributed 14 and 10%, respectively. Overall, this study revealed the relative roles of temperature, water

  2. Radiology of bacterial pneumonia

    Energy Technology Data Exchange (ETDEWEB)

    Vilar, Jose E-mail: vilar_jlu@gva.es; Domingo, Maria Luisa; Soto, Cristina; Cogollos, Jonathan

    2004-08-01

    Bacterial pneumonia is commonly encountered in clinical practice. Radiology plays a prominent role in the evaluation of pneumonia. Chest radiography is the most commonly used imaging tool in pneumonias due to its availability and excellent cost benefit ratio. CT should be used in unresolved cases or when complications of pneumonia are suspected. The main applications of radiology in pneumonia are oriented to detection, characterisation and follow-up, especially regarding complications. The classical classification of pneumonias into lobar and bronchial pneumonia has been abandoned for a more clinical classification. Thus, bacterial pneumonias are typified into three main groups: Community acquired pneumonia (CAD), Aspiration pneumonia and Nosocomial pneumonia (NP).The usual pattern of CAD is that of the previously called lobar pneumonia; an air-space consolidation limited to one lobe or segment. Nevertheless, the radiographic patterns of CAD may be variable and are often related to the causative agent. Aspiration pneumonia generally involves the lower lobes with bilateral multicentric opacities. Nosocomial Pneumonia (NP) occurs in hospitalised patients. The importance of NP is related to its high mortality and, thus, the need to obtain a prompt diagnosis. The role of imaging in NP is limited but decisive. The most valuable information is when the chest radiographs are negative and rule out pneumonia. The radiographic patterns of NP are very variable, most commonly showing diffuse multifocal involvement and pleural effusion. Imaging plays also an important role in the detection and evaluation of complications of bacterial pneumonias. In many of these cases, especially in hospitalised patients, chest CT must be obtained in order to better depict these associate findings.

  3. Radiology of bacterial pneumonia

    International Nuclear Information System (INIS)

    Vilar, Jose; Domingo, Maria Luisa; Soto, Cristina; Cogollos, Jonathan

    2004-01-01

    Bacterial pneumonia is commonly encountered in clinical practice. Radiology plays a prominent role in the evaluation of pneumonia. Chest radiography is the most commonly used imaging tool in pneumonias due to its availability and excellent cost benefit ratio. CT should be used in unresolved cases or when complications of pneumonia are suspected. The main applications of radiology in pneumonia are oriented to detection, characterisation and follow-up, especially regarding complications. The classical classification of pneumonias into lobar and bronchial pneumonia has been abandoned for a more clinical classification. Thus, bacterial pneumonias are typified into three main groups: Community acquired pneumonia (CAD), Aspiration pneumonia and Nosocomial pneumonia (NP).The usual pattern of CAD is that of the previously called lobar pneumonia; an air-space consolidation limited to one lobe or segment. Nevertheless, the radiographic patterns of CAD may be variable and are often related to the causative agent. Aspiration pneumonia generally involves the lower lobes with bilateral multicentric opacities. Nosocomial Pneumonia (NP) occurs in hospitalised patients. The importance of NP is related to its high mortality and, thus, the need to obtain a prompt diagnosis. The role of imaging in NP is limited but decisive. The most valuable information is when the chest radiographs are negative and rule out pneumonia. The radiographic patterns of NP are very variable, most commonly showing diffuse multifocal involvement and pleural effusion. Imaging plays also an important role in the detection and evaluation of complications of bacterial pneumonias. In many of these cases, especially in hospitalised patients, chest CT must be obtained in order to better depict these associate findings

  4. Bacterial Degradation of Pesticides

    DEFF Research Database (Denmark)

    Knudsen, Berith Elkær

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

  5. Bacterial mitotic machineries

    DEFF Research Database (Denmark)

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

    2004-01-01

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

  6. Changes in bacterial meningitis.

    OpenAIRE

    Carter, P E; Barclay, S M; Galloway, W H; Cole, G F

    1990-01-01

    In 1964, one of us (WHG) undertook a retrospective study of bacterial meningitis in childhood in the north east of Scotland during the period 1946-61. We have recently carried out a similar review of cases occurring during 1971-86, to compare the incidence, mortality, and bacteriological patterns. During the earlier period 285 cases occurred, a total incidence of 16.9/100,000 children per year. In the later period 274 children were affected, an annual incidence of 17.8/100,000. The overall mo...

  7. Understanding PISA

    Directory of Open Access Journals (Sweden)

    Stephen DOWNES

    2005-04-01

    Full Text Available Understanding PISA Stephen DOWNESMoncton, CANADA ABSTRACT The headline was dramatic enough to cause a ripple in the reading public. "Students who use computers a lot at school have worse maths and reading performance," noted the BBC news article, citing a 2004 study by Ludger Woessmann and Thomas Fuchs (Fuchs and Woessman, 2004. It was not long before the blogosphere took notice. Taking the theme and running with it, Alice and Bill ask, "Computers Make School Kids Dumber?" They theorize, "If you track the admitted decline of education, you'll probably notice that it follows along with the increase of technology in the classroom." In a similar vein, James Bartholomew asks, "Do you think that the government will turn down the volume of its boasting about how it has spent billions introducing computers in schools (while keeping down the pay of teachers so much that there are shortages? Do you think it will stop sending governors of state schools glossy pamphlets about insisting that computers are used in their schools as much as possible?" In this study, therefore, PISA looks well beyond educational attainment, and also includes school demographics, such as whether it is a public or private school, has large or small classes, or has access or not to technological resources. Finally, it does measure student information-their family background, access to books and computers and parental support as well. The PISA survey departs from previous surveys in disregarding the stated curricula of the schools being measured. Therefore, the conclusion is not surprising, nor even wrong for him to consider independently of any parental or teacher support, considered without reference to the software running on it, considered without reference to student attitudes and interests, does not positively impact an education. Finally, he focus on missing the reporting of results

  8. Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs

    Directory of Open Access Journals (Sweden)

    Giuseppe D’Auria

    2018-01-01

    Full Text Available New biotechnology applications require in-depth preliminary studies of biodiversity. The methods of massive sequencing using metagenomics and bioinformatics tools offer us sufficient and reliable knowledge to understand environmental diversity, to know new microorganisms, and to take advantage of their functional genes. Villa Luz caves, in the southern Mexican state of Tabasco, are fed by at least 26 groundwater inlets, containing 300–500 mg L-1 H2S and <0.1 mg L-1 O2. We extracted environmental DNA for metagenomic analysis of collected samples in five selected Villa Luz caves sites, with pH values from 2.5 to 7. Foreign organisms found in this underground ecosystem can oxidize H2S to H2SO4. These include: biovermiculites, a bacterial association that can grow on the rock walls; snottites, that are whitish, viscous biofilms hanging from the rock walls, and sacks or bags of phlegm, which live within the aquatic environment of the springs. Through the emergency food assistance program (TEFAP pyrosequencing, a total of 20,901 readings of amplification products from hypervariable regions V1 and V3 of 16S rRNA bacterial gene in whole and pure metagenomic DNA samples were generated. Seven bacterial phyla were identified. As a result, Proteobacteria was more frequent than Acidobacteria. Finally, acidophilic Proteobacteria was detected in UJAT5 sample

  9. Bacterial community analysis during fermentation of ten representative kinds of kimchi with barcoded pyrosequencing.

    Science.gov (United States)

    Park, Eun-Jin; Chun, Jongsik; Cha, Chang-Jun; Park, Wan-Soo; Jeon, Che Ok; Bae, Jin-Woo

    2012-05-01

    Kimchi, a food made of fermented vegetables, is densely populated by indigenous microorganisms that originate from the raw ingredients under normal conditions. Most microbiological studies on kimchi have been on the most popular dish, baechu-kimchi (Chinese cabbage kimchi). Therefore, relatively little is known about the various other kinds of kimchi (depending on the region, season, main ingredient, starter culture inoculation and recipe). In this study, we collected 100 samples periodically during the fermentation of ten representative kinds of kimchi (including starter-inoculated kimchi) that were stored in the refrigerator (4 °C) during the 30-35 days fermentation period. The multiplex barcoded pyrosequencing of a hypervariable V1-V3 region of the 16S ribosomal RNA (rRNA) gene tagged with sample-specific barcodes for multiplex identifiers was employed for bacterial community profiling. We found that bacterial communities differed between starter-inoculated and non-inoculated kimchi at the early stages of fermentation, but overall there were no significant differences in the late phases. Also, the diversity and richness of bacterial communities varied depending on the various types of kimchi, and these differences could largely be explained by the major ingredients and the manufacture processes of each types of kimchi. This study provides the comprehensive understanding of the factors influencing the biodiversity of the kimchi ecosystem. Copyright © 2011 Elsevier Ltd. All rights reserved.

  10. Structural correlations in bacterial metabolic networks

    Directory of Open Access Journals (Sweden)

    Lizana Ludvig

    2011-01-01

    Full Text Available Abstract Background Evolution of metabolism occurs through the acquisition and loss of genes whose products acts as enzymes in metabolic reactions, and from a presumably simple primordial metabolism the organisms living today have evolved complex and highly variable metabolisms. We have studied this phenomenon by comparing the metabolic networks of 134 bacterial species with known phylogenetic relationships, and by studying a neutral model of metabolic network evolution. Results We consider the 'union-network' of 134 bacterial metabolisms, and also the union of two smaller subsets of closely related species. Each reaction-node is tagged with the number of organisms it belongs to, which we denote organism degree (OD, a key concept in our study. Network analysis shows that common reactions are found at the centre of the network and that the average OD decreases as we move to the periphery. Nodes of the same OD are also more likely to be connected to each other compared to a random OD relabelling based on their occurrence in the real data. This trend persists up to a distance of around five reactions. A simple growth model of metabolic networks is used to investigate the biochemical constraints put on metabolic-network evolution. Despite this seemingly drastic simplification, a 'union-network' of a collection of unrelated model networks, free of any selective pressure, still exhibit similar structural features as their bacterial counterpart. Conclusions The OD distribution quantifies topological properties of the evolutionary history of bacterial metabolic networks, and lends additional support to the importance of horizontal gene transfer during bacterial metabolic evolution where new reactions are attached at the periphery of the network. The neutral model of metabolic network growth can reproduce the main features of real networks, but we observe that the real networks contain a smaller common core, while they are more similar at the periphery

  11. Structural correlations in bacterial metabolic networks.

    Science.gov (United States)

    Bernhardsson, Sebastian; Gerlee, Philip; Lizana, Ludvig

    2011-01-20

    Evolution of metabolism occurs through the acquisition and loss of genes whose products acts as enzymes in metabolic reactions, and from a presumably simple primordial metabolism the organisms living today have evolved complex and highly variable metabolisms. We have studied this phenomenon by comparing the metabolic networks of 134 bacterial species with known phylogenetic relationships, and by studying a neutral model of metabolic network evolution. We consider the 'union-network' of 134 bacterial metabolisms, and also the union of two smaller subsets of closely related species. Each reaction-node is tagged with the number of organisms it belongs to, which we denote organism degree (OD), a key concept in our study. Network analysis shows that common reactions are found at the centre of the network and that the average OD decreases as we move to the periphery. Nodes of the same OD are also more likely to be connected to each other compared to a random OD relabelling based on their occurrence in the real data. This trend persists up to a distance of around five reactions. A simple growth model of metabolic networks is used to investigate the biochemical constraints put on metabolic-network evolution. Despite this seemingly drastic simplification, a 'union-network' of a collection of unrelated model networks, free of any selective pressure, still exhibit similar structural features as their bacterial counterpart. The OD distribution quantifies topological properties of the evolutionary history of bacterial metabolic networks, and lends additional support to the importance of horizontal gene transfer during bacterial metabolic evolution where new reactions are attached at the periphery of the network. The neutral model of metabolic network growth can reproduce the main features of real networks, but we observe that the real networks contain a smaller common core, while they are more similar at the periphery of the network. This suggests that natural selection and

  12. Corticosteroids for acute bacterial meningitis.

    Science.gov (United States)

    Brouwer, Matthijs C; McIntyre, Peter; Prasad, Kameshwar; van de Beek, Diederik

    2015-09-12

    In experimental studies, the outcome of bacterial meningitis has been related to the severity of inflammation in the subarachnoid space. Corticosteroids reduce this inflammatory response. To examine the effect of adjuvant corticosteroid therapy versus placebo on mortality, hearing loss and neurological sequelae in people of all ages with acute bacterial meningitis. We searched CENTRAL (2015, Issue 1), MEDLINE (1966 to January week 4, 2015), EMBASE (1974 to February 2015), Web of Science (2010 to February 2015), CINAHL (2010 to February 2015) and LILACS (2010 to February 2015). Randomised controlled trials (RCTs) of corticosteroids for acute bacterial meningitis. We scored RCTs for methodological quality. We collected outcomes and adverse effects. We performed subgroup analyses for children and adults, causative organisms, low-income versus high-income countries, time of steroid administration and study quality. We included 25 studies involving 4121 participants (2511 children and 1517 adults; 93 mixed population). Four studies were of high quality with no risk of bias, 14 of medium quality and seven of low quality, indicating a moderate risk of bias for the total analysis. Nine studies were performed in low-income countries and 16 in high-income countries.Corticosteroids were associated with a non-significant reduction in mortality (17.8% versus 19.9%; risk ratio (RR) 0.90, 95% confidence interval (CI) 0.80 to 1.01, P value = 0.07). A similar non-significant reduction in mortality was observed in adults receiving corticosteroids (RR 0.74, 95% CI 0.53 to 1.05, P value = 0.09). Corticosteroids were associated with lower rates of severe hearing loss (RR 0.67, 95% CI 0.51 to 0.88), any hearing loss (RR 0.74, 95% CI 0.63 to 0.87) and neurological sequelae (RR 0.83, 95% CI 0.69 to 1.00).Subgroup analyses for causative organisms showed that corticosteroids reduced mortality in Streptococcus pneumoniae (S. pneumoniae) meningitis (RR 0.84, 95% CI 0.72 to 0.98), but not in

  13. Dynamics of bacterial communities in two unpolluted soils after spiking with phenanthrene: soil type specific and common responders

    Directory of Open Access Journals (Sweden)

    Guo-Chun eDing

    2012-08-01

    Full Text Available Considering their key role for ecosystem processes, it is important to understand the response of microbial communities in unpolluted soils to pollution with polycyclic aromatic hydrocarbons (PAH. Phenanthrene, a model compound for PAH, was spiked to a Cambisol and a Luvisol soil. Total community DNA from phenanthrene-spiked and control soils collected on days 0, 21 and 63 were analyzed based on PCR-amplified 16S rRNA genefragments. Denaturing gradient gel electrophoresis (DGGE fingerprints of bacterial communities increasingly deviated with time between spiked and control soils. In taxon specific DGGE, significant responses of Alphaproteobacteria and Actinobacteria became only detectable after 63 days, while significant effects on Betaproteobacteria were detectable in both soils after 21 days. Comparison of the taxonomic distribution of bacteria in spiked and control soils on day 63 as revealed by pyrosequencing indicated soil type specific negative effects of phenanthrene on several taxa, many of them belonging to the Gamma-, Beta- or Deltaproteobacteria. Bacterial richness and evenness decreased in spiked soils. Despite the significant differences in the bacterial community structure between both soils on day 0, similar genera increased in relative abundance after PAH spiking, especially Sphingomonas and Polaromonas. However, this did not result in an increased overall similarity of the bacterial communities in both soils.

  14. Drylands soil bacterial community is affected by land use change and different irrigation practices in the Mezquital Valley, Mexico.

    Science.gov (United States)

    Lüneberg, Kathia; Schneider, Dominik; Siebe, Christina; Daniel, Rolf

    2018-01-23

    Dryland agriculture nourishes one third of global population, although crop irrigation is often mandatory. As freshwater sources are scarce, treated and untreated wastewater is increasingly used for irrigation. Here, we investigated how the transformation of semiarid shrubland into rainfed farming or irrigated agriculture with freshwater, dam-stored or untreated wastewater affects the total (DNA-based) and active (RNA-based) soil bacterial community composition, diversity, and functionality. To do this we collected soil samples during the dry and rainy seasons and isolated DNA and RNA. Soil moisture, sodium content and pH were the strongest drivers of the bacterial community composition. We found lineage-specific adaptations to drought and sodium content in specific land use systems. Predicted functionality profiles revealed gene abundances involved in nitrogen, carbon and phosphorous cycles differed among land use systems and season. Freshwater irrigated bacterial community is taxonomically and functionally susceptible to seasonal environmental changes, while wastewater irrigated ones are taxonomically susceptible but functionally resistant to them. Additionally, we identified potentially harmful human and phytopathogens. The analyses of 16 S rRNA genes, its transcripts and deduced functional profiles provided extensive understanding of the short-term and long-term responses of bacterial communities associated to land use, seasonality, and water quality used for irrigation in drylands.

  15. Illumina MiSeq sequencing investigation on the contrasting soil bacterial community structures in different iron mining areas.

    Science.gov (United States)

    Hong, Chen; Si, Yanxiao; Xing, Yi; Li, Yang

    2015-07-01

    Mine activities leaked heavy metals into surrounding soil and may affected indigenous microbial communities. In the present study, the diversity and composition of the bacterial community in soil collected from three regions which have different pollution degree, heavy pollution, moderate pollution, and non-pollution, within the catchment of Chao River in Beijing City, were compared using the Illumina MiSeq sequencing technique. Rarefaction results showed that the polluted area had significant higher bacterial alpha diversity than those from unpolluted area. Principal component analysis (PCA) showed that microbial communities in the polluted areas had significant differences compared with the unpolluted area. Moreover, PCA at phylum level and Matastats results demonstrated that communities in locations shared similar phyla diversity, indicating that the bacterial community changes under metal pollution were not reflected on phyla structure. At genus level, the relative abundance of dominant genera changed in sites with degrees of pollution. Genera Bradyrhizobium, Rhodanobacter, Reyranella, and Rhizomicrobium significantly decreased with increasing pollution degree, and their dominance decreased, whereas several genera (e.g., Steroidobacter, Massilia, Arthrobacter, Flavisolibacter, and Roseiflexus) increased and became new dominant genera in the heavily metal-polluted area. The potential resistant bacteria, found within the genera of Thiobacillus, Pseudomonas, Arthrobacter, Microcoleus, Leptolyngbya, and Rhodobacter, are less than 2.0 % in the indigenous bacterial communities, which play an important role in soil ecosystem. This effort to profile the background diversity may set the first stage for better understanding the mechanism underlying the community structure changes under in situ mild heavy metal pollution.

  16. Bacterial Inclusion Bodies: Discovering Their Better Half.

    Science.gov (United States)

    Rinas, Ursula; Garcia-Fruitós, Elena; Corchero, José Luis; Vázquez, Esther; Seras-Franzoso, Joaquin; Villaverde, Antonio

    2017-09-01

    Bacterial inclusion bodies (IBs) are functional, non-toxic amyloids occurring in recombinant bacteria showing analogies with secretory granules of the mammalian endocrine system. The scientific interest in these mesoscale protein aggregates has been historically masked by their status as a hurdle in recombinant protein production. However, progressive understanding of how the cell handles the quality of recombinant polypeptides and the main features of their intriguing molecular organization has stimulated the interest in inclusion bodies and spurred their use in diverse technological fields. The engineering and tailoring of IBs as functional protein particles for materials science and biomedicine is a good example of how formerly undesired bacterial byproducts can be rediscovered as promising functional materials for a broad spectrum of applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Collection Mapping and Collection Development.

    Science.gov (United States)

    Murray, William; And Others

    1985-01-01

    Describes the use of collection mapping to assess media collections of Aurora, Colorado, Public Schools. Case studies of elementary, middle, and high school media centers describe materials selection and weeding and identify philosophies that library collections should support school curriculum, and teacher-library media specialist cooperation in…

  18. Animal Models of Bacterial Keratitis

    Science.gov (United States)

    Marquart, Mary E.

    2011-01-01

    Bacterial keratitis is a disease of the cornea characterized by pain, redness, inflammation, and opacity. Common causes of this disease are Pseudomonas aeruginosa and Staphylococcus aureus. Animal models of keratitis have been used to elucidate both the bacterial factors and the host inflammatory response involved in the disease. Reviewed herein are animal models of bacterial keratitis and some of the key findings in the last several decades. PMID:21274270

  19. Bacterial selection by mycospheres of Atlantic Rainforest mushrooms.

    Science.gov (United States)

    Halsey, Joshua Andrew; de Cássia Pereira E Silva, Michele; Andreote, Fernando Dini

    2016-10-01

    This study focuses on the selection exerted on bacterial communities in the mycospheres of mushrooms collected in the Brazilian Atlantic Rainforest. A total of 24 paired samples (bulk soil vs. mycosphere) were assessed to investigate potential interactions between fungi and bacteria present in fungal mycospheres. Prevalent fungal families were identified as Marasmiaceae and Lepiotaceae (both Basidiomycota) based on ITS partial sequencing. We used culture-independent techniques to analyze bacterial DNA from soil and mycosphere samples. Bacterial communities in the samples were distinguished based on overall bacterial, alphaproteobacterial, and betaproteobacterial PCR-DGGE patterns, which were different in fungi belonging to different taxa. These results were confirmed by pyrosequencing the V4 region of the 16S rRNA gene (based on five bulk soil vs. mycosphere pairs), which revealed the most responsive bacterial families in the different conditions generated beneath the mushrooms, identified as Bradyrhizobiaceae, Burkholderiaceae, and Pseudomonadaceae. The bacterial families Acetobacteraceae, Chrhoniobacteraceae, Planctomycetaceae, Conexibacteraceae, and Burkholderiaceae were found in all mycosphere samples, composing the core mycosphere microbiome. Similarly, some bacterial groups identified as Koribacteriaceae, Acidobacteria (Solibacteriaceae) and an unclassified group of Acidobacteria were preferentially present in the bulk soil samples (found in all of them). In this study we depict the mycosphere effect exerted by mushrooms inhabiting the Brazilian Atlantic Rainforest, and identify the bacteria with highest response to such a specific niche, possibly indicating the role bacteria play in mushroom development and dissemination within this yet-unexplored environment.

  20. Bacterial Succession on Rat Carcasses and Applications for PMI Estimation.

    Science.gov (United States)

    Zhang, Lin; Guo, Juan-juan; Telet-Siyit; Peng, Yu-long; Xie, Dan; Guo, Ya-dong; Yan, Jie; Zha, Lagabaiyila; Cai, Ji-feng

    2016-02-01

    Abstract: To investigate the bacterial succession on rat carcasses and to evaluate the use of bacterial succession for postmortem interval (PMI) estimation. Adult female SD rat remains were placed in carton boxes. The bacterial colonization of circumocular skin, mouth and vagina was collected to be identified using culture-dependent biochemical methods. The changes in community composition were regularly documented. The bacterial succession in three habitats showed that Staphylococcus and Neisseria were predominated in early PMI, especially Staphylococcus aureus and Neisseria lactamica in 6 hours after death. Lactobacillus casei developed on the 3-4 days regularly, and kept stable at a certain level in late PMI. The involvement of normal and putrefactive bacteria in three body habitats of rat remains can be used for PMI estimation.

  1. Bacterial intermediate filaments

    DEFF Research Database (Denmark)

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

    2009-01-01

    Crescentin, which is the founding member of a rapidly growing family of bacterial cytoskeletal proteins, was previously proposed to resemble eukaryotic intermediate filament (IF) proteins based on structural prediction and in vitro polymerization properties. Here, we demonstrate that crescentin...... also shares in vivo properties of assembly and dynamics with IF proteins by forming stable filamentous structures that continuously incorporate subunits along their length and that grow in a nonpolar fashion. De novo assembly of crescentin is biphasic and involves a cell size-dependent mechanism...... a new function for MreB and providing a parallel to the role of actin in IF assembly and organization in metazoan cells. Additionally, analysis of an MreB localization mutant suggests that cell wall insertion during cell elongation normally occurs along two helices of opposite handedness, each...

  2. Bacterial polyhydroxyalkanoates: Still fabulous?

    Science.gov (United States)

    Możejko-Ciesielska, Justyna; Kiewisz, Robert

    2016-11-01

    Bacterial polyhydroxyalkanoates (PHA) are polyesters accumulated as carbon and energy storage materials under limited growth conditions in the presence of excess carbon sources. They have been developed as biomaterials with unique properties for the past many years being considered as a potential substitute for conventional non-degradable plastics. Due to the increasing concern towards global climate change, depleting petroleum resource and problems with an utilization of a growing number of synthetic plastics, PHAs have gained much more attention from industry and research. These environmentally friendly microbial polymers have great potential in biomedical, agricultural, and industrial applications. However, their production on a large scale is still limited. This paper describes the backgrounds of PHAs and discussed the current state of knowledge on the polyhydroxyalkanoates. Ability of bacteria to convert different carbon sources to PHAs, the opportunities and challenges of their introduction to global market as valuable renewable products have been also discussed. Copyright © 2016 Elsevier GmbH. All rights reserved.

  3. Biosensors of bacterial cells.

    Science.gov (United States)

    Burlage, Robert S; Tillmann, Joshua

    2017-07-01

    Biosensors are devices which utilize both an electrical component (transducer) and a biological component to study an environment. They are typically used to examine biological structures, organisms and processes. The field of biosensors has now become so large and varied that the technology can often seem impenetrable. Yet the principles which underlie the technology are uncomplicated, even if the details of the mechanisms are elusive. In this review we confine our analysis to relatively current advancements in biosensors for the detection of whole bacterial cells. This includes biosensors which rely on an added labeled component and biosensors which do not have a labeled component and instead detect the binding event or bound structure on the transducer. Methods to concentrate the bacteria prior to biosensor analysis are also described. The variety of biosensor types and their actual and potential uses are described. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Bacterial proteases and virulence

    DEFF Research Database (Denmark)

    Frees, Dorte; Brøndsted, Lone; Ingmer, Hanne

    2013-01-01

    with the proteases either encoded within the same polypeptide or on separate subunits. In contrast, substrate recognition by extracellular proteases is less selective and therefore these enzymes are generally expressed as zymogens to prevent premature proteolytic activity that would be detrimental to the cell......Bacterial pathogens rely on proteolysis for variety of purposes during the infection process. In the cytosol, the main proteolytic players are the conserved Clp and Lon proteases that directly contribute to virulence through the timely degradation of virulence regulators and indirectly by providing...... signalling to short-circuit host cell processes. Common to both intra- and extracellular proteases is the tight control of their proteolytic activities. In general, substrate recognition by the intracellular proteases is highly selective which is, in part, attributed to the chaperone activity associated...

  5. Generative collectives

    NARCIS (Netherlands)

    van Osch, W.; Avital, M.; Sabherwal, R.; Sumner, M.

    2010-01-01

    Analyzing generative group activities against the backdrop of an increasingly connected world, this theory development paper introduces the concept of "generative collectives" as a new framework for classifying internet-based collectives and a novel theoretical lens for explaining why some

  6. Jay's Collectibles

    Science.gov (United States)

    Cappel, James J.; Gillman, Jason R., Jr.

    2011-01-01

    There is growing interest in collectibles of many types, as indicated by the popularity of television programs such as the History Channel's "Pawn Stars" and "American Pickers" and the Public Broadcasting Service's "Antiques Road Show." The availability of online auction sites such as eBay has enabled many people to collect items of interest as a…

  7. Data collection

    NARCIS (Netherlands)

    Callaert, J.; Epping, Elisabeth; Federkeil, G.; Jongbloed, Benjamin W.A.; Kaiser, Franciscus; Tijssen, R.; van Vught, F.A.; Ziegele, F.

    2012-01-01

    This chapter describes the data collection instruments used in the development of U-Multirank. The first section is an overview of existing databases – mainly on bibliometrics and patents. The second describes the questionnaires and survey tools used for collecting data from the institutions – at

  8. Bacteriële meningitis

    NARCIS (Netherlands)

    Brouwer, M. C.; van de Beek, D.

    2012-01-01

    Bacterial meningitis is a severe disease which affects 35.000 Europeans each year and has a mortality rate of about 20%. During the past 25 years the epidemiology of bacterial meningitis has changed significantly due to the implementation of vaccination against Haemophilus influenzae, Neisseria

  9. Bacterial meningitis in immunocompromised patients

    NARCIS (Netherlands)

    van Veen, K.E.B.

    2018-01-01

    Bacterial meningitis is an acute infection of the meninges, in The Netherlands most commonly caused by Streptococcus pneumoniae and Neisseria meningitides. Risk factors for acquiring bacterial meningitis include a decreased function of the immune system. The aim of this thesis was to study

  10. Culture collections.

    Science.gov (United States)

    Smith, David

    2012-01-01

    Culture collections no matter their size, form, or institutional objectives play a role in underpinning microbiology, supplying the resources for study, innovation, and discovery. Their basic roles include providing a mechanism for ex situ conservation of organisms; they are repositories for strains subject to publication, taking in safe, confidential, and patent deposits from researchers. They supply strains for use; therefore, the microorganisms provided must be authentic and preserved well, and any associated information must be valid and sufficient to facilitate the confirmation of their identity and to facilitate their use. The organisms must be collected in compliance with international conventions, international and national legislation and distributed to users indicating clearly the terms and conditions under which they are received and can be used. Collections are harmonizing approaches and characterizing strains to meet user needs. No one single collection can carry out this task alone, and therefore, it is important that output and strategy are coordinated to ensure culture collections deliver the basic resources and services microbiological innovation requires. This chapter describes the types of collection and how they can implement quality management systems and operate to deliver their basic functions. The links to information sources given not only provide support for the practitioners within collections but also provide guidance to users on accessing the huge resource available and how they can help ensure microbiology has the resources and a solid platform for future development. Copyright © 2012 Elsevier Inc. All rights reserved.

  11. The Laboratory Diagnosis of Bacterial Vaginosis

    Directory of Open Access Journals (Sweden)

    Deborah Money

    2005-01-01

    Full Text Available Bacterial vaginosis (BV is an extremely common health problem for women. In addition to the troublesome symptoms often associated with a disruption in the balance of vaginal flora, BV is associated with adverse gynecological and pregnancy outcomes. Although not technically a sexually transmitted infection, BV is a sexually associated condition. Diagnostic tests include real-time clinical/microbiological diagnosis, and the current gold standard, the standardized evaluation of morphotypes on Gram stain analysis. The inappropriate use of vaginal culture can be misleading. Future developments into molecular-based diagnostics will be important to further understand this complex endogenous flora disruption.

  12. The enzymes of bacterial census and censorship.

    Science.gov (United States)

    Fast, Walter; Tipton, Peter A

    2012-01-01

    N-Acyl-L-homoserine lactones (AHLs) are a major class of quorum-sensing signals used by Gram-negative bacteria to regulate gene expression in a population-dependent manner, thereby enabling group behavior. Enzymes capable of generating and catabolizing AHL signals are of significant interest for the study of microbial ecology and quorum-sensing pathways, for understanding the systems that bacteria have evolved to interact with small-molecule signals, and for their possible use in therapeutic and industrial applications. The recent structural and functional studies reviewed here provide a detailed insight into the chemistry and enzymology of bacterial communication. Copyright © 2011 Elsevier Ltd. All rights reserved.

  13. The role of metabolism in bacterial persistence

    Directory of Open Access Journals (Sweden)

    Stephanie M. Amato

    2014-03-01

    Full Text Available Bacterial persisters are phenotypic variants with extraordinary tolerances toward antibiotics. Persister survival has been attributed to inhibition of essential cell functions during antibiotic stress, followed by reversal of the process and resumption of growth upon removal of the antibiotic. Metabolism plays a critical role in this process, since it participates in the entry, maintenance, and exit from the persister phenotype. Here, we review the experimental evidence that demonstrates the importance of metabolism to persistence, highlight the successes and potential for targeting metabolism in the search for anti-persister therapies, and discuss the current methods and challenges to understand persister physiology.

  14. Chemoporation using saponins or cholates: an alternative method for transformation of bacterial cells.

    Science.gov (United States)

    Ravnikar, Matjaz; Irman, Andreja; Radić, Natasa; Lunder, Mojca; Strukelj, Borut

    2009-12-01

    A new method for fast transformation of competent bacterial cells has been developed. The transformation is induced with cholic acid analogues or saponins which cause reversible disruption of the bacterial membrane. This method shortens the time of transformation without significant loss of transformation efficiency in comparison to heat shock method and is the first reported chemically-induced transformation. New data about interactions between cholates and biomembranes is revealed that may contribute to better understanding of bacterial transformation.

  15. Bacterial proteases, untapped antimicrobial drug targets.

    Science.gov (United States)

    Culp, Elizabeth; Wright, Gerard D

    2017-04-01

    Bacterial proteases are an extensive collection of enzymes that have vital roles in cell viability, stress response and pathogenicity. Although their perturbation clearly offers the potential for antimicrobial drug development, both as traditional antibiotics and anti-virulence drugs, they are not yet the target of any clinically used therapeutics. Here we describe the potential for and recent progress in the development of compounds targeting bacterial proteases with a focus on AAA+ family proteolytic complexes and signal peptidases (SPs). Caseinolytic protease (ClpP) belongs to the AAA+ family of proteases, a group of multimeric barrel-shaped complexes whose activity is tightly regulated by associated AAA+ ATPases. The opportunity for chemical perturbation of these complexes is demonstrated by compounds targeting ClpP for inhibition, activation or perturbation of its associated ATPase. Meanwhile, SPs are also a proven antibiotic target. Responsible for the cleavage of targeting peptides during protein secretion, both type I and type II SPs have been successfully targeted by chemical inhibitors. As the threat of pan-antibiotic resistance continues to grow, these and other bacterial proteases offer an arsenal of novel antibiotic targets ripe for development.

  16. Bacterial - Fungal Interactions: ecology, mechanisms and challenges.

    Science.gov (United States)

    Deveau, A; Bonito, G; Uehling, J; Paoletti, M; Becker, M; Bindschedler, S; Hacquard, S; Hervé, V; Labbé, J; Lastovetsky, O A; Mieszkin, S; Millet, L J; Vajna, B; Junier, P; Bonfante, P; Krom, B P; Olsson, S; Elsas, J D van; Wick, L Y

    2018-02-19

    Fungi and bacteria are found living together in a wide variety of environments. Their interactions are significant drivers of many ecosystem functions and are important for the health of plants and animals. A large number of fungal and bacterial families are engaged in complex interactions that lead to critical behavioural shifts of the microorganisms ranging from mutualism to pathogenicity. The importance of bacterial-fungal interactions (BFI) in environmental science, medicine and biotechnology has led to the emergence of a dynamic and multidisciplinary research field that combines highly diverse approaches including molecular biology, genomics, geochemistry, chemical and microbial ecology, biophysics and ecological modelling. In this review, we discuss most recent advances that underscore the roles of BFI across relevant habitats and ecosystems. A particular focus is placed on the understanding of BFI within complex microbial communities and in regards of the metaorganism concept. We also discuss recent discoveries that clarify the (molecular) mechanisms involved in bacterial-fungal relationships, and the contribution of new technologies to decipher generic principles of BFI in terms of physical associations and molecular dialogues. Finally, we discuss future directions for researches in order to catalyse a synergy within the BFI research area and to resolve outstanding questions.

  17. Bacterial ferrous iron transport: the Feo system.

    Science.gov (United States)

    Lau, Cheryl K Y; Krewulak, Karla D; Vogel, Hans J

    2016-03-01

    To maintain iron homeostasis within the cell, bacteria have evolved various types of iron acquisition systems. Ferric iron (Fe(3+)) is the dominant species in an oxygenated environment, while ferrous iron (Fe(2+)) is more abundant under anaerobic conditions or at low pH. For organisms that must combat oxygen limitation for their everyday survival, pathways for the uptake of ferrous iron are essential. Several bacterial ferrous iron transport systems have been described; however, only the Feo system appears to be widely distributed and is exclusively dedicated to the transport of iron. In recent years, many studies have explored the role of the FeoB and FeoA proteins in ferrous iron transport and their contribution toward bacterial virulence. The three-dimensional structures for the Feo proteins have recently been determined and provide insight into the molecular details of the transport system. A highly select group of bacteria also express the FeoC protein from the same operon. This review will provide a comprehensive look at the structural and functional aspects of the Feo system. In addition, bioinformatics analyses of the feo operon and the Feo proteins have been performed to complement our understanding of this ubiquitous bacterial uptake system, providing a new outlook for future studies. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  18. Autonomously responsive pumping by a bacterial flagellar forest: A mean-field approach

    Science.gov (United States)

    Martindale, James D.; Fu, Henry C.

    2017-09-01

    This study is motivated by a microfluidic device that imparts a magnetic torque on an array of bacterial flagella. Bacterial flagella can transform their helical geometry autonomously in response to properties of the background fluid, which provides an intriguing mechanism allowing their use as an engineered element for the regulation or transport of chemicals in microscale applications. The synchronization of flagellar phase has been widely studied in biological contexts, but here we examine the synchronization of flagellar tilt, which is necessary for effective pumping. We first examine the effects of helical geometry and tilt on the pumping flows generated by a single rotating flagellum. Next, we explore a mean-field model for an array of helical flagella to understand how collective tilt arises and influences pumping. The mean-field methodology allows us to take into account possible phase differences through a time-averaging procedure and to model an infinite array of flagella. We find array separation distances, magnetic field strengths, and rotation frequencies that produce nontrivial self-consistent pumping solutions. For individual flagella, pumping is reversed when helicity or rotation is reversed; in contrast, when collective effects are included, self-consistent tilted pumping solutions become untilted nonpumping solutions when helicity or rotation is reversed.

  19. Distinct Bacterial Communities Associated with the Coral Model Aiptasia in Aposymbiotic and Symbiotic States with Symbiodinium

    KAUST Repository

    Röthig, Till

    2016-11-18

    Coral reefs are in decline. The basic functional unit of coral reefs is the coral metaorganism or holobiont consisting of the cnidarian host animal, symbiotic algae of the genus Symbiodinium, and a specific consortium of bacteria (among others), but research is slow due to the difficulty of working with corals. Aiptasia has proven to be a tractable model system to elucidate the intricacies of cnidarian-dinoflagellate symbioses, but characterization of the associated bacterial microbiome is required to provide a complete and integrated understanding of holobiont function. In this work, we characterize and analyze the microbiome of aposymbiotic and symbiotic Aiptasia and show that bacterial associates are distinct in both conditions. We further show that key microbial associates can be cultured without their cnidarian host. Our results suggest that bacteria play an important role in the symbiosis of Aiptasia with Symbiodinium, a finding that underlines the power of the Aiptasia model system where cnidarian hosts can be analyzed in aposymbiotic and symbiotic states. The characterization of the native microbiome and the ability to retrieve culturable isolates contributes to the resources available for the Aiptasia model system. This provides an opportunity to comparatively analyze cnidarian metaorganisms as collective functional holobionts and as separated member species. We hope that this will accelerate research into understanding the intricacies of coral biology, which is urgently needed to develop strategies to mitigate the effects of environmental change.

  20. Understanding Ebola Virus Transmission

    Directory of Open Access Journals (Sweden)

    Seth Judson

    2015-02-01

    Full Text Available An unprecedented number of Ebola virus infections among healthcare workers and patients have raised questions about our understanding of Ebola virus transmission. Here, we explore different routes of Ebola virus transmission between people, summarizing the known epidemiological and experimental data. From this data, we expose important gaps in Ebola virus research pertinent to outbreak situations. We further propose experiments and methods of data collection that will enable scientists to fill these voids in our knowledge about the transmission of Ebola virus.

  1. Elucidating Duramycin’s Bacterial Selectivity and Mode of Action on the Bacterial Cell Envelope

    Directory of Open Access Journals (Sweden)

    Sahar Hasim

    2018-02-01

    Full Text Available The use of naturally occurring antimicrobial peptides provides a promising route to selectively target pathogenic agents and to shape microbiome structure. Lantibiotics, such as duramycin, are one class of bacterially produced peptidic natural products that can selectively inhibit the growth of other bacteria. However, despite longstanding characterization efforts, the microbial selectivity and mode of action of duramycin are still obscure. We describe here a suite of biological, chemical, and physical characterizations that shed new light on the selective and mechanistic aspects of duramycin activity. Bacterial screening assays have been performed using duramycin and Populus-derived bacterial isolates to determine species selectivity. Lipidomic profiles of selected resistant and sensitive strains show that the sensitivity of Gram-positive bacteria depends on the presence of phosphatidylethanolamine (PE in the cell membrane. Further the surface and interface morphology were studied by high resolution atomic force microscopy and showed a progression of cellular changes in the cell envelope after treatment with duramycin for the susceptible bacterial strains. Together, these molecular and cellular level analyses provide insight into duramycin’s mode of action and a better understanding of its selectivity.

  2. Growth of bacterial phytopathogens in animal manures.

    Science.gov (United States)

    Sledz, Wojciech; Zoledowska, Sabina; Motyka, Agata; Kadziński, Leszek; Banecki, Bogdan

    2017-01-01

    Animal manures are routinely applied to agricultural lands to improve crop yield, but the possibility to spread bacterial phytopathogens through field fertilization has not been considered yet. We monitored 49 cattle, horse, swine, sheep or chicken manure samples collected in 14 Polish voivodeships for the most important plant pathogenic bacteria - Ralstonia solanacearum (Rsol), Xanthomonas campestris pv. campestris (Xcc), Pectobacterium carotovorum subsp. carotovorum (Pcc), Pectobacterium atrosepticum (Pba), Erwinia amylovora (Eam), Clavibacter michiganensis subsp. sepedonicus (Cms) and Dickeya sp. (Dsp). All of the tested animal fertilizers were free of these pathogens. Subsequently, the growth dynamics of Pba, Pcc, Rsol, and Xcc in cattle, horse, swine, sheep and chicken manures sterilized either by autoclaving or filtration was evaluated. The investigated phytopathogens did not exhibit any growth in the poultry manure. However, the manure filtrates originating from other animals were suitable for microbial growth, which resulted in the optical density change of 0.03-0.22 reached within 26 h (48 h Rsol, 120 h Xcc), depending on bacterial species and the manure source. Pcc and Pba multiplied most efficiently in the cattle manure filtrate. These bacteria grew faster than Rsol and Xcc in all the tested manure samples, both the filtrates and the autoclaved semi-solid ones. Though the growth dynamics of investigated strains in different animal fertilizers was unequal, all of the tested bacterial plant pathogens were proven to use cattle, horse, swine and sheep manures as the sources of nutrients. These findings may contribute to further research on the alternative routes of spread of bacterial phytopathogens, especially because of the fact that the control of pectionolytic bacteria is only based on preventive methods.

  3. Assessment of bacterial diversity in the cattle tick Rhipicephalus (Boophilus microplus through tag-encoded pyrosequencing

    Directory of Open Access Journals (Sweden)

    Bendele Kylie G

    2011-01-01

    Full Text Available Abstract Background Ticks are regarded as the most relevant vectors of disease-causing pathogens in domestic and wild animals. The cattle tick, Rhipicephalus (Boophilus microplus, hinders livestock production in tropical and subtropical parts of the world where it is endemic. Tick microbiomes remain largely unexplored. The objective of this study was to explore the R. microplus microbiome by applying the bacterial 16S tag-encoded FLX-titanium amplicon pyrosequencing (bTEFAP technique to characterize its bacterial diversity. Pyrosequencing was performed on adult males and females, eggs, and gut and ovary tissues from adult females derived from samples of R. microplus collected during outbreaks in southern Texas. Results Raw data from bTEFAP were screened and trimmed based upon quality scores and binned into individual sample collections. Bacteria identified to the species level include Staphylococcus aureus, Staphylococcus chromogenes, Streptococcus dysgalactiae, Staphylococcus sciuri, Serratia marcescens, Corynebacterium glutamicum, and Finegoldia magna. One hundred twenty-one bacterial genera were detected in all the life stages and tissues sampled. The total number of genera identified by tick sample comprised: 53 in adult males, 61 in adult females, 11 in gut tissue, 7 in ovarian tissue, and 54 in the eggs. Notable genera detected in the cattle tick include Wolbachia, Coxiella, and Borrelia. The molecular approach applied in this study allowed us to assess the relative abundance of the microbiota associated with R. microplus. Conclusions This report represents the first survey of the bacteriome in the cattle tick using non-culture based molecular approaches. Comparisons of our results with previous bacterial surveys provide an indication of geographic variation in the assemblages of bacteria associated with R. microplus. Additional reports on the identification of new bacterial species maintained in nature by R. microplus that may be

  4. Assessment of bacterial diversity in the cattle tick Rhipicephalus (Boophilus) microplus through tag-encoded pyrosequencing

    Science.gov (United States)

    2011-01-01

    Background Ticks are regarded as the most relevant vectors of disease-causing pathogens in domestic and wild animals. The cattle tick, Rhipicephalus (Boophilus) microplus, hinders livestock production in tropical and subtropical parts of the world where it is endemic. Tick microbiomes remain largely unexplored. The objective of this study was to explore the R. microplus microbiome by applying the bacterial 16S tag-encoded FLX-titanium amplicon pyrosequencing (bTEFAP) technique to characterize its bacterial diversity. Pyrosequencing was performed on adult males and females, eggs, and gut and ovary tissues from adult females derived from samples of R. microplus collected during outbreaks in southern Texas. Results Raw data from bTEFAP were screened and trimmed based upon quality scores and binned into individual sample collections. Bacteria identified to the species level include Staphylococcus aureus, Staphylococcus chromogenes, Streptococcus dysgalactiae, Staphylococcus sciuri, Serratia marcescens, Corynebacterium glutamicum, and Finegoldia magna. One hundred twenty-one bacterial genera were detected in all the life stages and tissues sampled. The total number of genera identified by tick sample comprised: 53 in adult males, 61 in adult females, 11 in gut tissue, 7 in ovarian tissue, and 54 in the eggs. Notable genera detected in the cattle tick include Wolbachia, Coxiella, and Borrelia. The molecular approach applied in this study allowed us to assess the relative abundance of the microbiota associated with R. microplus. Conclusions This report represents the first survey of the bacteriome in the cattle tick using non-culture based molecular approaches. Comparisons of our results with previous bacterial surveys provide an indication of geographic variation in the assemblages of bacteria associated with R. microplus. Additional reports on the identification of new bacterial species maintained in nature by R. microplus that may be pathogenic to its vertebrate hosts

  5. Zoonotic bacterial meningitis in human adults

    NARCIS (Netherlands)

    van Samkar, Anusha; Brouwer, Matthijs C.; van der Ende, Arie; van de Beek, Diederik

    2016-01-01

    To describe the epidemiology, etiology, clinical characteristics, treatment, outcome, and prevention of zoonotic bacterial meningitis in human adults. We identified 16 zoonotic bacteria causing meningitis in adults. Zoonotic bacterial meningitis is uncommon compared to bacterial meningitis caused by

  6. Evolution of Bacterial Suicide

    Science.gov (United States)

    Tchernookov, Martin; Nemenman, Ilya

    2013-03-01

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

  7. Electromagnetism of Bacterial Growth

    Science.gov (United States)

    Ainiwaer, Ailiyasi

    2011-10-01

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

  8. The metabolic footprint of the airway bacterial community in cystic fibrosis.

    Science.gov (United States)

    Narayanamurthy, Vaishnavi; Sweetnam, John M; Denner, Darcy R; Chen, Lena W; Naureckas, Edward T; Laxman, Bharathi; White, Steven R

    2017-06-30

    Progressive, chronic bacterial infection of the airways is a leading cause of death in cystic fibrosis (CF). Culture-independent methods based on sequencing of the bacterial 16S rRNA gene describe a distinct microbial community that decreases in richness and diversity with disease progression. Understanding the functional characteristics of the microbial community may aid in identifying potential therapies and may assist in management, but current methods are cumbersome. Here, we demonstrate the use of an oxidative metabolic assay as a complement to sequencing methods to describe the microbiome in the airways of patients with CF. Expectorated sputum was collected from 16 CF subjects and 8 control subjects. The Biolog Gen III Microplate was used in a community-level physiological profiling (CLPP)-based assay to examine oxidative metabolic activity. 16S rRNA V4 amplicon sequencing was used to characterize the taxonomy and diversity of the samples. Correlations were then identified among the oxidative activity and taxonomy data. In an additional paired analysis, sputum from seven CF subjects were collected at two separate clinic visits and compared for oxidative activity, taxonomy, and diversity. Significant differences in oxidative metabolic activity, microbial taxonomy, and diversity were found between the CF and control sputum samples. Oxidative activity correlated positively with total genera but not with other measures of diversity or taxonomy, demonstrating that the metabolic assay complements the structural aspects of the microbiome. As expected, Pseudomonas was significantly enriched in CF samples, while Streptococcus and Prevotella were similarly abundant in both CF and control samples. Paired analysis of CF samples at separate clinic visits revealed comparable oxidative activity that correlated with similar stability in taxonomy and diversity. The CLPP assay used in this study complements existing sequencing methods to delineate the oxidative metabolic

  9. Molecular Survey of Bacterial Zoonotic Agents in Bats from the Country of Georgia (Caucasus.

    Directory of Open Access Journals (Sweden)

    Ying Bai

    Full Text Available Bats are important reservoirs for many zoonotic pathogens. However, no surveys of bacterial pathogens in bats have been performed in the Caucasus region. To understand the occurrence and distribution of bacterial infections in these mammals, 218 bats belonging to eight species collected from four regions of Georgia were examined for Bartonella, Brucella, Leptospira, and Yersinia using molecular approaches. Bartonella DNA was detected in 77 (35% bats from all eight species and was distributed in all four regions. The prevalence ranged 6-50% per bat species. The Bartonella DNA represented 25 unique genetic variants that clustered into 21 lineages. Brucella DNA was detected in two Miniopterus schreibersii bats and in two Myotis blythii bats, all of which were from Imereti (west-central region. Leptospira DNA was detected in 25 (13% bats that included four M. schreibersii bats and 21 M. blythii bats collected from two regions. The Leptospira sequences represented five genetic variants with one of them being closely related to the zoonotic pathogen L. interrogans (98.6% genetic identity. No Yersinia DNA was detected in the bats. Mixed infections were observed in several cases. One M. blythii bat and one M. schreibersii bat were co-infected with Bartonella, Brucella, and Leptospira; one M. blythii bat and one M. schreibersii bat were co-infected with Bartonella and Brucella; 15 M. blythii bats and three M. schreibersii bats were co-infected with Bartonella and Leptospira. Our results suggest that bats in Georgia are exposed to multiple bacterial infections. Further studies are needed to evaluate pathogenicity of these agents to bats and their zoonotic potential.

  10. Survey of bacterial pathogens on leaves and seeds of red mangrove ...

    African Journals Online (AJOL)

    Bacterial pathogens of red mangrove (Rhizophora mangle) were investigated. 50 samples each of leaves and seeds (healthy and diseased) were randomly collected and used for the analysis. Mean bacterial counts obtained were: healthy and diseased leaves; 8.26 x 103 and 5.9 l x l03 cfu/ml respectively; healthy seeds ...

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

    Science.gov (United States)

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

  12. Assessment of the bacterial organisms in water from a lead-zinc ...

    African Journals Online (AJOL)

    Twenty-four (24) bulk water samples collected from a lead-zinc mining pit in Ishiagu, Ebonyi State, Nigeria over a period of 2 years were used to assess the bacterial population of the mining pit water. Nine bacterial organisms, which included Bacillus sp., Pseudomonas aeruginosa, Proteus sp., Escherichia coli, ...

  13. Bacterial carbohydrate structure database 3: principles and realization.

    Science.gov (United States)

    Toukach, Philip V

    2011-01-24

    Bacterial carbohydrate structure database (BCSDB) is an open-access project that collects primary publication data on carbohydrate structures originating from bacteria, their biological properties, bibliographic and taxonomic annotations, NMR spectra, etc. Almost complete coverage and outstanding data consistency are achieved. BCSDB version 3 and the principles lying behind it, including glycan description language, are reported.

  14. Acute bacterial meningitis in children admitted to the Queen ...

    African Journals Online (AJOL)

    In order to design appropriate interventioos, we collected clinical and demographic data prospectively on all children aged one day to 14 years admitted with a diagnosis of bacterial meningitis (BM) from April 1st 1996 to March 31st 1997 to the Queen Elizabeth Central Hospital (QECH), Blantyre Malawi. During the study ...

  15. Prevalence of Bacterial Meningitis among Infants in a Tertiary ...

    African Journals Online (AJOL)

    Bacterial meningitis remains a major cause of mortality and long–term neurological sequelae worldwide. Pathogens responsible for the infection vary with time, geographical location and patient age, thus necessitating periodic review. Against this background, this study was conducted. Cerebrospinal fluid was collected ...

  16. Semen bacterial flora of Rhode Island Breeder cocks in Zaria ...

    African Journals Online (AJOL)

    The semen used in this study was collected from 77 Rhode Island Breeder cocks reared in battery cages under intensive management from a private farm in Zaria, Kaduna State, Nigeria using the back massage procedure, 27 of the 77 semen samples (35.1%) contained bacterial isolates. None of the samples grew fungi.

  17. Evaluation of enset clones against enset bacterial wilt | Welde ...

    African Journals Online (AJOL)

    A large number of enset clones collected from the Sidama, Gurage, Kembata Tembaro and Hadyia zones were assessed for resistance/tolerance to enset bacterial wilt, Xanthomonas campestris pv. musacearum (Xcm) at the Awassa Agricultural Research Center, Awassa in Ethiopia, during the period 1994 to 2000.

  18. Bacterial aetiologic agents associated with upper respiratory tract ...

    African Journals Online (AJOL)

    Objectives: To identify the bacterial agents associated with upper respiratory tract infections in children less than five years old in Jos, Nigeria. Materials and Methods: Throat swabs were collected from a total of 200 children reporting at four (4) hospitals/clinics: Paediatric Units of OLA and Evangel hospitals and Primary ...

  19. A Survey of Collectives

    Science.gov (United States)

    Tumer, Kagan; Wolpert, David

    2004-01-01

    Due to the increasing sophistication and miniaturization of computational components, complex, distributed systems of interacting agents are becoming ubiquitous. Such systems, where each agent aims to optimize its own performance, but where there is a well-defined set of system-level performance criteria, are called collectives. The fundamental problem in analyzing/designing such systems is in determining how the combined actions of self-interested agents leads to 'coordinated' behavior on a iarge scale. Examples of artificial systems which exhibit such behavior include packet routing across a data network, control of an array of communication satellites, coordination of multiple deployables, and dynamic job scheduling across a distributed computer grid. Examples of natural systems include ecosystems, economies, and the organelles within a living cell. No current scientific discipline provides a thorough understanding of the relation between the structure of collectives and how well they meet their overall performance criteria. Although still very young, research on collectives has resulted in successes both in understanding and designing such systems. It is eqected that as it matures and draws upon other disciplines related to collectives, this field will greatly expand the range of computationally addressable tasks. Moreover, in addition to drawing on them, such a fully developed field of collective intelligence may provide insight into already established scientific fields, such as mechanism design, economics, game theory, and population biology. This chapter provides a survey to the emerging science of collectives.

  20. Bacterial growth on macrophyte leachate and fate of bacterial production

    International Nuclear Information System (INIS)

    Findlay, S.; Carlough, L.; Crocker, M.T.; Gill, H.K.; Meyer, J.L.; Smith, P.J.

    1986-01-01

    The role bacteria play in transferring organic carbon to other trophic levels in aquatic ecosystems depends on the efficiency with which they convert dissolved organic [ 14 C]-labelled carbon into bacterial biomass and on the ability of consumers to graze bacteria. The authors have measured the conversion efficiency for bacteria growing on macrophyte-derived dissolved organic carbon and estimated the amount of bacterial production removed by grazing. Bacteria converted this DOC into new tissue with an efficiency of 53%, substantially higher than the apparent conversion efficiency of macrophyte-derived particulate organic carbon or other types of DOC. Two estimates of grazing indicate that the decline in bacterial numbers after the bloom was probably due to grazing by flagellates. These results show the significance of the bacterial link between DOC and other trophic levels

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

    Directory of Open Access Journals (Sweden)

    Yongjin Qiu

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

  2. Bacterial communities in semen from men of infertile couples: metagenomic sequencing reveals relationships of seminal microbiota to semen quality.

    Directory of Open Access Journals (Sweden)

    Shun-Long Weng

    Full Text Available Some previous studies have identified bacteria in semen as being a potential factor in male infertility. However, only few types of bacteria were taken into consideration while using PCR-based or culturing methods. Here we present an analysis approach using next-generation sequencing technology and bioinformatics analysis to investigate the associations between bacterial communities and semen quality. Ninety-six semen samples collected were examined for bacterial communities, measuring seven clinical criteria for semen quality (semen volume, sperm concentration, motility, Kruger's strict morphology, antisperm antibody (IgA, Atypical, and leukocytes. Computer-assisted semen analysis (CASA was also performed. Results showed that the most abundant genera among all samples were Lactobacillus (19.9%, Pseudomonas (9.85%, Prevotella (8.51% and Gardnerella (4.21%. The proportion of Lactobacillus and Gardnerella was significantly higher in the normal samples, while that of Prevotella was significantly higher in the low quality samples. Unsupervised clustering analysis demonstrated that the seminal bacterial communities were clustered into three main groups: Lactobacillus, Pseudomonas, and Prevotella predominant group. Remarkably, most normal samples (80.6% were clustered in Lactobacillus predominant group. The analysis results showed seminal bacteria community types were highly associated with semen health. Lactobacillus might not only be a potential probiotic for semen quality maintenance, but also might be helpful in countering the negative influence of Prevotella and Pseudomonas. In this study, we investigated whole seminal bacterial communities and provided the most comprehensive analysis of the association between bacterial community and semen quality. The study significantly contributes to the current understanding of the etiology of male fertility.

  3. Adjunctive Therapies for Bacterial Keratitis.

    Science.gov (United States)

    Dakhil, Turki Abdulaziz Bin; Stone, Donald U; Gritz, David C

    2017-01-01

    Bacterial keratitis is the most common type among all types of infectious keratitis. Currently, antibiotics are the main-stay of treatment. The objective of this systematic review is to review published clinical studies which discuss the adjunctive treatment of bacterial keratitis to guide clinical decision-making. We reviewed the role of a variety of medications and surgeries which can help in managing bacterial keratitis complications, which include as thinning, perforation, and impaired wound healing. We have included appropriate animal and laboratory studies, case reports and case series, and randomized clinical trials regarding each therapy.

  4. Molecular detection of human bacterial pathogens

    National Research Council Canada - National Science Library

    Liu, Dongyou

    2011-01-01

    .... Molecular Detection of Human Bacterial Pathogens addresses this issue, with international scientists in respective bacterial pathogen research and diagnosis providing expert summaries on current...

  5. Evaluation of different lactic acid bacterial strains for probiotic characteristics

    OpenAIRE

    B. Srinu,; T. Madhava Rao,; P. V. Mallikarjuna Reddy; K. Kondal Reddy

    2013-01-01

    Objective: The objective of the present study was to collect different Lactic acid bacterial strains from culture collection centers and screen their functional probiotic characteristics such as acid tolerance, bile tolerance, antibacterial activity and antibiotic sensitivity for their commercial use. Materials and Methods: Acid and bile tolerence of selected LAB(Lactic acid bacteria) was determined. The antibiotic resistance of Lactobacillus species was assessed using different antibiotic di...

  6. Locals Collection

    Directory of Open Access Journals (Sweden)

    Stephen Hastings-King

    2010-03-01

    Full Text Available A locals collection is a set of parameters that are used to delimit data-mining operations. This piece uses a collection of locals from around Essex Massachusetts to shape and delimit an interrogation of post-reality in contemporary America. It explores the notion of crisis, the possibility of a crisis of empire that may or may not emerge in a media-space that does not allow crisis of empire to be mentioned and relations this maybe-crisis to the various levels of economic dysfunction that have become evident since late 2008. But mostly this piece explores ways in which particular stories about particular people do and do not link/link to these larger-scale narratives. This is the first of a potential series of locals collections that will mine the American post-real.

  7. Hijacking Complement Regulatory Proteins for Bacterial Immune Evasion.

    Science.gov (United States)

    Hovingh, Elise S; van den Broek, Bryan; Jongerius, Ilse

    2016-01-01

    The human complement system plays an important role in the defense against invading pathogens, inflammation and homeostasis. Invading microbes, such as bacteria, directly activate the complement system resulting in the formation of chemoattractants and in effective labeling of the bacteria for phagocytosis. In addition, formation of the membrane attack complex is responsible for direct killing of Gram-negative bacteria. In turn, bacteria have evolved several ways to evade complement activation on their surface in order to be able to colonize and invade the human host. One important mechanism of bacterial escape is attraction of complement regulatory proteins to the microbial surface. These molecules are present in the human body for tight regulation of the complement system to prevent damage to host self-surfaces. Therefore, recruitment of complement regulatory proteins to the bacterial surface results in decreased complement activation on the microbial surface which favors bacterial survival. This review will discuss recent advances in understanding the binding of complement regulatory proteins to the bacterial surface at the molecular level. This includes, new insights that have become available concerning specific conserved motives on complement regulatory proteins that are favorable for microbial binding. Finally, complement evasion molecules are of high importance for vaccine development due to their dominant role in bacterial survival, high immunogenicity and homology as well as their presence on the bacterial surface. Here, the use of complement evasion molecules for vaccine development will be discussed.

  8. Current understanding of multi-species biofilms

    DEFF Research Database (Denmark)

    Yang, Liang; Liu, Yang; Wu, Hong

    2011-01-01

    Direct observation of a wide range of natural microorganisms has revealed the fact that the majority of microbes persist as surface-attached communities surrounded by matrix materials, called biofilms. Biofilms can be formed by a single bacterial strain. However, most natural biofilms are actually...... formed by multiple bacterial species. Conventional methods for bacterial cleaning, such as applications of antibiotics and/or disinfectants are often ineffective for biofilm populations due to their special physiology and physical matrix barrier. It has been estimated that billions of dollars are spent...... every year worldwide to deal with damage to equipment, contaminations of products, energy losses, and infections in human beings resulted from microbial biofilms. Microorganisms compete, cooperate, and communicate with each other in multi-species biofilms. Understanding the mechanisms of multi...

  9. Soil bacterial community responses to global changes

    DEFF Research Database (Denmark)

    Bergmark, Lasse

    -pyrosequencing and qPCR with a range of soil measurements and analyses to provide a better understanding of the drivers in soil microbial communities. The thesis contains a brief introduction where the most important concepts of global change, soil as a habitat, the nitrogen cycle and nitrification are being...... overall importance for ecosystem function in soil is poorly understood. Global change factors may affect the diversity and functioning of soil prokaryotes and thereby ecosystem functioning. To gain a better understanding of the effects of global changes it is of fundamental importance to classify...... the bacterial soil population. The thesis addresses the effects of different global change manipulations on the soil microbial community composition (climate change in Manuscript 1-4 and unconventional urban fertilizers in Manuscript 5-6). A special emphasis was put on combining molecular techniques like 454...

  10. Soil bacterial communities associated with natural and commercial Cyclopia spp.

    Science.gov (United States)

    Postma, Anneke; Slabbert, Etienne; Postma, Ferdinand; Jacobs, Karin

    2016-03-01

    The commercially important plants in the genus Cyclopia spp. are indigenous to the Cape Floristic Region of South Africa and are used to manufacture an herbal tea known as honeybush tea. Growing in the low nutrient fynbos soils, these plants are highly dependent on symbiotic interactions with soil microorganisms for nutrient acquisition. The aim of this study was to investigate the soil bacterial communities associated with two commercially important Cyclopia species, namely C. subternata and C. longifolia. Specific interest was the differences between rhizosphere and bulk soil collected from natural sites and commercially grown plants. Samples were collected on two occasions to include a dry summer and wet winter season. Results showed that the dominant bacterial taxa associated with these plants included Acidobacteria, Actinobacteria, Bacteroidetes and Proteobacteria. Commercial and natural as well as rhizosphere and bulk soil samples were highly similar in bacterial diversity and species richness. Significant differences were detected in bacterial community structures and co-occurrence patterns between the wet and dry seasons. The results of this study improved our knowledge on what effect commercial Cyclopia plantations and seasonal changes can have on soil bacterial communities within the endemic fynbos biome. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. Distribution and ecology of Frankliniella occidentalis (Thysanoptera: Thripidae) bacterial symbionts.

    Science.gov (United States)

    Chanbusarakum, Lisa J; Ullman, Diane E

    2009-08-01

    Bacterial populations in Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae) collected in diverse California environments consisted of two bacterial symbionts: BFo-1 and BFo-2 (B = bacteria, Fo = Frankliniella occidentalis, numbers reflect different types). Dual infections of BFo-1 and BFo-2 were found in 50% of the thrips, 18% had neither bacterium, and 24 and 8% were infected solely with BFo-1 and BFo-2, respectively. No other bacteria consistently infected F. occidentalis. Dual infections occurred more often in male thrips and in thrips of both sexes from southern mountain and valley sites. As average collection year or month minimum temperature decreased, infections of BFo-1, alone or in dual infections, increased significantly. As yearly precipitation increased, infection with BFo-1 alone also increased. F. occidentalis color morphology did not affect bacterial infection. BFo-1 created weak biofilms at 25 and 32 degrees C; BFo-2 made strong biofilms at 25 degrees C and no biofilms at 32 degrees C. When the bacteria were grown in culture together, weak biofilms formed at both temperatures studied, although there was no way to determine what each bacterium contributed to the biofilm. BFo-1 and BFo-2 grew at similar rates at 25 and 30 degrees C. Our data show BFo-1 and BFo-2 occur in natural populations of F. occidentalis and support the hypothesis BFo have a symbiotic relationship with F. occidentalis. Regional differences in bacterial prevalence suggest bacterial infection is associated with environmental conditions, and altitude, temperature, and precipitation may be important factors.

  12. Bacterial sepsis and chemokines.

    Science.gov (United States)

    Kobayashi, Makiko; Tsuda, Yasuhiro; Yoshida, Tsuyoshi; Takeuchi, Dan; Utsunomiya, Tokuichiro; Takahashi, Hitoshi; Suzuki, Fujio

    2006-01-01

    Bacterial sepsis causes a high mortality rate when it occurs in patients with compromised host defenses. Severely burned patients, typical immunocompromised hosts, are extremely susceptible to infections from various pathogens, and a local wound infection frequently escalates into sepsis. In these patients, Staphylococcus aureus, Enterococcus faecalis and Pseudomonas aeruginosa are familiar pathogens that cause opportunistic infections. Also, polymicrobial sepsis frequently occurs in these patients. In this review, therefore, the roles of chemokines in thermally injured patients infected with these 3 pathogens and polymicrobial sepsis will be discussed. These infections in thermally injured patients may be controlled immunologically, because immunocompetent hosts are resistant to infections with these pathogens. Classically activated macrophages (M1Mphi) are major effector cells for host innate immune responses against these infections. However, M1Mphi are not generated in thermally injured patients whose alternatively activated macrophages (M2Mphi) predominate. M2Mphi appear in patients early after severe burn injuries. M2Mphi inhibit M1Mphi generation through the secretion of CCL17 and IL-10. As a modulator of Mphi, two different subsets of neutrophils (PMN-I, PMN-II) are described. PMN-I direct the polarization of resident Mphi into M1Mphi through the production of CCL3. M2Mphi are induced from resident Mphi by CCL2 released from PMN-II. Therefore, as an inhibitor of CCL2, glycyrrhizin protects individuals infected with S. aureus. Sepsis stemming from P. aeruginosa wound infection is also influenced by CCL2 released from immature myeloid cells. A large number of immature myeloid cells appear in association with burn injuries. Host resistance to S. aureus, E. faecalis, P. aeruginosa or polymicrobial infections may be improved in thermally injured patients through the induction of M1Mphi, elimination of CCL2 and/or depletion of M2Mphi induced by CCL2.

  13. Subdural Empyema in Bacterial Meningitis

    Directory of Open Access Journals (Sweden)

    J Gordon Millichap

    2013-01-01

    Full Text Available Researchers at the University of Amsterdam, the Netherlands, evaluated the occurrence, treatment, and outcome of subdural empyema as a complication of community-acquired bacterial meningitis in 28 (2.7% adults.

  14. Brain ventricular dimensions and relationship to outcome in adult patients with bacterial meningitis

    DEFF Research Database (Denmark)

    Sporrborn, Janni L; Knudsen, Gertrud B; Sølling, Mette

    2015-01-01

    BACKGROUND: Experimental studies suggest that changes in brain ventricle size are key events in bacterial meningitis. This study investigated the relationship between ventricle size, clinical condition and risk of poor outcome in patients with bacterial meningitis. METHODS: Adult patients diagnosed...... with bacterial meningitis admitted to two departments of infectious diseases from 2003 through 2010 were identified. Clinical and biochemical data as well as cerebral computed tomographic images were collected. The size of the brain ventricles were presented as a Ventricle to Brain Ratio (VBR). Normal range...... changes in size as a consequence of meningitis. Increased brain ventricle size in the acute phase of bacterial meningitis was associated with increased mortality....

  15. MECHANISMS OF BACTERIAL POLYHOSTALITY

    Directory of Open Access Journals (Sweden)

    Markova Yu.A.

    2007-12-01

    Full Text Available In the review data about factors of pathogenicity of the bacteria, capable to amaze both animals, and a plant are collected. Such properties of microorganisms as adhesion, secretion of some enzymes, mobility, a phenomenon of cooperative sensitivity - play an essential role at defeat of different organisms. They are used for many universal offensive strategy overcoming protection of an organism, irrespective of its evolutionary origin. Studying of these mechanisms, will allow to provide new approaches to monitoring illnesses.

  16. Collective excitations in nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Chomaz, Ph. [Grand Accelerateur National d`Ions Lourds (GANIL), 14 - Caen (France); Collaboration: La Direction des Sciences de la Matiere du CEA (FR); Le Fonds National de la Recherche Scientifique de Belgique (BE)

    1998-12-31

    The properties of the nucleus cannot be reduced to the properties of its constituents: it is a complex system. The fact that many properties of the nucleus are consequences of the existence of mean-field potential is a manifestation of this complexity. In particular, the nucleons can thus self-organize in collective motions such as giant resonances. Therefore the study of this collective motions is a very good tool to understand the properties of the nucleus itself. The purpose of this article is to stress some aspects of these collective vibrations. We have studied how an ensemble of fermions as the nucleus can self-organize in collective vibrations which are behaving like a gas of bosons in weak interaction. Understanding of these phenomena remains one of the important subjects of actuality in the context of quantal systems in strong interaction. In particular, the study of the states with one or two vibration quanta provides a direct information on the structure of nuclei close to their ground states. Moreover, some collective states appear to be very robust against the onset of chaos. This is the case of the hot giant dipole built on top of a hot nucleus which seems to survive up to rather high temperatures. Their sudden disappearance is still a subject of controversy. It may be that the mean-field and the associated collective states are playing a crucial role also in catastrophic processes such as the phase-transitions. Indeed, when the system is diluted the collective vibrations may become unstable and it seems that these unstable modes provide a natural explanation to the self organization of the system in drops. Finally, considering the diversity of the different structures of exotic nuclei one may expect new vibration types. All these studies are showing the diversity of the collective motions of strongly correlated quantum systems such as the nucleus but many open questions remain to be solved. (authors) 304 refs., 53 figs., 5 tabs.

  17. Collective excitations in nuclei

    International Nuclear Information System (INIS)

    Chomaz, Ph.

    1998-01-01

    The properties of the nucleus cannot be reduced to the properties of its constituents: it is a complex system. The fact that many properties of the nucleus are consequences of the existence of mean-field potential is a manifestation of this complexity. In particular, the nucleons can thus self-organize in collective motions such as giant resonances. Therefore the study of this collective motions is a very good tool to understand the properties of the nucleus itself. The purpose of this article is to stress some aspects of these collective vibrations. We have studied how an ensemble of fermions as the nucleus can self-organize in collective vibrations which are behaving like a gas of bosons in weak interaction. Understanding of these phenomena remains one of the important subjects of actuality in the context of quantal systems in strong interaction. In particular, the study of the states with one or two vibration quanta provides a direct information on the structure of nuclei close to their ground states. Moreover, some collective states appear to be very robust against the onset of chaos. This is the case of the hot giant dipole built on top of a hot nucleus which seems to survive up to rather high temperatures. Their sudden disappearance is still a subject of controversy. It may be that the mean-field and the associated collective states are playing a crucial role also in catastrophic processes such as the phase-transitions. Indeed, when the system is diluted the collective vibrations may become unstable and it seems that these unstable modes provide a natural explanation to the self organization of the system in drops. Finally, considering the diversity of the different structures of exotic nuclei one may expect new vibration types. All these studies are showing the diversity of the collective motions of strongly correlated quantum systems such as the nucleus but many open questions remain to be solved. (authors)

  18. Arsenic uptake in bacterial calcite

    Energy Technology Data Exchange (ETDEWEB)

    Catelani, Tiziano; Perito, Brunella; Bellucci, Francesco; Lee, Sang Soo; Fenter, Paul; Newville, Matthew G.; Rimondi, Valentina; Pratesi, Giovanni; Costagliola, Pilario

    2018-02-01

    Bio-mediated processes for arsenic (As) uptake in calcite were investigated by means of X-ray Diffraction (XRD) and Xray Absorption Spectroscopy (XAS) coupled with X-ray Fluorescence measurements. The environmental bacterial strain Bacillus licheniformis BD5, sampled at the Bullicame Hot Springs (Viterbo, Central Italy), was used to synthesize calcite from As-enriched growth media. Both liquid and solid cultures were applied to simulate planktonic and biofilm community environments, respectively. Bacterial calcite samples cultured in liquid media had an As enrichment factor (Kd) 50 times higher than that from solid media. The XRD analysis revealed an elongation of the crystal lattice along the c axis (by 0.03Å) for biogenic calcite, which likely resulted from the substitution of larger arsenate for carbonate in the crystal. The XAS data also showed a clear difference in the oxidation state of sorbed As between bacterial and abiotic calcite. Abiotic chemical processes yielded predominantly As(V) uptake whereas bacterial precipitation processes led to the uptake of both As(III) and As(V). The presence of As(III) in bacterial calcite is proposed to result from subsequent reduction of arsenate to arsenite by bacterial activities. To the best of our knowledge, this is the first experimental observation of the incorporation of As(III) in the calcite crystal lattice, revealing a critical role of biochemical processes for the As cycling in nature.

  19. Arsenic uptake in bacterial calcite

    Science.gov (United States)

    Catelani, Tiziano; Perito, Brunella; Bellucci, Francesco; Lee, Sang Soo; Fenter, Paul; Newville, Matthew; Rimondi, Valentina; Pratesi, Giovanni; Costagliola, Pilario

    2018-02-01

    Bio-mediated processes for arsenic (As) uptake in calcite were investigated by means of X-ray Diffraction (XRD) and X-ray Absorption Spectroscopy (XAS) coupled with X-ray Fluorescence measurements. The environmental bacterial strain Bacillus licheniformis BD5, sampled at the Bullicame Hot Springs (Viterbo, Central Italy), was used to synthesize calcite from As-enriched growth media. Both liquid and solid cultures were applied to simulate planktonic and biofilm community environments, respectively. Bacterial calcite samples cultured in liquid media had an As enrichment factor (Kd) 50 times higher than that from solid media. The XRD analysis revealed an elongation of the crystal lattice along the c axis (by 0.03 Å) for biogenic calcite, which likely resulted from the substitution of larger arsenate for carbonate in the crystal. The XAS data also showed a clear difference in the oxidation state of sorbed As between bacterial and abiotic calcite. Abiotic chemical processes yielded predominantly As(V) uptake whereas bacterial precipitation processes led to the uptake of both As(III) and As(V). The presence of As(III) in bacterial calcite is proposed to result from subsequent reduction of arsenate to arsenite by bacterial activities. To the best of our knowledge, this is the first experimental observation of the incorporation of As(III) in the calcite crystal lattice, revealing a critical role of biochemical processes for the As cycling in nature.

  20. Collective Success or Collective Failure?

    DEFF Research Database (Denmark)

    Fayyaz, Anjum

    , industrial cluster, and corporate social responsibility literatures with the aim of explaining why collective cluster action through industry associations and/or public private partnerships succeed or fail in facilitating cluster-wide compliance with CSR standards. I then use this framework to analyze a case...... study of soccer village project to learn how various attempts at facilitating joint CSR action in the Pakistani football manufacturing have consistently failed in addressing international CSR compliance demands. I conclude that this form of collective failure – along with technological changes, lack...

  1. Recent functional insights into the role of (p)ppGpp in bacterial physiology

    DEFF Research Database (Denmark)

    Hauryliuk, Vasili; Atkinson, Gemma C.; Murakami, Katsuhiko S.

    2015-01-01

    The alarmones guanosine tetraphosphate and guanosine pentaphosphate (collectively referred to as (p)ppGpp) are involved in regulating growth and several different stress responses in bacteria. In recent years, substantial progress has been made in our understanding of the molecular mechanisms of ...... of transcriptional regulation by (p)ppGpp and the role of (p)ppGpp in GTP metabolism and in the emergence of bacterial persisters.......)ppGpp metabolism and (p)ppGpp-mediated regulation. In this Review, we summarize these recent insights, with a focus on the molecular mechanisms governing the activity of the RelA/SpoT homologue (RSH) proteins, which are key players that regulate the cellular levels of (p)ppGpp. We also discuss the structural basis...

  2. Bacterial Communities of Two Parthenogenetic Aphid Species Cocolonizing Two Host Plants across the Hawaiian Islands ▿

    Science.gov (United States)

    Jones, Ryan T.; Bressan, Alberto; Greenwell, April M.; Fierer, Noah

    2011-01-01

    Aphids (Hemiptera: Aphididae) have been the focus of several studies with respect to their interactions with inherited symbionts, but bacterial communities of most aphid species are still poorly characterized. In this research, we used bar-coded pyrosequencing to characterize bacterial communities in aphids. Specifically, we examined the diversity of bacteria in two obligately parthenogenetic aphid species (the melon aphid, Aphis gossypii, and the cardamom aphid, Pentalonia caladii) cocolonizing two plant species (taro, Colocasia esculenta, and ginger, Alpinia purpurata) across four Hawaiian Islands (Hawaii, Kauai, Maui, and Oahu). Results from this study revealed that heritable symbionts dominated the bacterial communities for both aphid species. The bacterial communities differed significantly between the two species, and A. gossypii harbored a more diverse bacterial community than P. caladii. The bacterial communities also differed across aphid populations sampled from the different islands; however, communities did not differ between aphids collected from the two host plants. PMID:21965398

  3. Bacterial communities of two parthenogenetic aphid species cocolonizing two host plants across the Hawaiian Islands.

    Science.gov (United States)

    Jones, Ryan T; Bressan, Alberto; Greenwell, April M; Fierer, Noah

    2011-12-01

    Aphids (Hemiptera: Aphididae) have been the focus of several studies with respect to their interactions with inherited symbionts, but bacterial communities of most aphid species are still poorly characterized. In this research, we used bar-coded pyrosequencing to characterize bacterial communities in aphids. Specifically, we examined the diversity of bacteria in two obligately parthenogenetic aphid species (the melon aphid, Aphis gossypii, and the cardamom aphid, Pentalonia caladii) cocolonizing two plant species (taro, Colocasia esculenta, and ginger, Alpinia purpurata) across four Hawaiian Islands (Hawaii, Kauai, Maui, and Oahu). Results from this study revealed that heritable symbionts dominated the bacterial communities for both aphid species. The bacterial communities differed significantly between the two species, and A. gossypii harbored a more diverse bacterial community than P. caladii. The bacterial communities also differed across aphid populations sampled from the different islands; however, communities did not differ between aphids collected from the two host plants.

  4. Concurrent Collections

    OpenAIRE

    Budimlić, Zoran; Burke, Michael; Cavé, Vincent; Knobe, Kathleen; Lowney, Geoff; Newton, Ryan; Palsberg, Jens; Peixotto, David; Sarkar, Vivek; Schlimbach, Frank; Taşırlar, Sağnak

    2010-01-01

    We introduce the Concurrent Collections (CnC) programming model. CnC supports flexible combinations of task and data parallelism while retaining determinism. CnC is implicitly parallel, with the user providing high-level operations along with semantic ordering constraints that together form a CnC graph. We formally describe the execution semantics of CnC and prove that the model guarantees deterministic computation. We evaluate the performance of CnC implementations on several applications an...

  5. Bacterial utilization of size-fractionated dissolved organic matter

    Digital Repository Service at National Institute of Oceanography (India)

    Khodse, V.B.; Bhosle, N.B.

    or groups developed during the period of incubation (Covert & Moran 2001, Cherrier & Bauer 2004). BGE is an important factor in understanding bacterial influence on carbon flow in aquatic ecosystems. According to del Giorgio and Cole (1998) numerous... DOM than in LMW DOM (del Giorgio and Cole, 1998). Conclusion Bacterial utilization of HMW DOM (>30 kDa to 0.22 µm) and LMW DOM (>10 kDa to 30 kDa) isolated from Dona Paula Bay, west coast of India was measured. δ 13 C values suggest that HMW DOM...

  6. A robust platform for chemical genomics in bacterial systems.

    Science.gov (United States)

    French, Shawn; Mangat, Chand; Bharat, Amrita; Côté, Jean-Philippe; Mori, Hirotada; Brown, Eric D

    2016-03-15

    While genetic perturbation has been the conventional route to probing bacterial systems, small molecules are showing great promise as probes for cellular complexity. Indeed, systematic investigations of chemical-genetic interactions can provide new insights into cell networks and are often starting points for understanding the mechanism of action of novel chemical probes. We have developed a robust and sensitive platform for chemical-genomic investigations in bacteria. The approach monitors colony volume kinetically using transmissive scanning measurements, enabling acquisition of growth rates and conventional endpoint measurements. We found that chemical-genomic profiles were highly sensitive to concentration, necessitating careful selection of compound concentrations. Roughly 20,000,000 data points were collected for 15 different antibiotics. While 1052 chemical-genetic interactions were identified using the conventional endpoint biomass approach, adding interactions in growth rate resulted in 1564 interactions, a 50-200% increase depending on the drug, with many genes uncharacterized or poorly annotated. The chemical-genetic interaction maps generated from these data reveal common genes likely involved in multidrug resistance. Additionally, the maps identified deletion backgrounds exhibiting class-specific potentiation, revealing conceivable targets for combination approaches to drug discovery. This open platform is highly amenable to kinetic screening of any arrayable strain collection, be it prokaryotic or eukaryotic. © 2016 French et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  7. Metabolic bacterial genes and the construction of high-level composite lineages of life.

    Science.gov (United States)

    Méheust, Raphaël; Lopez, Philippe; Bapteste, Eric

    2015-03-01

    Understanding how major organismal lineages originated is fundamental for understanding processes by which life evolved. Major evolutionary transitions, like eukaryogenesis, merging genetic material from distantly related organisms, are rare events, hence difficult ones to explain causally. If most archaeal lineages emerged after massive acquisitions of bacterial genes, a rule however arises: metabolic bacterial genes contributed to all major evolutionary transitions. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

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

    Science.gov (United States)

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

    2016-03-01

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

  9. Bacterial disease management: challenges, experience, innovation and future prospects: Challenges in Bacterial Molecular Plant Pathology.

    Science.gov (United States)

    Sundin, George W; Castiblanco, Luisa F; Yuan, Xiaochen; Zeng, Quan; Yang, Ching-Hong

    2016-12-01

    Plant diseases caused by bacterial pathogens place major constraints on crop production and cause significant annual losses on a global scale. The attainment of consistent effective management of these diseases can be extremely difficult, and management potential is often affected by grower reliance on highly disease-susceptible cultivars because of consumer preferences, and by environmental conditions favouring pathogen development. New and emerging bacterial disease problems (e.g. zebra chip of potato) and established problems in new geographical regions (e.g. bacterial canker of kiwifruit in New Zealand) grab the headlines, but the list of bacterial disease problems with few effective management options is long. The ever-increasing global human population requires the continued stable production of a safe food supply with greater yields because of the shrinking areas of arable land. One major facet in the maintenance of the sustainability of crop production systems with predictable yields involves the identification and deployment of sustainable disease management solutions for bacterial diseases. In addition, the identification of novel management tactics has also come to the fore because of the increasing evolution of resistance to existing bactericides. A number of central research foci, involving basic research to identify critical pathogen targets for control, novel methodologies and methods of delivery, are emerging that will provide a strong basis for bacterial disease management into the future. Near-term solutions are desperately needed. Are there replacement materials for existing bactericides that can provide effective disease management under field conditions? Experience should inform the future. With prior knowledge of bactericide resistance issues evolving in pathogens, how will this affect the deployment of newer compounds and biological controls? Knowledge is critical. A comprehensive understanding of bacterial pathosystems is required to not

  10. Co-acclimation of bacterial communities under stresses of hydrocarbons with different structures

    Science.gov (United States)

    Wang, Hui; Wang, Bin; Dong, Wenwen; Hu, Xiaoke

    2016-01-01

    Crude oil is a complex mixture of hydrocarbons with different structures; its components vary in bioavailability and toxicity. It is important to understand how bacterial communities response to different hydrocarbons and their co-acclimation in the process of degradation. In this study, microcosms with the addition of structurally different hydrocarbons were setup to investigate the successions of bacterial communities and the interactions between different bacterial taxa. Hydrocarbons were effectively degraded in all microcosms after 40 days. High-throughput sequencing offered a great quantity of data for analyzing successions of bacterial communities. The results indicated that the bacterial communities responded dramatically different to various hydrocarbons. KEGG database and PICRUSt were applied to predict functions of individual bacterial taxa and networks were constructed to analyze co-acclimations between functional bacterial groups. Almost all functional genes catalyzing degradation of different hydrocarbons were predicted in bacterial communities. Most of bacterial taxa were believed to conduct biodegradation processes via interactions with each other. This study addressed a few investigated area of bacterial community responses to structurally different organic pollutants and their co-acclimation and interactions in the process of biodegradation. The study could provide useful information to guide the bioremediation of crude oil pollution. PMID:27698451

  11. Subversion of the Endocytic and Secretory Pathways by Bacterial Effector Proteins

    Directory of Open Access Journals (Sweden)

    Mary M. Weber

    2018-01-01

    Full Text Available Intracellular bacteria have developed numerous strategies to hijack host vesicular trafficking pathways to form their unique replicative niches. To promote intracellular replication, the bacteria must interact with host organelles and modulate host signaling pathways to acquire nutrients and membrane for the growing parasitophorous vacuole all while suppressing activation of the immune response. To facilitate host cell subversion, bacterial pathogens use specialized secretion systems to deliver bacterial virulence factors, termed effectors, into the host cell that mimic, agonize, and/or antagonize the function of host proteins. In this review we will discuss how bacterial effector proteins from Coxiella burnetii, Brucella abortus, Salmonella enterica serovar Typhimurium, Legionella pneumophila, Chlamydia trachomatis, and Orientia tsutsugamushi manipulate the endocytic and secretory pathways. Understanding how bacterial effector proteins manipulate host processes not only gives us keen insight into bacterial pathogenesis, but also enhances our understanding of how eukaryotic membrane trafficking is regulated.

  12. Subversion of the Endocytic and Secretory Pathways by Bacterial Effector Proteins.

    Science.gov (United States)

    Weber, Mary M; Faris, Robert

    2018-01-01

    Intracellular bacteria have developed numerous strategies to hijack host vesicular trafficking pathways to form their unique replicative niches. To promote intracellular replication, the bacteria must interact with host organelles and modulate host signaling pathways to acquire nutrients and membrane for the growing parasitophorous vacuole all while suppressing activation of the immune response. To facilitate host cell subversion, bacterial pathogens use specialized secretion systems to deliver bacterial virulence factors, termed effectors, into the host cell that mimic, agonize, and/or antagonize the function of host proteins. In this review we will discuss how bacterial effector proteins from Coxiella burnetii, Brucella abortus, Salmonella enterica serovar Typhimurium, Legionella pneumophila, Chlamydia trachomatis , and Orientia tsutsugamushi manipulate the endocytic and secretory pathways. Understanding how bacterial effector proteins manipulate host processes not only gives us keen insight into bacterial pathogenesis, but also enhances our understanding of how eukaryotic membrane trafficking is regulated.

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

    Science.gov (United States)

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

    2011-03-01

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

  14. Unraveling plant responses to bacterial pathogens through proteomics

    KAUST Repository

    Zimaro, Tamara

    2011-11-03

    Plant pathogenic bacteria cause diseases in important crops and seriously and negatively impact agricultural production. Therefore, an understanding of the mechanisms by which plants resist bacterial infection at the stage of the basal immune response or mount a successful specific R-dependent defense response is crucial since a better understanding of the biochemical and cellular mechanisms underlying these interactions will enable molecular and transgenic approaches to crops with increased biotic resistance. In recent years, proteomics has been used to gain in-depth understanding of many aspects of the host defense against pathogens and has allowed monitoring differences in abundance of proteins as well as posttranscriptional and posttranslational processes, protein activation/inactivation, and turnover. Proteomics also offers a window to study protein trafficking and routes of communication between organelles. Here, we summarize and discuss current progress in proteomics of the basal and specific host defense responses elicited by bacterial pathogens. Copyright 2011 Tamara Zimaro et al.

  15. Bacterial and Archaeal Lipids Recovered from Subsurface Evaporites of Dalangtan Playa on the Tibetan Plateau and Their Astrobiological Implications

    Science.gov (United States)

    Cheng, Ziye; Xiao, Long; Wang, Hongmei; Yang, Huan; Li, Jingjing; Huang, Ting; Xu, Yi; Ma, Nina

    2017-11-01

    Qaidam Basin (Tibetan Plateau) is considered an applicable analogue to Mars with regard to sustained extreme aridity and abundant evaporites. To investigate the possibility of the preservation of microbial lipids under these Mars analog conditions, we conducted a mineralogical and organic geochemistry study on samples collected from two Quaternary sections in Dalangtan Playa, northwestern Qaidam Basin, which will enhance our understanding of the potential preservation of molecular biomarkers on Mars. Two sedimentary units were identified along two profiles: one salt unit characterized by a predominance of gypsum and halite, and one detrital unit with a decrease of gypsum and halite and enrichment in siliciclastic minerals. Bacterial fatty acids and archaeal acyclic diether and tetraether membrane lipids were detected, and they varied throughout the sections in concentration and abundance. Bacterial and archaeal biomolecules indicate a dominance of Gram-positive bacteria and halophilic archaea in this hypersaline ecosystem that is similar to those in other hypersaline environments. Furthermore, the abundance of bacterial lipids decreases with the increase of salinity, whereas archaeal lipids showed a reverse trend. The detection of microbial lipids in hypersaline environments would indicate, for example on Mars, a high potential for the detection of microbial biomarkers in evaporites over geological timescales.

  16. The Human Vaginal Bacterial Biota and Bacterial Vaginosis

    Directory of Open Access Journals (Sweden)

    Sujatha Srinivasan

    2008-01-01

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

  17. Shape understanding system machine understanding and human understanding

    CERN Document Server

    Les, Zbigniew

    2015-01-01

    This is the third book presenting selected results of research on the further development of the shape understanding system (SUS) carried out by authors in the newly founded Queen Jadwiga Research Institute of Understanding. In this book the new term Machine Understanding is introduced referring to a new area of research aiming to investigate the possibility of building machines with the ability to understand. It is presented that SUS needs to some extent mimic human understanding and for this reason machines are evaluated according to the rules applied for the evaluation of human understanding. The book shows how to formulate problems and how it can be tested if the machine is able to solve these problems.    

  18. A novel ion-beam-mutation effect application in identification of gene involved in bacterial antagonism to fungal infection of ornamental crops

    International Nuclear Information System (INIS)

    Mahadtanapuk, S.; Teraarusiri, W.; Nanakorn, W.; Yu, L.D.; Thongkumkoon, P.; Anuntalabhochai, S.

    2014-01-01

    Highlights: • Ion beam bombardment induced mutation in bacterial B. licheniformis. • A mutant lost antifungal activity. • DNA fingerprint of the mutant was analyzed. • The lost gene was indentified to code for TrxR gene. • TrxR gene from B. licheniformis expressed the flower antagonism to fungi. - Abstract: This work is on a novel application of ion beam effect on biological mutation. Bacillus licheniformis (B. licheniformis) is a common soil bacterium with an antagonistic effect on Curcuma alismatifolia Gagnep. and Chrysanthemum indicum Linn. In an attempt to control fungal diseases of local crops by utilizing B. licheniformis, we carried out gene analysis of the bacterium to understand the bacterial antagonistic mechanism. The bacterial cells were bombarded to induce mutations using nitrogen ion beam. After ion bombardment, DNA analysis revealed that the modified polymorphism fragment present in the wild type was missing in a bacterial mutant which lost the antifungal activity. The fragments conserved in the wild type but lost in the mutant bacteria was identified to code for the thioredoxin reductase (TrxR) gene. The gene analysis showed that the TrxR gene from B. licheniformis had the expression of the antagonism to fungi in a synchronous time evolution with the fungus inhibition when the bacteria were co-cultivated with the fungi. The collective results indicate the TrxR gene responsible for the antagonism of bacteria B. licheniformis to fungal infection

  19. A novel ion-beam-mutation effect application in identification of gene involved in bacterial antagonism to fungal infection of ornamental crops

    Energy Technology Data Exchange (ETDEWEB)

    Mahadtanapuk, S. [Faculty of Agriculture and Natural Resources, University of Phayao, Maeka, Muang, Phayao 56000 (Thailand); Teraarusiri, W. [Central Laboratory, University of Phayao, Maeka, Muang, Phayao 56000 (Thailand); Nanakorn, W. [The Crown Property Bureau, 173 Nakhonratchasrima Road, Dusit, Bangkok 10300 (Thailand); Yu, L.D., E-mail: yuld@thep-center.org [Plasma and Beam Physics Research Facility, Department of Physics and Materials Science, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Thailand Center of Excellence in Physics, Commission on Higher Education, 328 Si Ayutthaya Road, Bangkok 10400 (Thailand); Thongkumkoon, P. [Plasma and Beam Physics Research Facility, Department of Physics and Materials Science, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand); Anuntalabhochai, S., E-mail: soanu.1@gmail.com [Molecular Biology Laboratory, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200 (Thailand)

    2014-05-01

    Highlights: • Ion beam bombardment induced mutation in bacterial B. licheniformis. • A mutant lost antifungal activity. • DNA fingerprint of the mutant was analyzed. • The lost gene was indentified to code for TrxR gene. • TrxR gene from B. licheniformis expressed the flower antagonism to fungi. - Abstract: This work is on a novel application of ion beam effect on biological mutation. Bacillus licheniformis (B. licheniformis) is a common soil bacterium with an antagonistic effect on Curcuma alismatifolia Gagnep. and Chrysanthemum indicum Linn. In an attempt to control fungal diseases of local crops by utilizing B. licheniformis, we carried out gene analysis of the bacterium to understand the bacterial antagonistic mechanism. The bacterial cells were bombarded to induce mutations using nitrogen ion beam. After ion bombardment, DNA analysis revealed that the modified polymorphism fragment present in the wild type was missing in a bacterial mutant which lost the antifungal activity. The fragments conserved in the wild type but lost in the mutant bacteria was identified to code for the thioredoxin reductase (TrxR) gene. The gene analysis showed that the TrxR gene from B. licheniformis had the expression of the antagonism to fungi in a synchronous time evolution with the fungus inhibition when the bacteria were co-cultivated with the fungi. The collective results indicate the TrxR gene responsible for the antagonism of bacteria B. licheniformis to fungal infection.

  20. Collective Security

    DEFF Research Database (Denmark)

    Galster, Kjeld

    and real defence of the country’s neutrality let alone a capability to support possible League of Nations action, should such need arise. The anti-militarist ideology of one party, led to regarding the armed services as harmful to designs for developing civic society and a waste of resources generally...... disinclination to accept that the collective security concept and international treaties and accords signed by Denmark should necessitate credible and real defence of the country’s neutrality let alone a capability to support possible League of Nations action, should such need arise. The anti-militarist ideology...

  1. Concurrent Collections

    Directory of Open Access Journals (Sweden)

    Zoran Budimlić

    2010-01-01

    Full Text Available We introduce the Concurrent Collections (CnC programming model. CnC supports flexible combinations of task and data parallelism while retaining determinism. CnC is implicitly parallel, with the user providing high-level operations along with semantic ordering constraints that together form a CnC graph. We formally describe the execution semantics of CnC and prove that the model guarantees deterministic computation. We evaluate the performance of CnC implementations on several applications and show that CnC offers performance and scalability equivalent to or better than that offered by lower-level parallel programming models.

  2. Bacterial contamination of blood products.

    Science.gov (United States)

    Palavecino, Elizabeth; Jacobs, Michael; Yomtovian, Roslyn

    2004-11-01

    The occurrence of a septic reaction resulting from bacterial contamination of blood products, particularly with room-temperature stored platelets, is the most common transfusion-associated infectious risk in the United States. Bacterial contamination of blood products was first identified more than 60 years ago; yet, strategies to resolve this problem have proved daunting despite ongoing awareness and increasing concern especially in the last few years. With the recent US Food and Drug Administration (FDA) approval of culture methods for quality control testing of platelet units and the promulgation of accreditation standards by the College of American Pathologists and American Association of Blood Banks to detect bacterially contaminated platelet units and to prevent transfusion of these units, blood banks and transfusion services have finally started to address this problem, in a more standardized manner. Furthermore, as new methods of interdicting, inactivating and detecting bacterially contaminated blood products emerge, it is hoped that the problem of bacterial contamination of blood products will be overcome.

  3. Community-acquired bacterial meningitis.

    Science.gov (United States)

    Costerus, Joost M; Brouwer, Matthijs C; Bijlsma, Merijn W; van de Beek, Diederik

    2017-02-01

    Bacterial meningitis is a medical emergency and is associated with a high disease burden. We reviewed recent progress in the management of patients with community-acquired bacterial meningitis. The worldwide burden of disease of bacterial meningitis remains high, despite the decreasing incidence following introduction of routine vaccination campaigns. Delay in diagnosis and treatment remain major concerns in the management of acute bacterial meningitis. European Society of Clinical Microbiology and Infectious Diseases guidelines strive for a door-to-antibiotic-time less than 1 h. Polymerase chain reaction (PCR) has emerged as an important diagnostic tool to identify the causative organism. Point-of-care tests using fast multiplex PCR have been developed, but additional value has not been proven. Although anecdotal observations advocate pressure-based management, a randomized controlled trial will need to be performed first to determine efficacy and safety of such an aggressive treatment approach. Adjunctive dexamethasone remains the only adjunctive therapy with proven efficacy. The incidence of bacterial meningitis has been decreasing after the implementation of effective vaccines. Treatment should be administered as soon as possible and time to treatment should not exceed 1 h.

  4. Salt Marsh Bacterial Communities before and after the Deepwater Horizon Oil Spill.

    Science.gov (United States)

    Engel, Annette Summers; Liu, Chang; Paterson, Audrey T; Anderson, Laurie C; Turner, R Eugene; Overton, Edward B

    2017-10-15

    communities in coastal marshes is poorly known, with limited investigation of potential changes in bacterial communities in response to various environmental stressors. The Deepwater Horizon oil spill provided an unprecedented opportunity to study the long-term effects of an oil spill on microbial systems in marshes. Compared to previous studies, the significance of our research stems from (i) a broader geographic range of studied marshes, (ii) an extended time frame of data collection that includes prespill conditions, (iii) a more accurate procedure using biomarker indices to understand oiling, and (iv) an examination of other potential stressors linked to in situ environmental changes, aside from oil exposure. Copyright © 2017 American Society for Microbiology.

  5. Antibiogram of bacterial species isolated from canine pyometra

    Directory of Open Access Journals (Sweden)

    Madhu Swamy

    2013-06-01

    Full Text Available Aim: The aim of the present work was to ascertain the bacterial flora causing pyometra in female dogs and their antibiotic sensitivity. Materials and Methods: A study was conducted to determine the antibiogram of bacterial species isolated from 20 female dogs diagnosed with pyometra. The vaginal discharge was collected by sterile swab and streaked smoothly over Mueller Hinton medium and sensitivity towards antibiotics was determined by measuring the zone of inhibition using a Hi-media scale. Results: The antobiogram showed that Gentamicin was the most sensitive (85% antibiotic followed by Enrofloxacin, Ciprofloxacin and Amoxicillin (65%, 65% and 55%, respectively. The isolates were most resistant to Oxytetracycline (85% followed by Tetracycline, Ampicillin, Chloramphenicol, Cloxacillin and Erythromycin (80%, 80%, 75%, 70% and 70%, respectively. Conclusion: Gentamicin was found to be most effective antibiotic against the bacterial species isolated from canine pyometra. [Vet World 2013; 6(8.000: 546-549

  6. Spectral imagery collection experiment

    Science.gov (United States)

    Romano, Joao M.; Rosario, Dalton; Farley, Vincent; Sohr, Brian

    2010-04-01

    The Spectral and Polarimetric Imagery Collection Experiment (SPICE) is a collaborative effort between the US Army ARDEC and ARL for the collection of mid-wave and long-wave infrared imagery using hyperspectral, polarimetric, and broadband sensors. The objective of the program is to collect a comprehensive database of the different modalities over the course of 1 to 2 years to capture sensor performance over a wide variety of adverse weather conditions, diurnal, and seasonal changes inherent to Picatinny's northern New Jersey location. Using the Precision Armament Laboratory (PAL) tower at Picatinny Arsenal, the sensors will autonomously collect the desired data around the clock at different ranges where surrogate 2S3 Self-Propelled Howitzer targets are positioned at different viewing perspectives at 549 and 1280m from the sensor location. The collected database will allow for: 1) Understand of signature variability under the different weather conditions; 2) Development of robust algorithms; 3) Development of new sensors; 4) Evaluation of hyperspectral and polarimetric technologies; and 5) Evaluation of fusing the different sensor modalities. In this paper, we will present the SPICE data collection objectives, the ongoing effort, the sensors that are currently deployed, and how this work will assist researches on the development and evaluation of sensors, algorithms, and fusion applications.

  7. Tiny but mighty: bacterial membrane vesicles in food biotechnological applications.

    Science.gov (United States)

    Liu, Yue; Alexeeva, Svetlana; Defourny, Kyra Ay; Smid, Eddy J; Abee, Tjakko

    2018-02-01

    Membrane vesicle (MV) production is observed in all domains of life. Evidence of MV production accumulated in recent years among bacterial species involved in fermentation processes. These studies revealed MV composition, biological functions and properties, which made us recognize the potential of MVs in food applications as delivery vehicles of various compounds to other bacteria or the human host. Moreover, MV producing strains can deliver benefits as probiotics or starters in fermentation processes. Next to the natural production of MVs, we also highlight possible methods for artificial generation of bacterial MVs and cargo loading to enhance their applicability. We believe that a more in-depth understanding of bacterial MVs opens new avenues for their exploitation in biotechnological applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. The quest for a unified view of bacterial land colonization.

    Science.gov (United States)

    Wu, Hao; Fang, Yongjun; Yu, Jun; Zhang, Zhang

    2014-07-01

    Exploring molecular mechanisms underlying bacterial water-to-land transition represents a critical start toward a better understanding of the functioning and stability of the terrestrial ecosystems. Here, we perform comprehensive analyses based on a large variety of bacteria by integrating taxonomic, phylogenetic and metagenomic data, in the quest for a unified view that elucidates genomic, evolutionary and ecological dynamics of the marine progenitors in adapting to nonaquatic environments. We hypothesize that bacterial land colonization is dominated by a single-gene sweep, that is, the emergence of dnaE2 derived from an early duplication event of the primordial dnaE, followed by a series of niche-specific genomic adaptations, including GC content increase, intensive horizontal gene transfer and constant genome expansion. In addition, early bacterial radiation may be stimulated by an explosion of land-borne hosts (for example, plants and animals) after initial land colonization events.

  9. Hindered bacterial mobility in porous media flow enhances dispersion

    Science.gov (United States)

    Dehkharghani, Amin; Waisbord, Nicolas; Dunkel, Jörn; Guasto, Jeffrey

    2017-11-01

    Swimming bacteria live in porous environments characterized by dynamic fluid flows, where they play a crucial role in processes ranging from the bioremediation to the spread of infections. We study bacterial transport in a quasi-two-dimensional porous microfluidic device, which is complemented by Langevin simulations. The cell trajectories reveal filamentous patterns of high cell concentration, which result from the accumulation of bacteria in the high-shear regions of the flow and their subsequent advection. Moreover, the effective diffusion coefficient of the motile bacteria is severely hindered in the transverse direction to the flow due to decorrelation of the cells' persistent random walk by shear-induced rotation. The hindered lateral diffusion has the surprising consequence of strongly enhancing the longitudinal bacterial transport through a dispersion effect. These results demonstrate the significant role of the flow and geometry in bacterial transport through porous media with potential implications for understanding ecosystem dynamics and engineering bioreactors. NSF CBET-1511340, NSF CAREER-1554095.

  10. Gram-negative and Gram-positive bacterial extracellular vesicles.

    Science.gov (United States)

    Kim, Ji Hyun; Lee, Jaewook; Park, Jaesung; Gho, Yong Song

    2015-04-01

    Like mammalian cells, Gram-negative and Gram-positive bacteria release nano-sized membrane vesicles into the extracellular environment either in a constitutive manner or in a regulated manner. These bacterial extracellular vesicles are spherical bilayered proteolipids enriched with bioactive proteins, lipids, nucleic acids, and virulence factors. Recent progress in this field supports the critical pathophysiological functions of these vesicles in both bacteria-bacteria and bacteria-host interactions. This review provides an overview of the current understanding on Gram-negative and Gram-positive bacterial extracellular vesicles, especially regarding the biogenesis, components, and functions in poly-species communities. We hope that this review will stimulate additional research in this emerging field of bacterial extracellular vesicles and contribute to the development of extracellular vesicle-based diagnostic tools and effective vaccines against pathogenic Gram-negative and Gram-positive bacteria. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Water microbiology. Bacterial pathogens and water.

    Science.gov (United States)

    Cabral, João P S

    2010-10-01

    Water is essential to life, but many people do not have access to clean and safe drinking water and many die of waterborne bacterial infections. In this review a general characterization of the most important bacterial diseases transmitted through water-cholera, typhoid fever and bacillary dysentery-is presented, focusing on the biology and ecology of the causal agents and on the diseases' characteristics and their life cycles in the environment. The importance of pathogenic Escherichia coli strains and emerging pathogens in drinking water-transmitted diseases is also briefly discussed. Microbiological water analysis is mainly based on the concept of fecal indicator bacteria. The main bacteria present in human and animal feces (focusing on their behavior in their hosts and in the environment) and the most important fecal indicator bacteria are presented and discussed (focusing on the advantages and limitations of their use as markers). Important sources of bacterial fecal pollution of environmental waters are also briefly indicated. In the last topic it is discussed which indicators of fecal pollution should be used in current drinking water microbiological analysis. It was concluded that safe drinking water for all is one of the major challenges of the 21st century and that microbiological control of drinking water should be the norm everywhere. Routine basic microbiological analysis of drinking water should be carried out by assaying the presence of Escherichia coli by culture methods. Whenever financial resources are available, fecal coliform determinations should be complemented with the quantification of enterococci. More studies are needed in order to check if ammonia is reliable for a preliminary screening for emergency fecal pollution outbreaks. Financial resources should be devoted to a better understanding of the ecology and behavior of human and animal fecal bacteria in environmental waters.

  12. Fluoroquinolones as imaging agents for bacterial infection.

    Science.gov (United States)

    Naqvi, Syed Ali Raza; Drlica, Karl

    2017-10-31

    Diagnosis of deep-seated bacterial infection is difficult, as neither standard anatomical imaging nor radiolabeled, autologous leukocytes distinguish sterile inflammation from infection. Two recent imaging efforts are receiving attention: (1) radioactive derivatives of sorbitol show good specificity with Gram-negative bacterial infections, and (2) success in combining anatomical and functional imaging for cancer diagnosis has rekindled interest in 99m Tc-fluoroquinolone-based imaging. With the latter, computed tomography (CT) would be combined with single-photon-emission-computed tomography (SPECT) to detect 99m Tc-fluoroquinolone-bacterial interactions. The present minireview provides a framework for advancing fluoroquinolone-based imaging by identifying gaps in our understanding of the process. One issue is the reliance of 99m Tc labeling on the reduction of sodium pertechnetate, which can lead to colloid formation and loss of specificity. Specificity problems may be reduced by altering the quinolone structure (for example, switching from ciprofloxacin to sitafloxacin). Another issue is the uncharacterized nature of 99m Tc-ciprofloxacin binding to, or sequestration in, bacteria: specific interactions with DNA gyrase, an intracellular fluoroquinolone target, are unlikely. Labeling with 68 Ga rather than 99m Tc enables detection by positron emission tomography, but with similar biological uncertainties. Replacing the C6-F of the fluoroquinolone with 18 F provides an alternative to pertechnetate and gallium that may lead to imaging based on drug interactions with gyrase. Gyrase-based imaging requires knowledge of fluoroquinolone action, which we update. We conclude that quinolone-based probes show promise for the diagnosis of infection, but improvements in specificity and sensitivity are needed. These improvements include the optimization of the quinolone structure; such chemistry efforts can be accelerated by refining microbiological assays.

  13. Water Microbiology. Bacterial Pathogens and Water

    Directory of Open Access Journals (Sweden)

    João P. S. Cabral

    2010-10-01

    Full Text Available Water is essential to life, but many people do not have access to clean and safe drinking water and many die of waterborne bacterial infections. In this review a general characterization of the most important bacterial diseases transmitted through water—cholera, typhoid fever and bacillary dysentery—is presented, focusing on the biology and ecology of the causal agents and on the diseases’ characteristics and their life cycles in the environment. The importance of pathogenic Escherichia coli strains and emerging pathogens in drinking water-transmitted diseases is also briefly discussed. Microbiological water analysis is mainly based on the concept of fecal indicator bacteria. The main bacteria present in human and animal feces (focusing on their behavior in their hosts and in the environment and the most important fecal indicator bacteria are presented and discussed (focusing on the advantages and limitations of their use as markers. Important sources of bacterial fecal pollution of environmental waters are also briefly indicated. In the last topic it is discussed which indicators of fecal pollution should be used in current drinking water microbiological analysis. It was concluded that safe drinking water for all is one of the major challenges of the 21st century and that microbiological control of drinking water should be the norm everywhere. Routine basic microbiological analysis of drinking water should be carried out by assaying the presence of Escherichia coli by culture methods. Whenever financial resources are available, fecal coliform determinations should be complemented with the quantification of enterococci. More studies are needed in order to check if ammonia is reliable for a preliminary screening for emergency fecal pollution outbreaks. Financial resources should be devoted to a better understanding of the ecology and behavior of human and animal fecal bacteria in environmental waters.

  14. Selective adsorption of bacterial cells onto zeolites.

    Science.gov (United States)

    Kubota, Munehiro; Nakabayashi, Tadashi; Matsumoto, Yuki; Shiomi, Tohru; Yamada, Yusuke; Ino, Keita; Yamanokuchi, Hiroyuki; Matsui, Masayoshi; Tsunoda, Tatsuo; Mizukami, Fujio; Sakaguchi, Kengo

    2008-06-15

    Zeolites adsorb microbial cells on their surfaces and selective adsorption for specific microorganisms was seen with certain zeolites. Tests for the adsorption ability of zeolites were conducted using various established microbial cell lines. Specific cell lines were shown to selectively absorb to certain zeolites, species to species. In order to understand the selectivity of adsorption, we tested adsorption under various pH conditions and determined the zeta-potentials of zeolites and cells. The adsorption of some cell lines depended on the pH, and some microorganisms were preferentially adsorbed at acidic pH. The values of zeta-potentials were used for calculating the electric double layer interaction energy between zeolites and microbial cells. There was a correlation between the experimental adsorption results and the interaction energy. Moreover, we evaluated the surface hydrophobicity of bacterial cells by using the microbial adherence to hydrocarbon (MATH) assay. In addition, we also applied this method for zeolites to quantify relative surface hydrophobicity. As a result, we found a correlation between the adsorption results and the hydrophobicity of bacterial cells and zeolites. These results suggested that adsorption could be explained mainly by electric double layer interactions and hydrophobic interactions. Finally, by using the zeolites Na-BEA and H-Y, we succeeded in clearly separating three representative microbes from a mixture of Escherichia coli, Bacillus subtilis and Staphylococcus aureus. Zeolites could adsorb each of the bacterial cell species with high selectivity even from a mixed suspension. Zeolites can therefore be used as effective carrier materials to provide an easy, rapid and accurate method for cell separation.

  15. Collective drawing

    Directory of Open Access Journals (Sweden)

    Roberto Grossa

    2009-10-01

    Full Text Available This paper is referred to the experiences run at Iuav in the framework of the EU-FSE founded Courses of Collaborative Composition. In these courses we built up some work/game thought as meaning of a distance collaborative game. Rally around these games, we delivered specific knowledge and portions of technical knowledge referred to the issue of formal structure, shape grammar, and codify of “behaviours role” for a networked distance collaboration. The subject of this didactic experience is the composition and of a collective figurative opera (an image processed by the whole group of students. The themes of the image have been different in each Course: a figurative opera, a facade of an urban street or a small square. The students shared a repertory of figures coming from the break down of paintings or pictures of palaces and used the repertory as a source in order to compose the final collective opera. On the other side we worked on the shape grammar roles, experimented tools and protocols of communication, analysed the best practice in this field and defined evaluation systems.

  16. Seasonal variability in airborne bacterial communities at a high elevation site and their relationship to other air studies and to potential sources

    Science.gov (United States)

    Bowers, R. M.; Mccubbin, I. B.; Hallar, A. G.; Fierer, N.

    2012-12-01

    Airborne bacteria are a large component of the near-surface atmospheric aerosol; however we know surprisingly little about their spatiotemporal dynamics and even less about their distributions at high-elevation. With this work, we describe seasonal shifts in bacterial abundances, total particle abundances, and bacterial community structure at a high-elevation research station located in Colorado, USA. In addition, we describe the unique composition of these high-elevation airborne bacterial communities as compared to the bacteria commonly observed throughout the lower elevation atmosphere as well as bacteria common to major sources such as leaf surfaces, soils, water bodies and various other surfaces. To address these knowledge gaps, we collected aerosol samples on the rooftop of Storm Peak Laboratory (3200 m ASL) over the course of 2-3 week periods during each of the four calendar seasons. Total bacterial abundances were assessed via flow cytometry, total particle abundances were calculated with an aerodynamic particle sizer, and bacterial communities were characterized using a high-throughput barcoded DNA sequencing approach. The airborne bacterial communities at Storm Peak Lab were then used in a meta-analysis comparing Storm Peak bacteria to other near-surface (lower elevation) bacterial communities and to the communities of likely source environments. Bacterial abundances varied by season, which was similar but not identical to the changes in total particle abundances across the same sampling period. Airborne bacterial community structure varied significantly by season, with the summer communities being the most distinct. Season specific bacterial groups were identified, suggesting that a large proportion of the airborne community may be derived from nearby sources. However following a multi-environment meta-analysis using several air and source derived bacterial community datasets, the high-elevation air communities were the most distinct as compared to the

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

    Directory of Open Access Journals (Sweden)

    Sinead E Miller

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

  18. Collective excitations in nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Chomaz, Ph

    1997-12-31

    The properties of the nucleus cannot be reduced to the properties of its constituents: it is a complex system. The fact that many properties of the nucleus are consequences of the existence of mean-field potential is a manifestation of this complexity. In particular the nucleons can thus self-organize in collective motions such as giant resonances. Therefore the study of these collective motions is a very good to understand the properties of the nucleus itself. The purpose of this article was to stress some aspects of these collective vibrations. In particular we have studied how an ensemble of fermions as the nucleus can self-organize in collective vibrations which are behaving like a gas of bosons in weak interaction. The understanding of these phenomena remains one of the important subjects of actually in the context of quantal systems in strong interaction. In particular the study of the states with one or two vibration quanta provides a direct information on the structure if nuclei close to their ground states. (author) 270 refs.

  19. Collective excitations in nuclei

    International Nuclear Information System (INIS)

    Chomaz, Ph.

    1997-01-01

    The properties of the nucleus cannot be reduced to the properties of its constituents: it is a complex system. The fact that many properties of the nucleus are consequences of the existence of mean-field potential is a manifestation of this complexity. In particular the nucleons can thus self-organize in collective motions such as giant resonances. Therefore the study of these collective motions is a very good to understand the properties of the nucleus itself. The purpose of this article was to stress some aspects of these collective vibrations. In particular we have studied how an ensemble of fermions as the nucleus can self-organize in collective vibrations which are behaving like a gas of bosons in weak interaction. The understanding of these phenomena remains one of the important subjects of actually in the context of quantal systems in strong interaction. In particular the study of the states with one or two vibration quanta provides a direct information on the structure if nuclei close to their ground states. (author)

  20. Molecular analysis of bacterial pathogens in otitis media with effusion.

    Science.gov (United States)

    Post, J C; Preston, R A; Aul, J J; Larkins-Pettigrew, M; Rydquist-White, J; Anderson, K W; Wadowsky, R M; Reagan, D R; Walker, E S; Kingsley, L A; Magit, A E; Ehrlich, G D

    To determine if the polymerase chain reaction (PCR) can detect bacterial DNA in pediatric middle ear effusions that are sterile by standard cultural methods. Single-center, blinded, comparative study of diagnostic assays. The PCR-based detection systems for Moraxella catarrhalis, Haemophilus influenzae, and Streptococcus pneumoniae were designed and validated using a battery of DNAs obtained from cultured bacteria. Chronic middle ear effusion specimens were collected and comparatively analyzed by culture and the PCR. Tertiary care pediatric hospital. A total of 97 middle ear effusions were collected from pediatric outpatients at Children's Hospital of Pittsburgh (Pa) during myringotomy and tube placement for chronic otitis media with effusion (duration > 3 months). All patients had failed multiple courses of antimicrobial therapy and were diagnosed by a combination of validated otoscopy and tympanograms. Differences in the percentage of positive test results between PCR-based assays and culture for M catarrhalis, H influenzae, and S pneumoniae. Of the 97 specimens of otitis media with effusion, 28 (28.9%) tested positive by both culture and PCR for M catarrhalis, H influenzae, or S pneumoniae. An additional 47 specimens (48%) were PCR positive/culture negative for these three bacterial species. Thus, 75 (77.3%) of the 97 specimens tested PCR positive for one or more of the three test organisms. The minimum number of bacterial genomic equivalents present in the average culture-negative ear was estimated to be greater than 10(4) based on dilutional experiments. The PCR-based assay systems can detect the presence of bacterial DNA in a significant percentage of culturally sterile middle ear effusions. While this finding is not proof of an active bacterial infectious process, the large number of bacterial genomic equivalents present in the ears is suggestive of an active process.

  1. Bacterial Attachment, Aggregation, and Alignment on Subcellular Nanogratings.

    Science.gov (United States)

    Lai, Chang Quan

    2018-04-03

    Recent investigations on the interactions of bacteria with micro/nanostructures have revealed a wide range of prokaryotic responses that were previously unknown. Despite these advances, however, it remains unclear how collective bacterial behavior on a surface would be influenced by the presence of anisotropic nanostructures with subcellular dimensions. To clarify this, the attachment, aggregation, and alignment of Pseudomonas aeruginosa on orderly subcellular nanogratings with systematically varied geometries were investigated. Compared with a flat surface, attachment and aggregation of bacteria on the nanogratings were reduced by up to 83 and 84% respectively, whereas alignment increased by a maximum of 850%. Using a semiempirical quantitative model, these results were shown to be caused by a lowering of physicochemical attraction between the substrate and bacteria, possible disruption to cell communication, and physical isolation of bacteria that were entrenched in the nanogratings by capillary action. Furthermore, the bacterial attachment level was generally found to be exponentially related to the contact area between the substrate and bacterial cells, except when there were significant deficits in the available contact area, which prompted the bacterial cells to employ their appendages to maintain a minimum attachment rate. Because the contact area for adhesion is strongly dependent on the geometry of the surface features and orientation of the bacterial cells, these results indicate that the conventional practice of using roughness parameters to draw quantitative relationships between surface topographies and bacterial attachment could suffer from inaccuracies due to the lack of shape and orientation information provided by these parameters. On the basis of these insights, design principles for generating maximal and minimal bacterial attachment on a surface were also proposed and verified with results reported in the literature.

  2. Abdominal radiation causes bacterial translocation

    International Nuclear Information System (INIS)

    Guzman-Stein, G.; Bonsack, M.; Liberty, J.; Delaney, J.P.

    1989-01-01

    The purpose of this study was to determine if a single dose of radiation to the rat abdomen leads to bacterial translocation into the mesenteric lymph nodes (MLN). A second issue addressed was whether translocation correlates with anatomic damage to the mucosa. The radiated group (1100 cGy) which received anesthesia also was compared with a control group and a third group which received anesthesia alone but no abdominal radiation. Abdominal radiation lead to 100% positive cultures of MLN between 12 hr and 4 days postradiation. Bacterial translocation was almost nonexistent in the control and anesthesia group. Signs of inflammation and ulceration of the intestinal mucosa were not seen until Day 3 postradiation. Mucosal damage was maximal by Day 4. Bacterial translocation onto the MLN after a single dose of abdominal radiation was not apparently dependent on anatomical, histologic damage of the mucosa

  3. Bacterial Degradation of Aromatic Compounds

    Directory of Open Access Journals (Sweden)

    Qing X. Li

    2009-01-01

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

  4. Precise, High-throughput Analysis of Bacterial Growth.

    Science.gov (United States)

    Kurokawa, Masaomi; Ying, Bei-Wen

    2017-09-19

    Bacterial growth is a central concept in the development of modern microbial physiology, as well as in the investigation of cellular dynamics at the systems level. Recent studies have reported correlations between bacterial growth and genome-wide events, such as genome reduction and transcriptome reorganization. Correctly analyzing bacterial growth is crucial for understanding the growth-dependent coordination of gene functions and cellular components. Accordingly, the precise quantitative evaluation of bacterial growth in a high-throughput manner is required. Emerging technological developments offer new experimental tools that allow updates of the methods used for studying bacterial growth. The protocol introduced here employs a microplate reader with a highly optimized experimental procedure for the reproducible and precise evaluation of bacterial growth. This protocol was used to evaluate the growth of several previously described Escherichia coli strains. The main steps of the protocol are as follows: the preparation of a large number of cell stocks in small vials for repeated tests with reproducible results, the use of 96-well plates for high-throughput growth evaluation, and the manual calculation of two major parameters (i.e., maximal growth rate and population density) representing the growth dynamics. In comparison to the traditional colony-forming unit (CFU) assay, which counts the cells that are cultured in glass tubes over time on agar plates, the present method is more efficient and provides more detailed temporal records of growth changes, but has a stricter detection limit at low population densities. In summary, the described method is advantageous for the precise and reproducible high-throughput analysis of bacterial growth, which can be used to draw conceptual conclusions or to make theoretical observations.

  5. Evidence of Ash Tree (Fraxinus spp. Specific Associations with Soil Bacterial Community Structure and Functional Capacity

    Directory of Open Access Journals (Sweden)

    Michael P. Ricketts

    2018-04-01

    Full Text Available The spread of the invasive emerald ash borer (EAB across North America has had enormous impacts on temperate forest ecosystems. The selective removal of ash trees (Fraxinus spp. has resulted in abnormally large inputs of coarse woody debris and altered forest tree community composition, ultimately affecting a variety of ecosystem processes. The goal of this study was to determine if the presence of ash trees influences soil bacterial communities and/or functions to better understand the impacts of EAB on forest successional dynamics and biogeochemical cycling. Using 16S rRNA amplicon sequencing of soil DNA collected from ash and non-ash plots in central Ohio during the early stages of EAB infestation, we found that bacterial communities in plots with ash differed from those without ash. These differences were largely driven by Acidobacteria, which had a greater relative abundance in non-ash plots. Functional genes required for sulfur cycling, phosphorus cycling, and carbohydrate metabolism (specifically those which breakdown complex sugars to glucose were estimated to be more abundant in non-ash plots, while nitrogen cycling gene abundance did not differ. This ash-soil microbiome association implies that EAB-induced ash decline may promote belowground successional shifts, altering carbon and nutrient cycling and changing soil properties beyond the effects of litter additions caused by ash mortality.

  6. Temporal changes in the diazotrophic bacterial communities associated with Caribbean sponges Ircinia stroblina and Mycale laxissima

    Directory of Open Access Journals (Sweden)

    Fan eZhang

    2014-10-01

    Full Text Available Sponges that harbor microalgal or cyanobacterial symbionts may benefit from photosynthetically derived carbohydrates, which are rich in carbon but devoid of nitrogen, and may therefore encounter nitrogen limitation. Diazotrophic communities associated with two Caribbean sponges, Ircinia strobilina and Mycale laxissima were studied in a time series during which three individuals of each sponge were collected in four time points (5:00 AM, 12:00 noon, 5:00 PM, 10:00 PM. nifH genes were successfully amplified from the corresponding gDNA and cDNA pools and sequenced by high throughput 454 amplicon sequencing. In both sponges, over half the nifH transcripts were classified as from cyanobacteria and the remainder from heterotrophic bacteria. We found various groups of bacteria actively expressing the nifH gene during the entire day-night cycle, an indication that the nitrogen fixation potential was fully exploited by different nitrogen fixing bacteria groups associated with their hosts. This study showed for the first time the dynamic changes in the activity of the diazotrophic bacterial communities in marine sponges. Our study expands understanding of the diazotrophic groups that contribute to the fixed nitrogen pool in the benthic community. Sponge bacterial community-associated diazotrophy may have an important impact on the nitrogen biogeochemical cycle in the coral reef ecosystem.

  7. Population structure of the bacterial pathogen Xylella fastidiosa among street trees in Washington D.C.

    Directory of Open Access Journals (Sweden)

    Jordan Lee Harris

    Full Text Available Bacterial leaf scorch, associated with the bacterial pathogen Xylella fastidiosa, is a widely established and problematic disease of landscape ornamentals in Washington D.C. A multi-locus sequence typing analysis was performed using 10 housekeeping loci for X. fastidiosa strains in order to better understand the epidemiology of leaf scorch disease in this municipal environment. Samples were collected from 7 different tree species located throughout the District of Columbia, consisting of 101 samples of symptomatic and asymptomatic foliage from 84 different trees. Five strains of the bacteria were identified. Consistent with prior data, these strains were host specific, with only one strain associated with members of the red oak family, one strain associated with American elm, one strain associated with American sycamore, and two strains associated with mulberry. Strains found for asymptomatic foliage were the same as strains from the symptomatic foliage on individual trees. Cross transmission of the strains was not observed at sites with multiple species of infected trees within an approx. 25 m radius of one another. X. fastidiosa strain specificity observed for each genus of tree suggests a highly specialized host-pathogen relationship.

  8. Saltwater intrusion history shapes the response of bacterial communities upon rehydration.

    Science.gov (United States)

    Nelson, Tiffanie M; Streten, Claire; Gibb, Karen S; Chariton, Anthony A

    2015-01-01

    Saltwater intrusion (SWI) can result in the loss of dominant vegetation from freshwater habitats. In northern Australia, sea level is predicted to rise 17-50 cm by 2030-2070. This will exacerbate the impact of SWI, threatening Ramsar-listed habitats. Soil bacteria in these habitats play a significant role in biogeochemical cycling, regulating availability of essential nutrients such as nitrogen to vegetation. However, there is limited understanding as to how SWI will impact these soil bacteria. Floodplain soil samples were collected from the South Alligator River floodplain in Northern Australia from sites with contrasting histories of SWI. A SWI event was simulated over 7 days with treatments of saltwater and freshwater. Bacterial community composition before and after treatment were measured using next generation sequencing of bacterial DNA. Sites with no history of SWI showed no significant changes in community taxonomic composition following treatments, suggesting the community at these sites have broad functional capacity which may be due to their historic conditioning over many years. Sites with a history of SWI showed a significant response to both treatments. Following saltwater treatment, there was an increase in sulfate-reducing bacteria, which are known to have an impact on carbon and nitrogen cycling. We suggest that the impact of SWI causes a shift in the soil bacteria which alters the community to one which is more specialised, with implications for the cycling of essential elements and nutrients. Copyright © 2014 Elsevier B.V. All rights reserved.

  9. Seasonal Variability of Airborne Particulate Matter and Bacterial Concentrations in Colorado Homes

    Directory of Open Access Journals (Sweden)

    Nicholas Clements

    2018-04-01

    Full Text Available Aerosol measurements were collected at fifteen homes over the course of one year in Colorado (USA to understand the temporal variability of indoor air particulate matter and bacterial concentrations and their relationship with home characteristics, inhabitant activities, and outdoor air particulate matter (PM. Indoor and outdoor PM2.5 concentrations averaged (±st. dev. 8.1 ± 8.1 μg/m3 and 6.8 ± 4.5 μg/m3, respectively. Indoor PM2.5 was statistically significantly higher during summer compared to spring and winter; outdoor PM2.5 was significantly higher for summer compared to spring and fall. The PM2.5 I/O ratio was 1.6 ± 2.4 averaged across all homes and seasons and was not statistically significantly different across the seasons. Average indoor PM10 was 15.4 ± 18.3 μg/m3 and was significantly higher during summer compared to all other seasons. Total suspended particulate bacterial biomass, as determined by qPCR, revealed very little seasonal differences across and within the homes. The qPCR I/O ratio was statistically different across seasons, with the highest I/O ratio in the spring and lowest in the summer. Using one-minute indoor PM10 data and activity logs, it was observed that elevated particulate concentrations commonly occurred when inhabitants were cooking and during periods with elevated outdoor concentrations.

  10. Population structure of the bacterial pathogen Xylella fastidiosa among street trees in Washington D.C.

    Science.gov (United States)

    Harris, Jordan Lee; Balci, Yilmaz

    2015-01-01

    Bacterial leaf scorch, associated with the bacterial pathogen Xylella fastidiosa, is a widely established and problematic disease of landscape ornamentals in Washington D.C. A multi-locus sequence typing analysis was performed using 10 housekeeping loci for X. fastidiosa strains in order to better understand the epidemiology of leaf scorch disease in this municipal environment. Samples were collected from 7 different tree species located throughout the District of Columbia, consisting of 101 samples of symptomatic and asymptomatic foliage from 84 different trees. Five strains of the bacteria were identified. Consistent with prior data, these strains were host specific, with only one strain associated with members of the red oak family, one strain associated with American elm, one strain associated with American sycamore, and two strains associated with mulberry. Strains found for asymptomatic foliage were the same as strains from the symptomatic foliage on individual trees. Cross transmission of the strains was not observed at sites with multiple species of infected trees within an approx. 25 m radius of one another. X. fastidiosa strain specificity observed for each genus of tree suggests a highly specialized host-pathogen relationship.

  11. Herpesviral-bacterial coinfection in periapical pathosis.

    Science.gov (United States)

    Sabeti, Mohammad; Slots, Jørgen

    2004-02-01

    Two members of the herpesvirus family, human cytomegalovirus (HCMV) and Epstein-Barr virus (EBV), seem to be important putative pathogens of human periodontitis and symptomatic periapical lesions, causing pathosis either by inducing immunosuppression with a subsequent risk of aggressive bacterial infections or by infecting of periodontal cells directly. This study aimed to relate periapical occurrence of HCMV, EBV, and herpes simplex virus active infections to clinical characteristics of periapical lesions and periapical bacterial flora. Microbial samples were collected from 34 periapical lesions in conjunction with periapical surgery. Part of the periapical specimen was frozen for virologic examination, and another part was transferred to anaerobic transport medium for bacteriologic examination. RNA was isolated by means of a guanidinium isothiocyanate-acid phenol procedure, and cDNA was produced using herpesvirus-specific primers and reverse-transcription polymerase chain reaction amplification. Bacteriologic examination was performed according to established anaerobic culture methods. Of the 34 periapical lesions studied, 20 showed both HCMV and EBV, seven showed only HCMV, one showed only EBV, and six showed neither HCMV nor EBV. Herpes simplex virus was detected in two lesions. Higher occurrence of herpesvirus was detected in large versus small periapical lesions (p aggressive types of periapical pathosis in humans.

  12. Bacterial communities in petroleum oil in stockpiles.

    Science.gov (United States)

    Yoshida, Nobuyuki; Yagi, Kazuhiro; Sato, Daisuke; Watanabe, Noriko; Kuroishi, Takeshi; Nishimoto, Kana; Yanagida, Akira; Katsuragi, Tohoru; Kanagawa, Takahiro; Kurane, Ryuichiro; Tani, Yoshiki

    2005-02-01

    Bacterial communities in crude-oil samples from Japanese oil stockpiles were investigated by 16S rRNA gene cloning, followed by denaturing gradient gel electrophoresis (DGGE) analysis. 16S rRNA genes were successfully amplified by PCR after isooctane treatment from three kinds of crude-oil sample collected at four oil stockpiles in Japan. DGGE profiles showed that bacteria related to Ochrobactrum anthropi, Burkholderia cepacia, Stenotrophomonas maltophilia, Propionibacterium acnes, and Brevundimonas diminuta were frequently detected in most crude-oil samples. The bacterial communities differed in the sampling time and layer. Among the predominant bacteria detected in the crude oil, only three species were found for bacteria isolated on agar plates and were related to Burkholderia, Stenotrophomonas, and Propionibacterium, while Ochrobactrum sp. could not be isolated although this species seemed to be the most abundant bacterium in crude oil from the DGGE profiles. Using an archaea-specific primer set, methanogens were found in crude-oil sludge but not in crude-oil samples, indicating that methanogens might be involved in sludge formation in oil stockpiles.

  13. Bacterial diversity of symptomatic primary endodontic infection by clonal analysis

    Directory of Open Access Journals (Sweden)

    Letícia Maria Menezes NÓBREGA

    Full Text Available Abstract The aim of this study was to explore the bacterial diversity of 10 root canals with acute apical abscess using clonal analysis. Samples were collected from 10 patients and submitted to bacterial DNA isolation, 16S rRNA gene amplification, cloning, and sequencing. A bacterial genomic library was constructed and bacterial diversity was estimated. The mean number of taxa per canal was 15, ranging from 11 to 21. A total of 689 clones were analyzed and 76 phylotypes identified, of which 47 (61.84% were different species and 29 (38.15% were taxa reported as yet-uncultivable or as yet-uncharacterized species. Prevotella spp., Fusobacterium nucleatum, Filifactor alocis, and Peptostreptococcus stomatis were the most frequently detected species, followed by Dialister invisus, Phocaeicola abscessus, the uncharacterized Lachnospiraceae oral clone, Porphyromonas spp., and Parvimonas micra. Eight phyla were detected and the most frequently identified taxa belonged to the phylum Firmicutes (43.5%, followed by Bacteroidetes (22.5% and Proteobacteria (13.2%. No species was detected in all studied samples and some species were identified in only one case. It was concluded that acute primary endodontic infection is characterized by wide bacterial diversity and a high intersubject variability was observed. Anaerobic Gram-negative bacteria belonging to the phylum Firmicutes, followed by Bacteroidetes, were the most frequently detected microorganisms.

  14. Understanding place brands as collective and territorial development processes

    NARCIS (Netherlands)

    Donner, M.I.M.

    2016-01-01

    Place branding strategies linking marketing to places have received increasing attention in practice and theory in the past two decades. It is generally assumed that place branding contributes to the economic, social, political and cultural development of cities, regions and countries. But there

  15. Understanding place brands as collective and territorial development processes

    NARCIS (Netherlands)

    Donner, M.I.M.

    2016-01-01

    Place branding strategies linking marketing to places have received increasing attention in practice and theory in the past two decades. It is generally assumed that place branding contributes to the economic, social, political and cultural development of cities, regions and countries. But there

  16. Understanding the Structure of Large, Diverse Collections of Shapes

    Science.gov (United States)

    2013-06-01

    Scaringella, G. Zoia, and D. Mlynek. Automatic genre classification of music content: a survey. Signal Processing Magazine, IEEE, 23(2):133 –141...Hoffman, David M. Blei, and Perry R. Cook. Content-based musical sim- ilarity computation using the hierarchical dirichlet process. In Juan Pablo...Bello, Elaine Chew, and Douglas Turnbull, editors, ISMIR 2008, 9th International Con- ference on Music Information Retrieval, Drexel University

  17. Cell cycle regulation by the bacterial nucleoid.

    Science.gov (United States)

    Adams, David William; Wu, Ling Juan; Errington, Jeff

    2014-12-01

    Division site selection presents a fundamental challenge to all organisms. Bacterial cells are small and the chromosome (nucleoid) often fills most of the cell volume. Thus, in order to maximise fitness and avoid damaging the genetic material, cell division must be tightly co-ordinated with chromosome replication and segregation. To achieve this, bacteria employ a number of different mechanisms to regulate division site selection. One such mechanism, termed nucleoid occlusion, allows the nucleoid to protect itself by acting as a template for nucleoid occlusion factors, which prevent Z-ring assembly over the DNA. These factors are sequence-specific DNA-binding proteins that exploit the precise organisation of the nucleoid, allowing them to act as both spatial and temporal regulators of bacterial cell division. The identification of proteins responsible for this process has provided a molecular understanding of nucleoid occlusion but it has also prompted the realisation that substantial levels of redundancy exist between the diverse systems that bacteria employ to ensure that division occurs in the right place, at the right time.

  18. Bacterial Enzymes and Antibiotic Resistance- Oral Presentation

    Energy Technology Data Exchange (ETDEWEB)

    Maltz, Lauren [SLAC National Accelerator Lab., Menlo Park, CA (United States)

    2015-08-25

    By using protein crystallography and X-ray diffraction, structures of bacterial enzymes were solved to gain a better understanding of how enzymatic modification acts as an antibacterial resistance mechanism. Aminoglycoside phosphotransferases (APHs) are one of three aminoglycoside modifying enzymes that confer resistance to the aminoglycoside antibiotics via enzymatic modification, rendering many drugs obsolete. Specifically, the APH(2”) family vary in their substrate specificities and also in their preference for the phosphate donor (ADP versus GDP). By solving the structures of members of the APH(2”) family of enzymes, we can see how domain movements are important to their substrate specificity. Our structure of the ternary complex of APH(2”)-IIIa with GDP and kanamycin, when compared to the known structures of APH(2”)-IVa, reveals that there are real physical differences between these two enzymes, a structural finding that explains why the two enzymes differ in their preferences for certain aminoglycosides. Another important group of bacterial resistance enzymes are the Class D β-lactamases. Oxacillinase carbapenemases (OXAs) are part of this enzyme class and have begun to confer resistance to ‘last resort’ drugs, most notably carbapenems. Our structure of OXA-143 shows that the conformational flexibility of a conserved hydrophobic residue in the active site (Val130) serves to control the entry of a transient water molecule responsible for a key step in the enzyme’s mechanism. Our results provide insight into the structural mechanisms of these two different enzymes.

  19. Use of adjunctive topical corticosteroids in bacterial keratitis.

    Science.gov (United States)

    Ni, Nina; Srinivasan, Muthiah; McLeod, Stephen D; Acharya, Nisha R; Lietman, Thomas M; Rose-Nussbaumer, Jennifer

    2016-07-01

    Topical corticosteroid use in the setting of infectious keratitis has been a controversial issue. The aim of this review is to provide an update on the evidence for use of topical corticosteroids in addition to antibiotics in bacterial keratitis. Judicious use of steroids is postulated to limit the inflammatory component of bacterial keratitis, but can theoretically retard healing. Three small randomized controlled trials and one large-scale trial, the Steroids for Corneal Ulcers Trial, have provided the most recent evidence to address this debate. Adjunctive topical corticosteroids initiated after at least 48 h of antibiotic usage in cases of culture-proven bacterial keratitis appear generally safe in the treatment of bacterial keratitis. They may be beneficial in cases of severe ulcers especially when initiated early in the course of the infection, in non-Nocardia ulcers, and in certain Pseudomonas ulcers. Several randomized controlled trials have greatly contributed to our understanding of the controversy over steroid use in the management of bacterial keratitis. Future studies are needed to confirm subgroup analysis findings and define optimal timing, dosage, and the most appropriate treatment populations.

  20. Bacterial Communities Associated with the Lichen Symbiosis▿ †

    Science.gov (United States)

    Bates, Scott T.; Cropsey, Garrett W. G.; Caporaso, J. Gregory; Knight, Rob; Fierer, Noah

    2011-01-01

    Lichens are commonly described as a mutualistic symbiosis between fungi and “algae” (Chlorophyta or Cyanobacteria); however, they also have internal bacterial communities. Recent research suggests that lichen-associated microbes are an integral component of lichen thalli and that the classical view of this symbiotic relationship should be expanded to include bacteria. However, we still have a limited understanding of the phylogenetic structure of these communities and their variability across lichen species. To address these knowledge gaps, we used bar-coded pyrosequencing to survey the bacterial communities associated with lichens. Bacterial sequences obtained from four lichen species at multiple locations on rock outcrops suggested that each lichen species harbored a distinct community and that all communities were dominated by Alphaproteobacteria. Across all samples, we recovered numerous bacterial phylotypes that were closely related to sequences isolated from lichens in prior investigations, including those from a lichen-associated Rhizobiales lineage (LAR1; putative N2 fixers). LAR1-related phylotypes were relatively abundant and were found in all four lichen species, and many sequences closely related to other known N2 fixers (e.g., Azospirillum, Bradyrhizobium, and Frankia) were recovered. Our findings confirm the presence of highly structured bacterial communities within lichens and provide additional evidence that these bacteria may serve distinct functional roles within lichen symbioses. PMID:21169444

  1. Bacterial computing with engineered populations.

    Science.gov (United States)

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

    2015-07-28

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

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

    KAUST Repository

    El Chakhtoura, Joline

    2015-05-01

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

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

    Science.gov (United States)

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

    2015-05-01

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

  4. Ceftaroline Fosamil for the Treatment of Staphylococcus aureus Bacteremia Secondary to Acute Bacterial Skin and Skin Structure Infections or Community-Acquired Bacterial Pneumonia

    OpenAIRE

    Vazquez, Jose A.; Maggiore, Christy R.; Cole, Phillip; Smith, Alexander; Jandourek, Alena; Friedland, H. David

    2014-01-01

    Background The Clinical Assessment Program and Teflaro? Utilization Registry is designed to collect information on the clinical use of ceftaroline fosamil in the Unites States. This report presents data on the treatment of patients with Staphylococcus aureus bacteremia (SAB) secondary to acute bacterial skin and skin structure infections (ABSSSIs) or community-acquired bacterial pneumonia (CABP). Methods Patients diagnosed with ABSSSI or CABP were identified through sequential review of rando...

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

    Directory of Open Access Journals (Sweden)

    Wataru Yamanaka

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

  6. Shellfish as reservoirs of bacterial pathogens

    Directory of Open Access Journals (Sweden)

    Harry Hariharan

    2016-04-01

    Full Text Available The objective of this article is to present an overview on bacterial pathogens associated with shellfish in Grenada and other countries including the authors’ experience. Although there have been considerable published work on vibrios, there is a lack of information on Salmonella serovars associated with various shellfish. In Grenada, for instance the blue land crabs collected from their habitats were found to harbor several Salmonella serovars. Also, it is notable that only minimal research has been done on shellfish such as conchs and whelks, which are common in the Caribbean and West Indies. Information on anaerobic bacteria, particularly, non-spore forming bacteria associated with shellfish, in general, is also scanty. This review re-examines this globally important topic based on the recent findings as well as past observations. Strategies for reduction of bacteria in oysters are briefly mentioned because of the fact that oysters are consumed commonly without complete cooking.

  7. BACTERIOLOGY AND RISK FACTORS OF BACTERIAL KERATITIS IN JIMMA, SOUTHWEST ETHIOPIA.

    Science.gov (United States)

    Gebremariam, Tewelde Tesfaye

    2015-10-01

    In East Africa, particularly in Ethiopia, bacterial keratitis is a major cause of blindness. The aims of this study were to identify risk factors of bacterial keratitis and the spectrum of bacterial etiologies, and to assess the in-vitro antimicrobial susceptibility of these bacterial isolates at Jimma University Specialized Hospital, Southwest Ethiopia. A prospective study was employed from January 2012 to June 2012 from which a total of 24 patients with bacterial keratitis were included in the study. Corneal scrapings were collected, transported and microbiologically processed using standard operating procedures. Four different predisposing factors for bacterial keratitis were identified: corneal trauma 9 (37.5%), blepharitis 7 (29.2%), herpetic keratitis, and use of contaminated medications 4. Bilateral corneal infection was found in 5 (20.8%) of the cases. A total of 24 corneal scrapings were collected for microbiological evaluation, of which 20 (83%) had bacterial growth. The isolated bacterial pathogens were Pseudomonas aeruginosa 10 (41.7%), Staphyloccus aureus 5 (20.8%), Serratia marcescens 3 (12.5%), followed by Streptococcus pneumoniae 2 (8.3%). Antimicrobial susceptibility testing revealed that 85% of Gram-negative bacilli were susceptible to gentamicin and ciprofloxacin, while 86% of Gram-positive cocci were susceptible to vancomycin and Ciprofloxacin. Corneal trauma was the most common risk factor for bacterial keratitis followed by blepharitis. Bacteriological analysis of corneal scrapings also revealed that P. aeruginosa was the most common isolate followed by S. aureus; the antibiotic with the highest susceptibility was ciprofloxacin. As drug resistance among bacterial pathogens is an evolving process, routine surveillance and monitoring studies should be conducted to provide an update and most effective empirical treatment for bacterial keratitis.

  8. Bacterial systems for production of heterologous proteins.

    Science.gov (United States)

    Zerbs, Sarah; Frank, Ashley M; Collart, Frank R

    2009-01-01

    Proteins are the working molecules of all biological systems and participate in a majority of cellular chemical reactions and biological processes. Knowledge of the properties and function of these molecules is central to an understanding of chemical and biological processes. In this context, purified proteins are a starting point for biophysical and biochemical characterization methods that can assist in the elucidation of function. The challenge for production of proteins at the scale and quality required for experimental, therapeutic and commercial applications has led to the development of a diverse set of methods for heterologous protein production. Bacterial expression systems are commonly used for protein production as these systems provide an economical route for protein production and require minimal technical expertise to establish a laboratory protein production system.

  9. The physical basis of bacterial quorum communication

    CERN Document Server

    2015-01-01

    This book aims to educate physical scientists and quantitatively-oriented biologists on the application of physical experimentation and analysis, together with appropriate modeling, to understanding and interpreting microbial chemical communication and especially quorum sensing (QS). Quorum sensing describes a chemical communication behavior that is nearly universal among bacteria. Individual cells release a diffusible small molecule (an autoinducer) into their environment. A high concentration of this autoinducer serves as a signal of high population density, triggering new patterns of gene expression throughout the population. However QS is often much more complex than simple census-taking. Many QS bacteria produce and detect multiple autoinducers, which generate quorum signal cross talk with each other and with other bacterial species. QS gene regulatory networks operate in physically complex environments and respond to a range of inputs in addition to autoinducer signals. While many individual QS systems ...

  10. Empiric Antibiotic Therapy of Nosocomial Bacterial Infections.

    Science.gov (United States)

    Reddy, Pramod

    2016-01-01

    Broad-spectrum antibiotics are commonly used by physicians to treat various infections. The source of infection and causative organisms are not always apparent during the initial evaluation of the patient, and antibiotics are often given empirically to patients with suspected sepsis. Fear of attempting cephalosporins and carbapenems in penicillin-allergic septic patients may result in significant decrease in the spectrum of antimicrobial coverage. Empiric antibiotic therapy should sufficiently cover all the suspected pathogens, guided by the bacteriologic susceptibilities of the medical center. It is important to understand the major pharmacokinetic properties of antibacterial agents for proper use and to minimize the development of resistance. In several septic patients, negative cultures do not exclude active infection and positive cultures may not represent the actual infection. This article will review the important differences in the spectrum of commonly used antibiotics for nosocomial bacterial infections with a particular emphasis on culture-negative sepsis and colonization.

  11. Polarimetric imagery collection experiment

    Science.gov (United States)

    Romano, Joao M.; Felton, Melvin; Chenault, David; Sohr, Brian

    2010-04-01

    The Spectral and Polarimetric Imagery Collection Experiment (SPICE) is a collaborative effort between the US Army ARDEC and ARL that is focused on the collection of mid-wave and long-wave infrared imagery using hyperspectral, polarimetric, and broadband sensors. The objective of the program is to collect a comprehensive database of the different modalities over the course of 1 to 2 years to capture sensor performance over a wide variety of weather conditions, diurnal, and seasonal changes inherent to Picatinny's northern New Jersey location. Using the Precision Armament Laboratory (PAL) tower at Picatinny Arsenal, the sensors will autonomously collect the desired data around the clock at different ranges where surrogate 2S3 Self-Propelled Howitzer targets are positioned at different viewing perspectives in an open field. The database will allow for: 1) Understanding of signature variability under adverse weather conditions; 2) Development of robust algorithms; 3) Development of new sensors; 4) Evaluation of polarimetric technology; and 5) Evaluation of fusing the different sensor modalities. In this paper, we will present the SPICE data collection objectives, the ongoing effort, the sensors that are currently deployed, and how this work will assist researches on the development and evaluation of sensors, algorithms, and fusion applications.

  12. Collective Success or Collective Failure?

    DEFF Research Database (Denmark)

    Fayyaz, Anjum

    In this article, I make a contribution to the literature on how industrial clusters in developing countries respond to corporate responsibility demands from international buyers in Europe and North America. I outline an analytical framework that integrates insights from the global value chain, in...... of innovation, and government failure - can partly explain why Sialkot has been marginalized in terms of its overall share of world football manufacturing in the last decade....... study of soccer village project to learn how various attempts at facilitating joint CSR action in the Pakistani football manufacturing have consistently failed in addressing international CSR compliance demands. I conclude that this form of collective failure – along with technological changes, lack...

  13. Biotechnological applications of bacterial cellulases

    Czech Academy of Sciences Publication Activity Database

    Menéndez, E.; García-Fraile, Paula; Rivas, R.

    2015-01-01

    Roč. 2, č. 3 (2015), s. 163-182 ISSN 2306-5354 R&D Projects: GA MŠk(CZ) EE2.3.30.0003 Institutional support: RVO:61388971 Keywords : Biotechnological applications * Bacterial cellulases * Cellulose degradation Subject RIV: EE - Microbiology, Virology

  14. Disease notes - Bacterial root rot

    Science.gov (United States)

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

  15. Metagenomic Diagnosis of Bacterial Infections

    Science.gov (United States)

    Nakamura, Shota; Maeda, Norihiro; Miron, Ionut Mihai; Yoh, Myonsun; Izutsu, Kaori; Kataoka, Chidoh; Honda, Takeshi; Yasunaga, Teruo; Nakaya, Takaaki; Kawai, Jun; Hayashizaki, Yoshihide; Horii, Toshihiro

    2008-01-01

    To test the ability of high-throughput DNA sequencing to detect bacterial pathogens, we used it on DNA from a patient’s feces during and after diarrheal illness. Sequences showing best matches for Campylobacter jejuni were detected only in the illness sample. Various bacteria may be detectable with this metagenomic approach. PMID:18976571

  16. Community-acquired bacterial meningitis

    NARCIS (Netherlands)

    van de Beek, Diederik; Brouwer, Matthijs; Hasbun, Rodrigo; Koedel, Uwe; Whitney, Cynthia G.; Wijdicks, Eelco

    2016-01-01

    Meningitis is an inflammation of the meninges and subarachnoid space that can also involve the brain cortex and parenchyma. It can be acquired spontaneously in the community - community-acquired bacterial meningitis - or in the hospital as a complication of invasive procedures or head trauma

  17. Molecular mechanisms underlying bacterial persisters

    DEFF Research Database (Denmark)

    Maisonneuve, Etienne; Gerdes, Kenn

    2014-01-01

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

  18. Biotechnological applications of bacterial cellulases

    Directory of Open Access Journals (Sweden)

    Esther Menendez

    2015-08-01

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

  19. Rumen bacterial community evaluated by 454 pyrosequencing and terminal restriction fragment length polymorphism analyses in dairy sheep fed marine algae.

    Science.gov (United States)

    Castro-Carrera, T; Toral, P G; Frutos, P; McEwan, N R; Hervás, G; Abecia, L; Pinloche, E; Girdwood, S E; Belenguer, A

    2014-03-01

    Developing novel strategies to increase the content of bioactive unsaturated fatty acids (FA) in ruminant-derived products requires a deeper understanding of rumen biohydrogenation and bacteria involved in this process. Although high-throughput pyrosequencing may allow for a great coverage of bacterial diversity, it has hardly been used to investigate the microbiology of ruminal FA metabolism. In this experiment, 454 pyrosequencing and a molecular fingerprinting technique (terminal restriction fragment length polymorphism; T-RFLP) were used concurrently to assess the effect of diet supplementation with marine algae (MA) on the rumen bacterial community of dairy sheep. Eleven lactating ewes were divided in 2 lots and offered a total mixed ration based on alfalfa hay and concentrate (40:60), supplemented with 0 (control) or 8 (MA) g of MA/kg of dry matter. After 54 d on treatments, animals were slaughtered and samples of rumen content and fluid were collected separately for microbial analysis. Pyrosequencing yielded a greater coverage of bacterial diversity than T-RFLP and allowed the identification of low abundant populations. Conversely, both molecular approaches pointed to similar conclusions and showed that relevant changes due to MA addition were observed within the major ruminal phyla, namely Bacteroidetes, Firmicutes, and Proteobacteria. Decreases in the abundance of unclassified Bacteroidales, Porphyromonadaceae, and Ruminococcaceae and increases in as-yet uncultured species of the family Succinivibrionaceae, might be related to a potential role of these groups in different pathways of rumen FA metabolism. Diet supplementation with MA, however, had no effect on the relative abundance of Butyrivibrio and Pseudobutyrivibrio genera. In addition, results from both 454 pyrosequencing and T-RFLP indicate that the effect of MA was rather consistent in rumen content or fluid samples, despite inherent differences between these fractions in their bacterial composition

  20. Antibiotic treatment delay and outcome in acute bacterial meningitis

    DEFF Research Database (Denmark)

    Køster-Rasmussen, Rasmus; Korshin, André; Meyer, Christian N

    2008-01-01

    OBJECTIVES: To identify to what degree in-hospital delay of antibiotic therapy correlated to outcome in community acquired bacterial meningitis. METHODS: All cases of culture-positive cerebrospinal fluids in east Denmark from 2002 to 2004 were included. Medical records were collected retrospectiv......OBJECTIVES: To identify to what degree in-hospital delay of antibiotic therapy correlated to outcome in community acquired bacterial meningitis. METHODS: All cases of culture-positive cerebrospinal fluids in east Denmark from 2002 to 2004 were included. Medical records were collected......=1.30/h, CI: 1.08-1.57). The median delay to the first dose of adequate antibiotics was 1h and 39min (1h and 14min in children vs. 2h in adults, pmeningitis. CONCLUSION: The delay in antibiotic therapy correlated...

  1. Enhanced mixing and spatial instability in concentrated bacterial suspensions.

    Energy Technology Data Exchange (ETDEWEB)

    Sokolov, A.; Goldstein, R. E.; Feldchtein, F. I.; Aranson, I. S.; Materials Science Division; Illinois Inst. of Tech.; Univ. of Cambridge; Imalux Corp.

    2009-09-01

    High-resolution optical coherence tomography is used to study the onset of a large-scale convective motion in free-standing thin films of adjustable thickness containing suspensions of swimming aerobic bacteria. Clear evidence is found that beyond a threshold film thickness there exists a transition from quasi-two-dimensional collective swimming to three-dimensional turbulent behavior. The latter state, qualitatively different from bioconvection in dilute bacterial suspensions, is characterized by enhanced diffusivities of oxygen and bacteria. These results emphasize the impact of self-organized bacterial locomotion on the onset of three-dimensional dynamics, and suggest key ingredients necessary to extend standard models of bioconvection to incorporate effects of large-scale collective motion.

  2. RNA–Stable-Isotope Probing Shows Utilization of Carbon from Inulin by Specific Bacterial Populations in the Rat Large Bowel

    Science.gov (United States)

    Lawley, Blair; Munro, Karen; Sims, Ian M.; Lee, Julian; Butts, Christine A.; Roy, Nicole

    2014-01-01

    Knowledge of the trophisms that underpin bowel microbiota composition is required in order to understand its complex phylogeny and function. Stable-isotope (13C)-labeled inulin was added to the diet of rats on a single occasion in order to detect utilization of inulin-derived substrates by particular members of the cecal microbiota. Cecal digesta from Fibruline-inulin-fed rats was collected prior to (0 h) and at 6, 12, 18 and 24 h following provision of the [13C]inulin diet. RNA was extracted from these cecal specimens and fractionated in isopycnic buoyant density gradients in order to detect 13C-labeled nucleic acid originating in bacterial cells that had metabolized the labeled dietary constituent. RNA extracted from specimens collected after provision of the labeled diet was more dense than 0-h RNA. Sequencing of 16S rRNA genes amplified from cDNA obtained from these fractions showed that Bacteroides uniformis, Blautia glucerasea, Clostridium indolis, and Bifidobacterium animalis were the main users of the 13C-labeled substrate. Culture-based studies of strains of these bacterial species enabled trophisms associated with inulin and its hydrolysis products to be identified. B. uniformis utilized Fibruline-inulin for growth, whereas the other species used fructo-oligosaccharide and monosaccharides. Thus, RNA–stable-isotope probing (RNA-SIP) provided new information about the use of carbon from inulin in microbiota metabolism. PMID:24487527

  3. Scholars in International Relations Cite Books More Frequently than Journals: More Research is Needed to Better Understand Research Behaviour and Use. A Review of: Zhang, Li. ʺCitation Analysis for Collection Development: A Study of International Relations Journal Literature.ʺ Library Collections, Acquisitions, and Technical Services 31.3‐4 (2007: 195‐207.

    Directory of Open Access Journals (Sweden)

    Megan von Isenburg

    2009-09-01

    representing quantitative research were randomly selected from each of the three journals for each of the six years. Subsequently, five citations from each of the resulting pool of 72 articles were randomly selected to create a sample of 360 citations. These citations were analyzed by material type and age of source.Main Results – Analysis of the citation data showed that books (including monographs, edited books, book chapters and dictionaries made up 48.2% of the total citations; journals (including scholarly and non‐scholarly titles made up 38.4% of the citations; and government publications made up 4.5% of the citations. Electronic resources, which primarily refer to Web sites and digital collections in this study, represented 1.7% of the citations. Other sources of citations included magazines (1.1%, newspapers (1.1%, working papers (1.1%, theses (0.9%, conference papers not yet published as articles (0.6%, and a miscellaneous category, which included items such as committee minutes, radio broadcasts, unpublished materials and personal communications (2.5%. The average age of book citations was 14.3 years and the median age was 8 years. Foreign language citations represented 3.7% of the 651 total citations. The top ranked foreign languages were German (7, French (5, Russian (4, Spanish (3, Korean (2 and Swedish (number not given. Subject analysis of the citations revealed that 38% of all citations were from international relations and two related disciplines, political science, political theory, and public administration. Subject areas outside international relations included social sciences (23.4% ‐ including economics, commerce, industries and finance, history (16.3%, sociology (6.2%, and law (5.9%. Citations from philosophy, psychology, military science and general works together made up 7.3% of the total citations. Citations from science, linguistics, literature, geography and medicine made up less than 2% of the total.Authors of qualitative research articles

  4. Morphology, chemical composition, and bacterial concentration of airborne particulate matter in rabbit farms

    Directory of Open Access Journals (Sweden)

    Elisa Adell

    2012-12-01

    Full Text Available Livestock houses are major sources of airborne particulate matter (PM, which can originate from manure, feed, feathers, skin and bedding and may contain and transport microorganisms. Improved knowledge of particle size, morphology, chemical and microbiological composition of PM in livestock houses can help identify major sources of PM and contribute to the development of appropriate source-specific reduction techniques. In rabbit production systems, however, there is limited information on specific particle characteristics. The objective of this study was to characterise airborne PM in rabbit farms in terms of morphology, chemical compositions and bacterial concentration in different size fractions. Size-fractioned PM was sampled in the air of 2 rabbit farms, 1 for fattening rabbits and 1 for reproductive does, using a virtual cascade impactor, which simultaneously collected total suspended PM (TSP, PM10 and PM2.5 size fractions. Airborne PM samples were examined by light microscopy and scanning electron microscopy combined with energy dispersive X-ray analysis. Representative samples from potential sources of PM were also collected and examined. Additionally, a methodology to extract bacteria from the collected samples of airborne PM was developed to determine the bacterial concentration per PM size fraction. Results showed that airborne PM in rabbit farms is highly complex in particle morphology, especially in size. Broken skin flakes, disintegrated particles from feed or faecal material from mechanical fracture are the main sources of airborne PM in rabbit farms. Major elements found in rabbit airborne PM were S, Ca, Mg, Na and Cl. Bacterial concentrations ranged from 1.7×104 to 1.6×106 colony forming units (CFU/m3 (TSP; from 3.6×103 to 3.0×104 CFU/m3 (PM10; and from 3.1×103 to 1.6×104 CFU/m3 (PM2.5. Our results will improve the knowledge on essential particle characteristics necessary to understand PM’s origin in rabbit farms and

  5. Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species

    Directory of Open Access Journals (Sweden)

    Isabelle Laforest-Lapointe

    2016-08-01

    Full Text Available Background The diversity and composition of the microbial community of tree leaves (the phyllosphere varies among trees and host species and along spatial, temporal, and environmental gradients. Phyllosphere community variation within the canopy of an individual tree exists but the importance of this variation relative to among-tree and among-species variation is poorly understood. Sampling techniques employed for phyllosphere studies include picking leaves from one canopy location to mixing randomly selected leaves from throughout the canopy. In this context, our goal was to characterize the relative importance of intra-individual variation in phyllosphere communities across multiple species, and compare this variation to inter-individual and interspecific variation of phyllosphere epiphytic bacterial communities in a natural temperate forest in Quebec, Canada. Methods We targeted five dominant temperate forest tree species including angiosperms and gymnosperms: Acer saccharum, Acer rubrum, Betula papyrifera, Abies balsamea and Picea glauca. For one randomly selected tree of each species, we sampled microbial communities at six distinct canopy locations: bottom-canopy (1–2 m height, the four cardinal points of mid-canopy (2–4 m height, and the top-canopy (4–6 m height. We also collected bottom-canopy leaves from five additional trees from each species. Results Based on an analysis of bacterial community structure measured via Illumina sequencing of the bacterial 16S gene, we demonstrate that 65% of the intra-individual variation in leaf bacterial community structure could be attributed to the effect of inter-individual and inter-specific differences while the effect of canopy location was not significant. In comparison, host species identity explains 47% of inter-individual and inter-specific variation in leaf bacterial community structure followed by individual identity (32% and canopy location (6%. Discussion Our results suggest that

  6. Bacterial cells with improved tolerance to polyamines

    DEFF Research Database (Denmark)

    2017-01-01

    Provided are bacterial cells genetically modified to improve their tolerance to certain commodity chemicals, such as polyamines, and methods of preparing and using such bacterial cells for production of polyamines and other compounds....

  7. Bacterial cells with improved tolerance to polyols

    DEFF Research Database (Denmark)

    2017-01-01

    The present invention relates to bacterial cells genetically modified to improve their tolerance to certain commodity chemicals, such as diols and other polyols, and to methods of preparing and using such bacterial cells for production of polyols and other compounds....

  8. Adjunctive Corticosteroids in Adults with Bacterial Meningitis

    NARCIS (Netherlands)

    van de Beek, Diederik; de Gans, Jan

    2005-01-01

    Bacterial meningitis is a complex disorder in which neurologic injury is caused, in part, by the causative organism and, in part, by the host's own inflammatory response. In studies of experimental bacterial meningitis, adjuvant treatment with corticosteroids, specifically dexamethasone, has

  9. Endocarditis in adults with bacterial meningitis

    NARCIS (Netherlands)

    Lucas, Marjolein J.; Brouwer, Matthijs C.; van der Ende, Arie; van de Beek, Diederik

    2013-01-01

    Endocarditis may precede or complicate bacterial meningitis, but the incidence and impact of endocarditis in bacterial meningitis are unknown. We assessed the incidence and clinical characteristics of patients with meningitis and endocarditis from a nationwide cohort study of adults with

  10. Dexamethasone in adults with bacterial meningitis

    NARCIS (Netherlands)

    de Gans, Jan; van de Beek, Diederik

    2002-01-01

    Background: Mortality and morbidity rates are high among adults with acute bacterial meningitis, especially those with pneumococcal meningitis. In studies of bacterial meningitis in animals, adjuvant treatment with corticosteroids has beneficial effects. Methods: We conducted a prospective,

  11. Cognitive outcome in adults after bacterial meningitis

    NARCIS (Netherlands)

    Hoogman, Martine; van de Beek, Diederik; Weisfelt, Martijn; de Gans, Jan; Schmand, Ben

    2007-01-01

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

  12. Cognitive outcome in adults after bacterial meningitis.

    NARCIS (Netherlands)

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

    2007-01-01

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

  13. Antimicrobial susceptibility in community-acquired bacterial ...

    African Journals Online (AJOL)

    Objectives: To determine the antimicrobial susceptibility patterns of Streptococcus pneumoniae and Haemophilus influenzae, two bacterial pathogens commonly associated with communityacquired pneumonia. Design: Cross-sectional study. Setting: Bacterial isolates were obtained from adults suspected to have ...

  14. (PCR) in the diagnosis of bacterial infections

    African Journals Online (AJOL)

    ... bacterial infections that can be diagnosed using the technique which include among others; Tuberculosis (TB), whooping cough, brain abscesses and spinal infection, otitis media with effusion, Mycoplasmal pneumonia, endophthalmitis and bacterial meningitis. Keywords: Polymerase chain reaction, Diagnosis, Bacteria, ...

  15. Comparative approach to capture bacterial diversity in coastal waters

    DEFF Research Database (Denmark)

    Na, Hyunsoo; Kim, Ok-Sun; Yoon, Suk-hwan

    2011-01-01

    to investigate the bacterial community structure of coastal seawater collected from the Yellow Sea, Korea. For culture-independent studies, we used the latest model pyrosequencer, Roche/454 Genome Sequencer FLX Titanium. Pyrosequencing captured a total of 52 phyla including 27 candidate divisions from the water...... techniques available in microbial ecology. As different methods yielded different coverage, we suggest choosing the approach after carefully examining the scientific questions being asked....

  16. Bacterial diversity in the oral cavity of ten healthy individuals

    OpenAIRE

    Bik, Elisabeth M.; Long, Clara Davis; Armitage, Gary C.; Loomer, Peter; Emerson, Joanne; Mongodin, Emmanuel F.; Nelson, Karen E.; Gill, Steven R.; Fraser-Liggett, Claire M.; Relman, David A.

    2010-01-01

    The composition of the oral microbiota from 10 individuals with healthy oral tissues was determined using culture-independent techniques. From each individual, 26 specimens, each from different oral sites at a single point in time, were collected and pooled. An eleventh pool was constructed using portions of the subgingival specimens from all 10 individuals. The 16S rRNA gene was amplified using broad-range bacterial primers, and clone libraries from the individual and subgingival pools were ...

  17. The Bacterial Sequential Markov Coalescent.

    Science.gov (United States)

    De Maio, Nicola; Wilson, Daniel J

    2017-05-01

    Bacteria can exchange and acquire new genetic material from other organisms directly and via the environment. This process, known as bacterial recombination, has a strong impact on the evolution of bacteria, for example, leading to the spread of antibiotic resistance across clades and species, and to the avoidance of clonal interference. Recombination hinders phylogenetic and transmission inference because it creates patterns of substitutions (homoplasies) inconsistent with the hypothesis of a single evolutionary tree. Bacterial recombination is typically modeled as statistically akin to gene conversion in eukaryotes, i.e. , using the coalescent with gene conversion (CGC). However, this model can be very computationally demanding as it needs to account for the correlations of evolutionary histories of even distant loci. So, with the increasing popularity of whole genome sequencing, the need has emerged for a faster approach to model and simulate bacterial genome evolution. We present a new model that approximates the coalescent with gene conversion: the bacterial sequential Markov coalescent (BSMC). Our approach is based on a similar idea to the sequential Markov coalescent (SMC)-an approximation of the coalescent with crossover recombination. However, bacterial recombination poses hurdles to a sequential Markov approximation, as it leads to strong correlations and linkage disequilibrium across very distant sites in the genome. Our BSMC overcomes these difficulties, and shows a considerable reduction in computational demand compared to the exact CGC, and very similar patterns in simulated data. We implemented our BSMC model within new simulation software FastSimBac. In addition to the decreased computational demand compared to previous bacterial genome evolution simulators, FastSimBac provides more general options for evolutionary scenarios, allowing population structure with migration, speciation, population size changes, and recombination hotspots. FastSimBac is

  18. Bacterial human virulence genes across diverse habitats as assessed by In silico analysis of environmental metagenomes

    DEFF Research Database (Denmark)

    Søborg, Ditte Andreasen; Hendriksen, Niels B.; Kilian, Mogens

    2016-01-01

    The occurrence and distribution of clinically relevant bacterial virulence genes across natural (non-human) environments is not well understood. We aimed to investigate the occurrence of homologs to bacterial human virulence genes in a variety of ecological niches to better understand the role...... of natural environments in the evolution of bacterial virulence. Twenty four bacterial virulence genes were analyzed in 46 diverse environmental metagenomic datasets, representing various soils, seawater, freshwater, marine sediments, hot springs, the deep-sea, hypersaline mats, microbialites, gutless worms...... and glacial ice. Homologs to 16 bacterial human virulence genes, involved in urinary tract infections, gastrointestinal diseases, skin diseases, and wound and systemic infections, showed global ubiquity. A principal component analysis did not demonstrate clear trends across the metagenomes with respect...

  19. Bacterial communities associated with apical periodontitis and dental implant failure

    Science.gov (United States)

    Dingsdag, Simon; Nelson, Stephen; Coleman, Nicholas V.

    2016-01-01

    Background Previously, we demonstrated that bacteria reside in apparently healed alveolar bone, using culture and Sanger sequencing techniques. Bacteria in apparently healed alveolar bone may have a role in peri-implantitis and dental implant failure. Objective To compare bacterial communities associated with apical periodontitis, those colonising a failed implant and alveolar bone with reference biofilm samples from healthy teeth. Methods and results The study consisted of 196 samples collected from 40 patients undergoing routine dental implant insertion or rehabilitation. The bacterial 16S ribosomal DNA sequences were amplified. Samples yielding sufficient polymerase chain reaction product for further molecular analyses were subjected to terminal restriction fragment length polymorphism (T-RFLP; 31 samples) and next generation DNA sequencing (454 GS FLX Titanium; 8 samples). T-RFLP analysis revealed that the bacterial communities in diseased tissues were more similar to each other (p<0.049) than those from the healthy reference samples. Next generation sequencing detected 13 bacterial phyla and 373 putative bacterial species, revealing an increased abundance of Gram-negative [Prevotella, Fusobacterium (p<0.004), Treponema, Veillonellaceae, TG5 (Synergistetes)] bacteria and a decreased abundance of Gram-positive [(Actinomyces, Corynebacterium (p<0.008)] bacteria in the diseased tissue samples (n=5) relative to reference supragingival healthy samples (n=3). Conclusion Increased abundances of Prevotella, Fusobacterium and TG5 (Synergistetes) were associated with apical periodontitis and a failed implant. A larger sample set is needed to confirm these trends and to better define the processes of bacterial pathogenesis in implant failure and apical periodontitis. The application of combined culture-based, microscopic and molecular technique-based approaches is suggested for future studies. PMID:27834171

  20. Bacterial communities associated with apical periodontitis and dental implant failure

    Directory of Open Access Journals (Sweden)

    Simon Dingsdag

    2016-11-01

    Full Text Available Background: Previously, we demonstrated that bacteria reside in apparently healed alveolar bone, using culture and Sanger sequencing techniques. Bacteria in apparently healed alveolar bone may have a role in peri-implantitis and dental implant failure. Objective: To compare bacterial communities associated with apical periodontitis, those colonising a failed implant and alveolar bone with reference biofilm samples from healthy teeth. Methods and results: The study consisted of 196 samples collected from 40 patients undergoing routine dental implant insertion or rehabilitation. The bacterial 16S ribosomal DNA sequences were amplified. Samples yielding sufficient polymerase chain reaction product for further molecular analyses were subjected to terminal restriction fragment length polymorphism (T-RFLP; 31 samples and next generation DNA sequencing (454 GS FLX Titanium; 8 samples. T-RFLP analysis revealed that the bacterial communities in diseased tissues were more similar to each other (p<0.049 than those from the healthy reference samples. Next generation sequencing detected 13 bacterial phyla and 373 putative bacterial species, revealing an increased abundance of Gram-negative [Prevotella, Fusobacterium (p<0.004, Treponema, Veillonellaceae, TG5 (Synergistetes] bacteria and a decreased abundance of Gram-positive [(Actinomyces, Corynebacterium (p<0.008] bacteria in the diseased tissue samples (n=5 relative to reference supragingival healthy samples (n=3. Conclusion: Increased abundances of Prevotella, Fusobacterium and TG5 (Synergistetes were associated with apical periodontitis and a failed implant. A larger sample set is needed to confirm these trends and to better define the processes of bacterial pathogenesis in implant failure and apical periodontitis. The application of combined culture-based, microscopic and molecular technique-based approaches is suggested for future studies.

  1. Biosynthesis and structural characterization of silver nanoparticles from bacterial isolates

    Energy Technology Data Exchange (ETDEWEB)

    Zaki, Sahar, E-mail: saharzaki@yahoo.com [Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute, Mubarak City for Scientific Research and Technology Applications, Alexandria, 21934 New Burgelarab City (Egypt); El Kady, M.F. [Fabrication Technology Department, Advanced Technology and New Materials Research Institute (ATNMRI), Mubarak City for Scientific Research and Technology Applications, Alexandria (Egypt); Abd-El-Haleem, Desouky [Environmental Biotechnology Department, Genetic Engineering and Biotechnology Research Institute, Mubarak City for Scientific Research and Technology Applications, Alexandria, 21934 New Burgelarab City (Egypt)

    2011-10-15

    Graphical abstract: In this study five bacterial isolates belong to different genera were found to be able to biosynthesize silver nanoparticles. Biosynthesis and spectral characterization are reported here. Highlights: {yields} About 300 bacterial isolates were screened for their ability to produce nanosilvers {yields} Five of them were potential candidates for synthesis of silver nanoparticles {yields} Production of silver nanoparticles was examined using UV-Vis, XRD, SEM and EDS. {yields} The presence of nanoparticles with all five bacterial isolates was confirmed. -- Abstract: This study aimed to develop a green process for biosynthesis of silver nanomaterials by some Egyptian bacterial isolates. This target was achieved by screening an in-house culture collection consists of 300 bacterial isolates for silver nanoparticle formation. Through screening process, it was observed that strains belonging to Escherichia coli (S30, S78), Bacillus megaterium (S52), Acinetobacter sp. (S7) and Stenotrophomonas maltophilia (S54) were potential candidates for synthesis of silver nanoparticles. The extracellular production of silver nanoparticles by positive isolates was investigated by UV-Vis spectroscopy, X-ray diffraction (XRD), transmission electron microscope (TEM), scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). The results demonstrated that UV-visible spectrum of the aqueous medium containing silver ion showed a peak at 420 nm corresponding to the plasmon absorbance of silver nanoparticles. Scanning electron microscopy micrograph showed formation of silver nanoparticles in the range of 15-50 nm. XRD-spectrum of the silver nanoparticles exhibited 2{theta} values corresponding to the silver nanocrystal that produce in hexagonal and cubic crystal configurations with different plane of orientation. In addition, the signals of the silver atoms were observed by EDS-spectrum analysis that confirms the presence of silver nanoparticles (Ag

  2. Architectural design drives the biogeography of indoor bacterial communities.

    Directory of Open Access Journals (Sweden)

    Steven W Kembel

    Full Text Available BACKGROUND: Architectural design has the potential to influence the microbiology of the built environment, with implications for human health and well-being, but the impact of design on the microbial biogeography of buildings remains poorly understood. In this study we combined microbiological data with information on the function, form, and organization of spaces from a classroom and office building to understand how design choices influence the biogeography of the built environment microbiome. RESULTS: Sequencing of the bacterial 16S gene from dust samples revealed that indoor bacterial communities were extremely diverse, containing more than 32,750 OTUs (operational taxonomic units, 97% sequence similarity cutoff, but most communities were dominated by Proteobacteria, Firmicutes, and Deinococci. Architectural design characteristics related to space type, building arrangement, human use and movement, and ventilation source had a large influence on the structure of bacterial communities. Restrooms contained bacterial communities that were highly distinct from all other rooms, and spaces with high human occupant diversity and a high degree of connectedness to other spaces via ventilation or human movement contained a distinct set of bacterial taxa when compared to spaces with low occupant diversity and low connectedness. Within offices, the source of ventilation air had the greatest effect on bacterial community structure. CONCLUSIONS: Our study indicates that humans have a guiding impact on the microbial biodiversity in buildings, both indirectly through the effects of architectural design on microbial community structure, and more directly through the effects of human occupancy and use patterns on the microbes found in different spaces and space types. The impact of design decisions in structuring the indoor microbiome offers the possibility to use ecological knowledge to shape our buildings in a way that will select for an indoor microbiome

  3. Architectural design drives the biogeography of indoor bacterial communities.

    Science.gov (United States)

    Kembel, Steven W; Meadow, James F; O'Connor, Timothy K; Mhuireach, Gwynne; Northcutt, Dale; Kline, Jeff; Moriyama, Maxwell; Brown, G Z; Bohannan, Brendan J M; Green, Jessica L

    2014-01-01

    Architectural design has the potential to influence the microbiology of the built environment, with implications for human health and well-being, but the impact of design on the microbial biogeography of buildings remains poorly understood. In this study we combined microbiological data with information on the function, form, and organization of spaces from a classroom and office building to understand how design choices influence the biogeography of the built environment microbiome. Sequencing of the bacterial 16S gene from dust samples revealed that indoor bacterial communities were extremely diverse, containing more than 32,750 OTUs (operational taxonomic units, 97% sequence similarity cutoff), but most communities were dominated by Proteobacteria, Firmicutes, and Deinococci. Architectural design characteristics related to space type, building arrangement, human use and movement, and ventilation source had a large influence on the structure of bacterial communities. Restrooms contained bacterial communities that were highly distinct from all other rooms, and spaces with high human occupant diversity and a high degree of connectedness to other spaces via ventilation or human movement contained a distinct set of bacterial taxa when compared to spaces with low occupant diversity and low connectedness. Within offices, the source of ventilation air had the greatest effect on bacterial community structure. Our study indicates that humans have a guiding impact on the microbial biodiversity in buildings, both indirectly through the effects of architectural design on microbial community structure, and more directly through the effects of human occupancy and use patterns on the microbes found in different spaces and space types. The impact of design decisions in structuring the indoor microbiome offers the possibility to use ecological knowledge to shape our buildings in a way that will select for an indoor microbiome that promotes our health and well-being.

  4. Temporal relationships exist between cecum, ileum and litter bacterial microbiomes in a commercial turkey flock, and subtherapeutic penicillin treatment impacts ileum bacterial community establishment

    Directory of Open Access Journals (Sweden)

    Jessica L Danzeisen

    2015-11-01

    Full Text Available Gut health is paramount for commercial poultry production, and improved methods to assess gut health are critically needed to better understand how the avian gastrointestinal tract matures over time. One important aspect of gut health is the totality of bacterial populations inhabiting different sites of the avian gastrointestinal tract, and associations of these populations with the poultry farm environment, since these bacteria are thought to drive metabolism and prime the developing host immune system. In this study, a single flock of commercial turkeys was followed over the course of twelve weeks to examine bacterial microbiome inhabiting the ceca, ileum, and corresponding poultry litter. Furthermore, the effects of low-dose, growth-promoting penicillin treatment (50 g/ton in feed on the ileum bacterial microbiome were also examined during the early brood period. The cecum and ileum bacterial communities of turkeys were distinct, yet shifted in parallel to one another over time during bird maturation. Corresponding poultry litter was also distinct yet more closely represented the ileal bacterial populations than cecal bacterial populations, and also changed parallel to ileum bacterial populations over time. Penicillin applied at low dose in feed significantly enhanced early weight gain in commercial poults, and this correlated with predictable shifts in the ileum bacterial populations in control versus treatment groups. Overall, this study identified the dynamics of the turkey gastrointestinal microbiome during development, correlations between bacterial populations in the gastrointestinal tract and the litter environment, and the impact of low-dose penicillin on modulation of bacterial communities in the ileum. Such modulations provide a target for alternatives to low-dose antibiotics.

  5. Bacterial reproductive pathogens of cats and dogs.

    Science.gov (United States)

    Graham, Elizabeth M; Taylor, David J

    2012-05-01

    With the notable exception of Brucella canis, exogenous bacterial pathogens are uncommon causes of reproductive disease in cats and dogs. Most bacterial reproductive infections are endogenous, and predisposing factors for infection are important. This article reviews the etiology, pathogenesis, clinical presentation, diagnosis, treatment, and public health significance of bacterial reproductive pathogens in cats and dogs.

  6. Characterization of metabolically active bacterial populations in subseafloor Nankai Trough sediments above, within and below the sulfate-methane transition zone

    Directory of Open Access Journals (Sweden)

    Heath J. Mills

    2012-04-01

    Full Text Available A remarkable number of microbial cells have been enumerated within subseafloor sediments, suggesting a biological impact on geochemical processes in the subseafloor habitat. However, the metabolically active fraction of these populations is largely uncharacterized. In this study, an RNA-based molecular approach was used to determine the diversity and community structure of metabolically active bacterial populations in the upper sedimentary formation of the Nankai Trough seismogenic zone. Samples used in this study were collected from the slope apron sediment overlying the accretionary prism at Site C0004 during the Integrated Ocean Drilling Program (IODP Expedition 316. The sediments represented microbial habitats above, within, and below the sulfate-methane transition zone (SMTZ, which was observed approximately 20 meters below the seafloor (mbsf. Small subunit ribosomal RNA (SSU rRNA were extracted, quantified, amplified and sequenced using high-throughput 454-pyrosequencing, indicating the occurrence of metabolically active bacterial populations to a depth of 57 mbsf. Transcript abundance and bacterial diversity decreased with increasing depth. The two communities below the SMTZ were similar at the phylum level, however only a 24% overlap was observed at the genus level. Active bacterial community composition was not confined to geochemically predicted redox stratification despite the deepest sample being more than 50 meters below the oxic/anoxic interface. Genus-level classification suggested that the metabolically active subseafloor bacterial populations had similarities to previously cultured organisms. This allowed predictions of physiological potential, expanding understanding of the subseafloor microbial ecosystem. Unique community structures suggest very diverse active populations compared to previous DNA-based diversity estimates, providing more support for enhancing community characterizations using more advanced sequencing

  7. Dynamics of bacterial gene regulation

    Science.gov (United States)

    Narang, Atul

    2009-03-01

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

  8. Bacterial cheating limits antibiotic resistance

    Science.gov (United States)

    Xiao Chao, Hui; Yurtsev, Eugene; Datta, Manoshi; Artemova, Tanya; Gore, Jeff

    2012-02-01

    The widespread use of antibiotics has led to the evolution of resistance in bacteria. Bacteria can gain resistance to the antibiotic ampicillin by acquiring a plasmid carrying the gene beta-lactamase, which inactivates the antibiotic. This inactivation may represent a cooperative behavior, as the entire bacterial population benefits from removing the antibiotic. The cooperative nature of this growth suggests that a cheater strain---which does not contribute to breaking down the antibiotic---may be able to take advantage of cells cooperatively inactivating the antibiotic. Here we find experimentally that a ``sensitive'' bacterial strain lacking the plasmid conferring resistance can invade a population of resistant bacteria, even in antibiotic concentrations that should kill the sensitive strain. We observe stable coexistence between the two strains and find that a simple model successfully explains the behavior as a function of antibiotic concentration and cell density. We anticipate that our results will provide insight into the evolutionary origin of phenotypic diversity and cooperative behaviors.

  9. Bacterial streamers in curved microchannels

    Science.gov (United States)

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

    2009-11-01

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

  10. Bacterial antagonist mediated protein molecules

    OpenAIRE

    Urbizu, Lucia Paola; Sparo, Mónica Delfina; Sanchez Bruni, Sergio Fabian

    2016-01-01

    Bacterial antagonism mediated by ribosomally synthesised peptides has gained considerable attention in recent years because of its potential applications in the control of undesirable microbiota. These peptides, generally referred to as bacteriocins, are defined as a heterogeneous group of ribosomally synthesised, proteinaceous substances (with or without further modifications) extracellularly secreted by many Gram-positive and some Gram-negative bacteria. Their mode of activity is primarily ...

  11. Bacterial Biofilms in Jones Tubes.

    Science.gov (United States)

    Ahn, Eric S; Hauck, Matthew J; Kirk Harris, Jonathan; Robertson, Charles E; Dailey, Roger A

    To investigate the presence and microbiology of bacterial biofilms on Jones tubes (JTs) by direct visualization with scanning electron microscopy and polymerase chain reaction (PCR) of representative JTs, and to correlate these findings with inflammation and/or infection related to the JT. In this study, prospective case series were performed. JTs were recovered from consecutive patients presenting to clinic for routine cleaning or recurrent irritation/infection. Four tubes were processed for scanning electron microscopy alone to visualize evidence of biofilms. Two tubes underwent PCR alone for bacterial quantification. One tube was divided in half and sent for scanning electron microscopy and PCR. Symptoms related to the JTs were recorded at the time of recovery. Seven tubes were obtained. Five underwent SEM, and 3 out of 5 showed evidence of biofilms (60%). Two of the 3 biofilms demonstrated cocci and the third revealed rods. Three tubes underwent PCR. The predominant bacteria identified were Pseudomonadales (39%), Pseudomonas (16%), and Staphylococcus (14%). Three of the 7 patients (43%) reported irritation and discharge at presentation. Two symptomatic patients, whose tubes were imaged only, revealed biofilms. The third symptomatic patient's tube underwent PCR only, showing predominantly Staphylococcus (56%) and Haemophilus (36%) species. Two of the 4 asymptomatic patients also showed biofilms. All symptomatic patients improved rapidly after tube exchange and steroid antibiotic drops. Bacterial biofilms were variably present on JTs, and did not always correlate with patients' symptoms. Nevertheless, routine JT cleaning is recommended to treat and possibly prevent inflammation caused by biofilms.

  12. Bacterial sex in dental plaque

    Directory of Open Access Journals (Sweden)

    Ingar Olsen

    2013-06-01

    Full Text Available Genes are transferred between bacteria in dental plaque by transduction, conjugation, and transformation. Membrane vesicles can also provide a mechanism for horizontal gene transfer. DNA transfer is considered bacterial sex, but the transfer is not parallel to processes that we associate with sex in higher organisms. Several examples of bacterial gene transfer in the oral cavity are given in this review. How frequently this occurs in dental plaque is not clear, but evidence suggests that it affects a number of the major genera present. It has been estimated that new sequences in genomes established through horizontal gene transfer can constitute up to 30% of bacterial genomes. Gene transfer can be both inter- and intrageneric, and it can also affect transient organisms. The transferred DNA can be integrated or recombined in the recipient's chromosome or remain as an extrachromosomal inheritable element. This can make dental plaque a reservoir for antimicrobial resistance genes. The ability to transfer DNA is important for bacteria, making them better adapted to the harsh environment of the human mouth, and promoting their survival, virulence, and pathogenicity.

  13. Polymorphism in Bacterial Flagella Suspensions

    Science.gov (United States)

    Schwenger, Walter J.

    Bacterial flagella are a type of biological polymer studied for its role in bacterial motility and the polymorphic transitions undertaken to facilitate the run and tumble behavior. The naturally rigid, helical shape of flagella gives rise to novel colloidal dynamics and material properties. This thesis studies methods in which the shape of bacterial flagella can be controlled using in vitro methods and the changes the shape of the flagella have on both single particle dynamics and bulk material properties. We observe individual flagellum in both the dilute and semidilute regimes to observe the effects of solvent condition on the shape of the filament as well as the effect the filament morphology has on reptation through a network of flagella. In addition, we present rheological measurements showing how the shape of filaments effects the bulk material properties of flagellar suspensions. We find that the individual particle dynamics in suspensions of flagella can vary with geometry from needing to reptate linearly via rotation for helical filaments to the prevention of long range diffusion for block copolymer filaments. Similarly, for bulk material properties of flagella suspensions, helical geometries show a dramatic enhancement in elasticity over straight filaments while block copolymers form an elastic gel without the aid of crosslinking agents.

  14. Detergent-compatible bacterial amylases.

    Science.gov (United States)

    Niyonzima, Francois N; More, Sunil S

    2014-10-01

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

  15. Diversity of aquatic bacterial populations

    International Nuclear Information System (INIS)

    Teska, J.D.

    1988-01-01

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

  16. Dialkylresorcinols as bacterial signaling molecules.

    Science.gov (United States)

    Brameyer, Sophie; Kresovic, Darko; Bode, Helge B; Heermann, Ralf

    2015-01-13

    It is well recognized that bacteria communicate via small diffusible molecules, a process termed quorum sensing. The best understood quorum sensing systems are those that use acylated homoserine lactones (AHLs) for communication. The prototype of those systems consists of a LuxI-like AHL synthase and a cognate LuxR receptor that detects the signal. However, many proteobacteria possess LuxR receptors, yet lack any LuxI-type synthase, and thus these receptors are referred to as LuxR orphans or solos. In addition to the well-known AHLs, little is known about the signaling molecules that are sensed by LuxR solos. Here, we describe a novel cell-cell communication system in the insect and human pathogen Photorhabdus asymbiotica. We identified the LuxR homolog PauR to sense dialkylresorcinols (DARs) and cyclohexanediones (CHDs) instead of AHLs as signals. The DarABC synthesis pathway produces the molecules, and the entire system emerged as important for virulence. Moreover, we have analyzed more than 90 different Photorhabdus strains by HPLC/MS and showed that these DARs and CHDs are specific to the human pathogen P. asymbiotica. On the basis of genomic evidence, 116 other bacterial species are putative DAR producers, among them many human pathogens. Therefore, we discuss the possibility of DARs as novel and widespread bacterial signaling molecules and show that bacterial cell-cell communication goes far beyond AHL signaling in nature.

  17. Acute bacterial meningitis in adults.

    Science.gov (United States)

    McGill, Fiona; Heyderman, Robert S; Panagiotou, Stavros; Tunkel, Allan R; Solomon, Tom

    2016-12-17

    Over the past several decades, the incidence of bacterial meningitis in children has decreased but there remains a significant burden of disease in adults, with a mortality of up to 30%. Although the pathogenesis of bacterial meningitis is not completely understood, knowledge of bacterial invasion and entry into the CNS is improving. Clinical features alone cannot determine whether meningitis is present and analysis of cerebrospinal fluid is essential for diagnosis. Newer technologies, such as multiplex PCR, and novel diagnostic platforms that incorporate proteomics and genetic sequencing, might help provide a quicker and more accurate diagnosis. Even with appropriate antimicrobial therapy, mortality is high and so attention has focused on adjunctive therapies; adjunctive corticosteroids are beneficial in certain circumstances. Any further improvements in outcome are likely to come from either modulation of the host response or novel approaches to therapy, rather than new antibiotics. Ultimately, the best hope to reduce the disease burden is with broadly protective vaccines. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Bacterial Carriers for Glioblastoma Therapy

    Directory of Open Access Journals (Sweden)

    Nalini Mehta

    2017-03-01

    Full Text Available Treatment of aggressive glioblastoma brain tumors is challenging, largely due to diffusion barriers preventing efficient drug dosing to tumors. To overcome these barriers, bacterial carriers that are actively motile and programmed to migrate and localize to tumor zones were designed. These carriers can induce apoptosis via hypoxia-controlled expression of a tumor suppressor protein p53 and a pro-apoptotic drug, Azurin. In a xenograft model of human glioblastoma in rats, bacterial carrier therapy conferred a significant survival benefit with 19% overall long-term survival of >100 days in treated animals relative to a median survival of 26 days in control untreated animals. Histological and proteomic analyses were performed to elucidate the safety and efficacy of these carriers, showing an absence of systemic toxicity and a restored neural environment in treated responders. In the treated non-responders, proteomic analysis revealed competing mechanisms of pro-apoptotic and drug-resistant activity. This bacterial carrier opens a versatile avenue to overcome diffusion barriers in glioblastoma by virtue of its active motility in extracellular space and can lead to tailored therapies via tumor-specific expression of tumoricidal proteins.

  19. A method to isolate bacterial communities and characterize ecosystems from food products: Validation and utilization in as a reproducible chicken meat model.

    Science.gov (United States)

    Rouger, Amélie; Remenant, Benoit; Prévost, Hervé; Zagorec, Monique

    2017-04-17

    Influenced by production and storage processes and by seasonal changes the diversity of meat products microbiota can be very variable. Because microbiotas influence meat quality and safety, characterizing and understanding their dynamics during processing and storage is important for proposing innovative and efficient storage conditions. Challenge tests are usually performed using meat from the same batch, inoculated at high levels with one or few strains. Such experiments do not reflect the true microbial situation, and the global ecosystem is not taken into account. Our purpose was to constitute live stocks of chicken meat microbiotas to create standard and reproducible ecosystems. We searched for the best method to collect contaminating bacterial communities from chicken cuts to store as frozen aliquots. We tested several methods to extract DNA of these stored communities for subsequent PCR amplification. We determined the best moment to collect bacteria in sufficient amounts during the product shelf life. Results showed that the rinsing method associated to the use of Mobio DNA extraction kit was the most reliable method to collect bacteria and obtain DNA for subsequent PCR amplification. Then, 23 different chicken meat microbiotas were collected using this procedure. Microbiota aliquots were stored at -80°C without important loss of viability. Their characterization by cultural methods confirmed the large variability (richness and abundance) of bacterial communities present on chicken cuts. Four of these bacterial communities were used to estimate their ability to regrow on meat matrices. Challenge tests performed on sterile matrices showed that these microbiotas were successfully inoculated and could overgrow the natural microbiota of chicken meat. They can therefore be used for performing reproducible challenge tests mimicking a true meat ecosystem and enabling the possibility to test the influence of various processing or storage conditions on complex meat

  20. Regulation of bacterial gene expression by ribosome stalling and rescuing.

    Science.gov (United States)

    Jin, Yongxin; Jin, Shouguang; Wu, Weihui

    2016-05-01

    Ribosome is responsible for protein synthesis and is able to monitor the sequence and structure of the nascent peptide. Such ability plays an important role in determining overall gene expression profile of the bacteria through ribosome stalling and rescuing. In this review, we briefly summarize our current understanding of the regulation of gene expression through ribosome stalling and rescuing in bacteria, as well as mechanisms that modulate ribosome activity. Understanding the mechanisms of how bacteria modulate ribosome activity will provide not only fundamental insights into bacterial gene regulation, but also new candidate targets for the development of novel antimicrobial agents.

  1. Spatial Distribution of Bacterial Communities Driven by Multiple Environmental Factors in a Beach Wetland of the Largest Freshwater Lake in China

    Directory of Open Access Journals (Sweden)

    Xia eDing

    2015-02-01

    Full Text Available The spatial distributions of bacterial communities may be driven by multiple environmental factors. Thus, understanding the relationships between bacterial distribution and environmental factors is critical for understanding wetland stability and the functioning of freshwater lakes. However, little research on the bacterial communities in deep sediment layers exists. In this study, thirty clone libraries of 16S rRNA were constructed from a beach wetland of the Poyang Lake along both horizontal (distance to the water-land junction and vertical (sediment depth gradients to assess the effects of sediment properties on bacterial community structure and diversity. Our results showed that bacterial diversity increased along the horizontal gradient and decreased along the vertical gradient. The heterogeneous sediment properties along gradients substantially affected the dominant bacterial groups at the phylum and species levels. For example, the NH4+ concentration decreased with increasing depth, which was positively correlated with the relative abundance of Alphaproteobacteria. The changes in bacterial diversity and dominant bacterial groups showed that the top layer had a different bacterial community structure than the deeper layers. Principal component analysis revealed that both gradients, not each gradient independently, contributed to the shift in the bacterial community structure. A multiple linear regression model explained the changes in bacterial diversity and richness along the depth and distance gradients. Overall, our results suggest that spatial gradients associated with sediment properties shaped the bacterial communities in the Poyang Lake beach wetland.

  2. Bacterial and fungal markers in tobacco smoke

    Energy Technology Data Exchange (ETDEWEB)

    Szponar, B., E-mail: szponar@iitd.pan.wroc.pl [Lund University, Dept. of Laboratory Medicine, Soelvegatan 23, 223 62 Lund (Sweden); Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114 Wroclaw (Poland); Pehrson, C.; Larsson, L. [Lund University, Dept. of Laboratory Medicine, Soelvegatan 23, 223 62 Lund (Sweden)

    2012-11-01

    Previous research has demonstrated that cigarette smoke contains bacterial and fungal components including lipopolysaccharide (LPS) and ergosterol. In the present study we used gas chromatography-mass spectrometry to analyze tobacco as well as mainstream and second hand smoke for 3-hydroxy fatty acids (3-OH FAs) of 10 to 18 carbon chain lengths, used as LPS markers, and ergosterol, used as a marker of fungal biomass. The air concentrations of LPS were 0.0017 nmol/m{sup 3} (N = 5) and 0.0007/m{sup 3} (N = 6) in the smoking vs. non-smoking rooms (p = 0.0559) of the studied private houses, and 0.0231 nmol/m{sup 3} (N = 5) vs. 0.0006 nmol/m{sup 3} (N = 5) (p = 0.0173), respectively, at the worksite. The air concentrations of ergosterol were also significantly higher in rooms with ongoing smoking than in rooms without smoking. A positive correlation was found between LPS and ergosterol in rooms with smoking but not in rooms without smoking. 3-OH C14:0 was the main 3-OH FA, followed by 3-OH C12:0, both in mainstream and second hand smoke and in phenol:water smoke extracts prepared in order to purify the LPS. The Limulus activity of the phenolic phase of tobacco was 3900 endotoxin units (EU)/cigarette; the corresponding amount of the smoke, collected on filters from 8 puffs, was 4 EU/cigarette. Tobacco smoking has been associated with a range of inflammatory airway conditions including COPD, asthma, bronchitis, alveolar hypersensitivity etc. Significant levels of LPS and ergosterol were identified in tobacco smoke and these observations support the hypothesis that microbial components of tobacco smoke contribute to inflammation and airway disease. -- Highlights: Black-Right-Pointing-Pointer Air concentration of bacterial and fungal markers is significantly higher in rooms with ongoing smoking than without smoking. Black-Right-Pointing-Pointer Bacterial LPS correlates with fungal marker in rooms with ongoing smoking but not without smoking. Black-Right-Pointing-Pointer LPS

  3. [Bacterial diversity within different sections of summer sea-ice samples from the Prydz Bay, Antarctica].

    Science.gov (United States)

    Ma, Jifei; Du, Zongjun; Luo, Wei; Yu, Yong; Zeng, Yixin; Chen, Bo; Li, Huirong

    2013-02-04

    In order to assess bacterial abundance and diversity within three different sections of summer sea-ice samples collected from the Prydz Bay, Antarctica. Fluorescence in situ hybridization was applied to determine the proportions of Bacteria in sea-ice. Bacterial community composition within sea ice was analyzed by 16S rRNA gene clone library construction. Correlation analysis was performed between the physicochemical parameters and the bacterial diversity and abundance within sea ice. The result of fluorescence in situ hybridization shows that bacteria were abundant in the bottom section, and the concentration of total organic carbon, total organic nitrogen and phosphate may be the main factors for bacterial abundance. In bacterial 16S rRNA gene libraries of sea-ice, nearly complete 16S rRNA gene sequences were grouped into three distinct lineages of Bacteria (gamma-Proteobacteria, alpha-Proteobacteria and Bacteroidetes). Most clone sequences were related to cultured bacterial isolates from the marine environment, arctic and Antarctic sea-ice with high similarity. The member of Bacteroidetes was not detected in the bottom section of sea-ice. The bacterial communities within sea-ice were little heterogeneous at the genus-level between different sections, and the concentration of NH4+ may cause this distribution. The number of bacteria was abundant in the bottom section of sea-ice. Gamma-proteobacteria was the dominant bacterial lineage in sea-ice.

  4. Diversity of Bacterial Communities of Fitness Center Surfaces in a U.S. Metropolitan Area

    Directory of Open Access Journals (Sweden)

    Nabanita Mukherjee

    2014-12-01

    Full Text Available Public fitness centers and exercise facilities have been implicated as possible sources for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial community residing on the surfaces in these indoor environments is still unknown. In this study, we investigated the overall bacterial ecology of selected fitness centers in a metropolitan area (Memphis, TN, USA utilizing culture-independent pyrosequencing of the 16S rRNA genes. Samples were collected from the skin-contact surfaces (e.g., exercise instruments, floor mats, handrails, etc. within fitness centers. Taxonomical composition revealed the abundance of Firmicutes phyla, followed by Proteobacter and Actinobacteria, with a total of 17 bacterial families and 25 bacterial genera. Most of these bacterial genera are of human and environmental origin (including, air, dust, soil, and water. Additionally, we found the presence of some pathogenic or potential pathogenic bacterial genera including Salmonella, Staphylococcus, Klebsiella, and Micrococcus. Staphylococcus was found to be the most prevalent genus. Presence of viable forms of these pathogens elevates risk of exposure of any susceptible individuals. Several factors (including personal hygiene, surface cleaning and disinfection schedules of the facilities may be the reasons for the rich bacterial diversity found in this study. The current finding underscores the need to increase public awareness on the importance of personal hygiene and sanitation for public gym users.

  5. Diversity of bacterial communities of fitness center surfaces in a U.S. metropolitan area.

    Science.gov (United States)

    Mukherjee, Nabanita; Dowd, Scot E; Wise, Andy; Kedia, Sapna; Vohra, Varun; Banerjee, Pratik

    2014-12-03

    Public fitness centers and exercise facilities have been implicated as possible sources for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial community residing on the surfaces in these indoor environments is still unknown. In this study, we investigated the overall bacterial ecology of selected fitness centers in a metropolitan area (Memphis, TN, USA) utilizing culture-independent pyrosequencing of the 16S rRNA genes. Samples were collected from the skin-contact surfaces (e.g., exercise instruments, floor mats, handrails, etc.) within fitness centers. Taxonomical composition revealed the abundance of Firmicutes phyla, followed by Proteobacter and Actinobacteria, with a total of 17 bacterial families and 25 bacterial genera. Most of these bacterial genera are of human and environmental origin (including, air, dust, soil, and water). Additionally, we found the presence of some pathogenic or potential pathogenic bacterial genera including Salmonella, Staphylococcus, Klebsiella, and Micrococcus. Staphylococcus was found to be the most prevalent genus. Presence of viable forms of these pathogens elevates risk of exposure of any susceptible individuals. Several factors (including personal hygiene, surface cleaning and disinfection schedules of the facilities) may be the reasons for the rich bacterial diversity found in this study. The current finding underscores the need to increase public awareness on the importance of personal hygiene and sanitation for public gym users.

  6. Substantial nutritional contribution of bacterial amino acids to earthworms and enchytraeids: A case study from organic grasslands

    DEFF Research Database (Denmark)

    Larsen, Thomas; Pollierer, Melanie M.; Holmstrup, Martin

    2016-01-01

    species, we employed δ13C fingerprinting of essential amino acids (EAA) for distinguishing between bacterial, fungal, and plant derived food sources. We collected earthworms and enchytraeids from organic grasslands with grass, clover, and mixtures of these two plants. Our results showed that the worms...... worms relied equally on bacterial and plant derived EAA. Our study provides answers to some of the long-standing questions in regards to the role of bacteria for earthworm nutrition. While bacterial EAA contribution to anecic worms was relatively modest, less than one-quarter, bacterial contribution...

  7. Bacterial Swarming: social behaviour or hydrodynamics?

    Science.gov (United States)

    Vermant, Jan

    2010-03-01

    Bacterial swarming of colonies is typically described as a social phenomenon between bacteria, whereby groups of bacteria collectively move atop solid surfaces. This multicellular behavior, during which the organized bacterial populations are embedded in an extracellular slime layer, is connected to important features such as biofilm formation and virulence. Despite the possible intricate quorum sensing mechanisms that regulate swarming, several physico-chemical phenomena may play a role in the dynamics of swarming and biofilm formation. Especially the striking fingering patterns formed by some swarmer colonies on relatively soft sub phases have attracted the attention as they could be the signatures of an instability. Recently, a parallel has been drawn between the swarming patterns and the spreading of viscous drops under the influence of a surfactant, which lead to similar patterns [1]. Starting from the observation that several of the molecules, essential in swarming systems, are strong biosurfactants, the possibility of flows driven by gradients in surface tension, has been proposed. This Marangoni flows are known to lead to these characteristic patterns. For Rhizobium etli not only the pattern formation, but also the experimentally observed spreading speed has been shown to be consistent with the one expected for Marangoni flows for the surface pressures, thickness, and viscosities that have been observed [2]. We will present an experimental study of swarming colonies of the bacteria Pseudomonas aeruginosa, the pattern formation, the surfactant gradients and height profiles in comparison with predictions of a thin film hydrodynamic model.[4pt] [1] Matar O.K. and Troian S., Phys. Fluids 11 : 3232 (1999)[0pt] [2] Daniels, R et al., PNAS, 103 (40): 14965-14970 (2006)

  8. Autogenic succession and deterministic recovery following disturbance in soil bacterial communities

    DEFF Research Database (Denmark)

    Jurburg, Stephanie D.; Nunes, Ines Marques; Stegen, James C.

    2017-01-01

    slowed down, and a stability phase (after 29 days), during which the community tended towards its original composition. Phylogenetic turnover patterns indicated that the community experienced stronger deterministic selection during recovery. Thus, soil bacterial communities, despite their extreme...... to understand the successional trajectory of soil bacterial communities following disturbances and the mechanisms controlling these dynamics at a scale relevant for these organisms, we subjected soil microcosms to a heat disturbance and followed the community composition of active bacteria over 50 days...

  9. Complementarity among plant growth promoting traits in rhizospheric bacterial communities promotes plant growth

    OpenAIRE

    Mangal Singh; Ashutosh Awasthi; Sumit K. Soni; Rakshapal Singh; Rajesh K. Verma; Alok Kalra

    2015-01-01

    An assessment of roles of rhizospheric microbial diversity in plant growth is helpful in understanding plant-microbe interactions. Using random combinations of rhizospheric bacterial species at different richness levels, we analysed the contribution of species richness, compositions, interactions and identity on soil microbial respiration and plant biomass. We showed that bacterial inoculation in plant rhizosphere enhanced microbial respiration and plant biomass with complementary relationshi...

  10. Lake Bacterial Assemblage Composition Is Sensitive to Biological Disturbance Caused by an Invasive Filter Feeder

    OpenAIRE

    Vincent J. Denef; Hunter J. Carrick; Joann Cavaletto; Edna Chiang; Thomas H. Johengen; Henry A. Vanderploeg; Angela D. Kent

    2017-01-01

    ABSTRACT One approach to improve forecasts of how global change will affect ecosystem processes is to better understand how anthropogenic disturbances alter bacterial assemblages that drive biogeochemical cycles. Species invasions are important contributors to global change, but their impacts on bacterial community ecology are rarely investigated. Here, we studied direct impacts of invasive dreissenid mussels (IDMs), one of many invasive filter feeders, on freshwater lake bacterioplankton. We...

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

    Science.gov (United States)

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

    2015-04-01

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

  12. Bacterial Communities of Three Saline Meromictic Lakes in Central Asia.

    Science.gov (United States)

    Baatar, Bayanmunkh; Chiang, Pei-Wen; Rogozin, Denis Yu; Wu, Yu-Ting; Tseng, Ching-Hung; Yang, Cheng-Yu; Chiu, Hsiu-Hui; Oyuntsetseg, Bolormaa; Degermendzhy, Andrey G; Tang, Sen-Lin

    2016-01-01

    Meromictic lakes located in landlocked steppes of central Asia (~2500 km inland) have unique geophysiochemical characteristics compared to other meromictic lakes. To characterize their bacteria and elucidate relationships between those bacteria and surrounding environments, water samples were collected from three saline meromictic lakes (Lakes Shira, Shunet and Oigon) in the border between Siberia and the West Mongolia, near the center of Asia. Based on in-depth tag pyrosequencing, bacterial communities were highly variable and dissimilar among lakes and between oxic and anoxic layers within individual lakes. Proteobacteria, Bacteroidetes, Cyanobacteria, Actinobacteria and Firmicutes were the most abundant phyla, whereas three genera of purple sulfur bacteria (a novel genus, Thiocapsa and Halochromatium) were predominant bacterial components in the anoxic layer of Lake Shira (~20.6% of relative abundance), Lake Shunet (~27.1%) and Lake Oigon (~9.25%), respectively. However, few known green sulfur bacteria were detected. Notably, 3.94% of all sequencing reads were classified into 19 candidate divisions, which was especially high (23.12%) in the anoxic layer of Lake Shunet. Furthermore, several hydro-parameters (temperature, pH, dissolved oxygen, H2S and salinity) were associated (P< 0.05) with variations in dominant bacterial groups. In conclusion, based on highly variable bacterial composition in water layers or lakes, we inferred that the meromictic ecosystem was characterized by high diversity and heterogenous niches.

  13. Metals affect soil bacterial and fungal functional diversity differently.

    Science.gov (United States)

    Stefanowicz, Anna M; Niklińska, Maria; Laskowski, Ryszard

    2008-03-01

    Heavy metals can cause a decrease in the taxonomic diversity of soil communities. Because of functional redundancy, it remains unclear to what extent different functions performed by the soil microbial communities may be affected by pollution. We studied the impact of metal contamination on soil bacterial and fungal functional diversity, active microbial biomass, and soil respiration rate. Soil samples were collected from 39 sites along three forest and five meadow pollution transects near an abandoned Pb/Zn smelter in Avonmouth (UK) and Ni smelter in Clydach (UK), in a Cu mining and smelting region near Glogów (Poland), and in a Zn/Pb mining and smelting region near Olkusz (Poland). Biolog GN2 and SFN2 plates were used to study the bacterial and fungal functional diversity, which subsequently was expressed as Shannon's diversity index (H'). The active microbial biomass was measured as substrate-induced respiration. We found that the bacterial functional diversity significantly decreased, whereas the fungal functional diversity slightly increased, with increasing metal concentration. We also observed a slight negative effect of metal pollution on the active microbial biomass. No relationship was found between metal contamination and total soil respiration rate. This suggests a higher sensitivity of bacterial functional diversity as an indicator for the effects of metal pollution compared with overall soil respiration. All microbial parameters were affected by nutrient concentrations and/or soil pH.

  14. Intestinal bacterial signatures of white feces syndrome in shrimp.

    Science.gov (United States)

    Hou, Dongwei; Huang, Zhijian; Zeng, Shenzheng; Liu, Jian; Wei, Dongdong; Deng, Xisha; Weng, Shaoping; Yan, Qingyun; He, Jianguo

    2018-04-01

    Increasing evidence suggests that the intestinal microbiota is closely correlated with the host's health status. Thus, a serious disturbance that disrupts the stability of the intestinal microecosystem could cause host disease. Shrimps are one of the most important products among fishery trading commodities. However, digestive system diseases, such as white feces syndrome (WFS), frequently occur in shrimp culture and have led to enormous economic losses across the world. The WFS occurrences are unclear. Here, we compared intestinal bacterial communities of WFS shrimp and healthy shrimp. Intestinal bacterial communities of WFS shrimp exhibited less diversity but were more heterogeneous than those of healthy shrimp. The intestinal bacterial communities were significantly different between WFS shrimp and healthy shrimp; compared with healthy shrimp, in WFS shrimp, Candidatus Bacilloplasma and Phascolarctobacterium were overrepresented, whereas Paracoccus and Lactococcus were underrepresented. PICRUSt functional predictions indicated that the relative abundances of genes involved in energy metabolism and genetic information processing were significantly greater in WFS shrimp. Collectively, we found that the composition and predicted functions of the intestinal bacterial community were markedly shifted by WFS. Significant increases in Candidatus Bacilloplasma and Phascolarctobacterium and decreases in Paracoccus and Lactococcus may contribute to WFS in shrimp.

  15. Molecular bacterial diversity and bioburden of commercial airliner cabin air

    Energy Technology Data Exchange (ETDEWEB)

    La Duc, M.T.; Stuecker, T.; Venkateswaran, K. [California Inst. of Technology, Pasadena, CA (United States). Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group

    2007-11-15

    Microorganisms that exist in aircraft air systems are considered to be the primary source of microbial contamination that can lead to illness shortly after flying. More than 600 million passengers board commercial airline flights annually in the United States alone. In this study, culture-independent, biomarker-targeted bacterial enumeration and identification strategies were used to estimate total bacterial burden and diversity within the cabin air of commercial airliners. Air-impingement was used to collect samples of microorganisms from 4 flights on 2 commercial carriers. The total viable microbial population ranged from below detection limits to 4.1 x 10{sup 6} cells/m{sup 3} of air. Microbes were found to gradually accumulate from the time of passenger boarding through mid-flight. A sharp decline in bacterial abundance was then observed. Representatives of the {alpha}, {beta} and {gamma} Proteobacteria, as well as Gram-positive bacteria, were isolated in varying abundance. Airline A had large abundances of Neisseria meningitidis rRNA gene sequences and Streptococcus oralis/mitis sequences. Airline B was dominated by pseudomonas synxantha sequences as well as N. meningitidis and S. oralis/mitis. The cabin air samples housed low bacterial diversity and were typically dominated by a particular subset of bacteria, notably opportunistic pathogenic inhabitants of the human respiratory tract and oral cavity. The microbes were found largely around the ventilation ducts and gasper conduits that supply cabin air. 45 refs., 4 tabs., 3 figs.

  16. Bacterial Communities of Three Saline Meromictic Lakes in Central Asia.

    Directory of Open Access Journals (Sweden)

    Bayanmunkh Baatar

    Full Text Available Meromictic lakes located in landlocked steppes of central Asia (~2500 km inland have unique geophysiochemical characteristics compared to other meromictic lakes. To characterize their bacteria and elucidate relationships between those bacteria and surrounding environments, water samples were collected from three saline meromictic lakes (Lakes Shira, Shunet and Oigon in the border between Siberia and the West Mongolia, near the center of Asia. Based on in-depth tag pyrosequencing, bacterial communities were highly variable and dissimilar among lakes and between oxic and anoxic layers within individual lakes. Proteobacteria, Bacteroidetes, Cyanobacteria, Actinobacteria and Firmicutes were the most abundant phyla, whereas three genera of purple sulfur bacteria (a novel genus, Thiocapsa and Halochromatium were predominant bacterial components in the anoxic layer of Lake Shira (~20.6% of relative abundance, Lake Shunet (~27.1% and Lake Oigon (~9.25%, respectively. However, few known green sulfur bacteria were detected. Notably, 3.94% of all sequencing reads were classified into 19 candidate divisions, which was especially high (23.12% in the anoxic layer of Lake Shunet. Furthermore, several hydro-parameters (temperature, pH, dissolved oxygen, H2S and salinity were associated (P< 0.05 with variations in dominant bacterial groups. In conclusion, based on highly variable bacterial composition in water layers or lakes, we inferred that the meromictic ecosystem was characterized by high diversity and heterogenous niches.

  17. Bacterial Diversity and Community Structure in Korean Ginseng Field Soil Are Shifted by Cultivation Time.

    Science.gov (United States)

    Nguyen, Ngoc-Lan; Kim, Yeon-Ju; Hoang, Van-An; Subramaniyam, Sathiyamoorthy; Kang, Jong-Pyo; Kang, Chang Ho; Yang, Deok-Chun

    2016-01-01

    Traditional molecular methods have been used to examine bacterial communities in ginseng-cultivated soil samples in a time-dependent manner. Despite these efforts, our understanding of the bacterial community is still inadequate. Therefore, in this study, a high-throughput sequencing approach was employed to investigate bacterial diversity in various ginseng field soil samples over cultivation times of 2, 4, and 6 years in the first and second rounds of cultivation. We used non-cultivated soil samples to perform a comparative study. Moreover, this study assessed changes in the bacterial community associated with soil depth and the health state of the ginseng. Bacterial richness decreased through years of cultivation. This study detected differences in relative abundance of bacterial populations between the first and second rounds of cultivation, years of cultivation, and health states of ginseng. These bacterial populations were mainly distributed in the classes Acidobacteria, Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Sphingobacteria. In addition, we found that pH, available phosphorus, and exchangeable Ca+ seemed to have high correlations with bacterial class in ginseng cultivated soil.

  18. Bacterial Diversity and Community Structure in Korean Ginseng Field Soil Are Shifted by Cultivation Time

    Science.gov (United States)

    Hoang, Van-An; Subramaniyam, Sathiyamoorthy; Kang, Jong-Pyo; Kang, Chang Ho; Yang, Deok-Chun

    2016-01-01

    Traditional molecular methods have been used to examine bacterial communities in ginseng-cultivated soil samples in a time-dependent manner. Despite these efforts, our understanding of the bacterial community is still inadequate. Therefore, in this study, a high-throughput sequencing approach was employed to investigate bacterial diversity in various ginseng field soil samples over cultivation times of 2, 4, and 6 years in the first and second rounds of cultivation. We used non-cultivated soil samples to perform a comparative study. Moreover, this study assessed changes in the bacterial community associated with soil depth and the health state of the ginseng. Bacterial richness decreased through years of cultivation. This study detected differences in relative abundance of bacterial populations between the first and second rounds of cultivation, years of cultivation, and health states of ginseng. These bacterial populations were mainly distributed in the classes Acidobacteria, Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Sphingobacteria. In addition, we found that pH, available phosphorus, and exchangeable Ca+ seemed to have high correlations with bacterial class in ginseng cultivated soil. PMID:27187071

  19. Sequencing of Bacterial Genomes: Principles and Insights into Pathogenesis and Development of Antibiotics

    Directory of Open Access Journals (Sweden)

    Eric S. Donkor

    2013-10-01

    Full Text Available The impact of bacterial diseases on public health has become enormous, and is partly due to the increasing trend of antibiotic resistance displayed by bacterial pathogens. Sequencing of bacterial genomes has significantly improved our understanding about the biology of many bacterial pathogens as well as identification of novel antibiotic targets. Since the advent of genome sequencing two decades ago, about 1,800 bacterial genomes have been fully sequenced and these include important aetiological agents such as Streptococcus pneumoniae, Mycobacterium tuberculosis, Escherichia coli O157:H7, Vibrio cholerae, Clostridium difficile and Staphylococcus aureus. Very recently, there has been an explosion of bacterial genome data and is due to the development of next generation sequencing technologies, which are evolving so rapidly. Indeed, the field of microbial genomics is advancing at a very fast rate and it is difficult for researchers to be abreast with the new developments. This highlights the need for regular updates in microbial genomics through comprehensive reviews. This review paper seeks to provide an update on bacterial genome sequencing generally, and to analyze insights gained from sequencing in two areas, including bacterial pathogenesis and the development of antibiotics.

  20. A Brief History of Bacterial Growth Physiology

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    Moselio eSchaechter

    2015-04-01

    Full Text Available Arguably, microbial physiology started when Leeuwenhoek became fascinated by observing a Vorticella beating its cilia, my point being that almost any observation of microbes has a physiological component. With the advent of modern microbiology in the mid 19th century, the field became recognizably distinctive with such discoveries as anaerobiosis, fermentation as a biological phenomenon, and the nutritional requirements of microbes. Soon came the discoveries of Winogradsky and his followers of the chemical changes in the environment that result from microbial activities. Later, during the first half of the 20th century, microbial physiology became the basis for much of the elucidation of central metabolism.Bacterial physiology then became a handmaiden of molecular biology and was greatly influenced by the discovery of cellular regulatory mechanisms. Microbial growth, which had come of age with the early work of Hershey, Monod, and others, was later pursued by studies on a whole cell level by what became known as the Copenhagen School. During this time, the exploration of physiological activities became coupled to modern inquiries into the structure of the bacterial cell.Recent years have seen the development of a further phase in microbial physiology, one seeking a deeper quantitative understanding of phenomena on a whole cell level. This pursuit is exemplified by the emergence of systems biology, which is made possible by the development of technologies that permit the gathering of information in huge amounts. As has been true through history, the research into microbial physiology continues to be guided by the development of new methods of analysis. Some of these developments may well afford the possibility of making stunning breakthroughs.

  1. Bacterial Community Diversity Harboured by Interacting Species.

    Directory of Open Access Journals (Sweden)

    Mikaël Bili

    Full Text Available All animals are infected by microbial partners that can be passengers or residents and influence many biological traits of their hosts. Even if important factors that structure the composition and abundance of microbial communities within and among host individuals have been recently described, such as diet, developmental stage or phylogeny, few studies have conducted cross-taxonomic comparisons, especially on host species related by trophic relationships. Here, we describe and compare the microbial communities associated with the cabbage root fly Delia radicum and its three major parasitoids: the two staphylinid beetles Aleochara bilineata and A. bipustulata and the hymenopteran parasitoid Trybliographa rapae. For each species, two populations from Western France were sampled and microbial communities were described through culture independent methods (454 pyrosequencing. Each sample harbored at least 59 to 261 different bacterial phylotypes but was strongly dominated by one or two. Microbial communities differed markedly in terms of composition and abundance, being mainly influenced by phylogenetic proximity but also geography to a minor extent. Surprisingly, despite their strong trophic interaction, parasitoids shared a very low proportion of microbial partners with their insect host. Three vertically transmitted symbionts from the genus Wolbachia, Rickettsia, and Spiroplasma were found in this study. Among them, Wolbachia and Spiroplasma were found in both the cabbage fly and at least one of its parasitoids, which could result from horizontal transfers through trophic interactions. Phylogenetic analysis showed that this hypothesis may explain some but not all cases. More work is needed to understand the dynamics of symbiotic associations within trophic network and the effect of these bacterial communities on the fitness of their hosts.

  2. Dynamics of genome rearrangement in bacterial populations.

    Directory of Open Access Journals (Sweden)

    Aaron E Darling

    2008-07-01

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

  3. Canadian guidelines for acute bacterial rhinosinusitis

    Science.gov (United States)

    Kaplan, Alan

    2014-01-01

    Objective To provide a clinical summary of the Canadian clinical practice guidelines for acute bacterial rhinosinusitis (ABRS) that includes relevant considerations for family physicians. Quality of evidence Guideline authors performed a systematic literature search and drafted recommendations. Recommendations received both strength of evidence and strength of recommendation ratings. Input from external content experts was sought, as was endorsement from Canadian medical societies (Association of Medical Microbiology and Infectious Disease Canada, Canadian Society of Allergy and Clinical Immunology, Canadian Society of Otolaryngology—Head and Neck Surgery, Canadian Association of Emergency Physicians, and the Family Physicians Airways Group of Canada). Main message Diagnosis of ABRS is based on the presence of specific symptoms and their duration; imaging or culture are not needed in uncomplicated cases. Treatment is dependent on symptom severity, with intranasal corticosteroids (INCSs) recommended as monotherapy for mild and moderate cases, although the benefit might be modest. Use of INCSs plus antibiotics is reserved for patients who fail to respond to INCSs after 72 hours, and for initial treatment of patients with severe symptoms. Antibiotic selection must account for the suspected pathogen, the risk of resistance, comorbid conditions, and local antimicrobial resistance trends. Adjunct therapies such as nasal saline irrigation are recommended. Failure to respond to treatment, recurrent episodes, and signs of complications should prompt referral to an otolaryngologist. The guidelines address situations unique to the Canadian health care environment, including actions to take during prolonged wait periods for specialist referral or imaging. Conclusion The Canadian guidelines provide up-to-date recommendations for diagnosis and treatment of ABRS that reflect an evolving understanding of the disease. In addition, the guidelines offer useful tools to help

  4. Oxygen isotopic fractionation during bacterial sulfate reduction

    Science.gov (United States)

    Balci, N.; Turchyn, A. V.; Lyons, T.; Bruchert, V.; Schrag, D. P.; Wall, J.

    2006-12-01

    Sulfur isotope fractionation during bacterial sulfate reduction (BSR) is understood to depend on a variety of environmental parameters, such as sulfate concentration, temperature, cell specific sulfate reduction rates, and the carbon substrate. What controls oxygen isotope fractionation during BSR is less well understood. Some studies have suggested that carbon substrate is important, whereas others concluded that there is a stoichiometric relationship between the fractionations of sulfur and oxygen during BSR. Studies of oxygen fractionation are complicated by isotopic equilibration between sulfur intermediates, particularly sulfite, and water. This process can modify the isotopic composition of the extracellular sulfate pool (δ18OSO4 ). Given this, the challenge is to distinguish between this isotopic equilibration and fractionations linked to the kinetic effects of the intercellular enzymes and the incorporation of sulfate into the bacterial cell. The δ18OSO4 , in concert with the sulfur isotope composition of sulfate (δ34SSO4), could be a powerful tool for understanding the pathways and environmental controls of BSR in natural systems. We will present δ18OSO4 data measured from batch culture growth of 14 different species of sulfate reducing bacteria for which sulfur isotope data were previously published. A general observation is that δ18OSO4 shows little isotopic change (kinetic effect during BSR and/or equilibration between sulfur intermediates and the isotopically light water (~-5‰) of the growth medium. Our present batch culture data do not allow us to convincingly isolate the magnitude and the controlling parameters of the kinetic isotope effect for oxygen. However, ongoing growth of mutant bacteria missing enzymes critical in the different steps of BSR may assist in this mission.

  5. Validation of hierarchical cluster analysis for identification of bacterial species using 42 bacterial isolates

    Science.gov (United States)

    Ghebremedhin, Meron; Yesupriya, Shubha; Luka, Janos; Crane, Nicole J.

    2015-03-01

    Recent studies have demonstrated the potential advantages of the use of Raman spectroscopy in the biomedical field due to its rapidity and noninvasive nature. In this study, Raman spectroscopy is applied as a method for differentiating between bacteria isolates for Gram status and Genus species. We created models for identifying 28 bacterial isolates using spectra collected with a 785 nm laser excitation Raman spectroscopic system. In order to investigate the groupings of these samples, partial least squares discriminant analysis (PLSDA) and hierarchical cluster analysis (HCA) was implemented. In addition, cluster analyses of the isolates were performed using various data types consisting of, biochemical tests, gene sequence alignment, high resolution melt (HRM) analysis and antimicrobial susceptibility tests of minimum inhibitory concentration (MIC) and degree of antimicrobial resistance (SIR). In order to evaluate the ability of these models to correctly classify bacterial isolates using solely Raman spectroscopic data, a set of 14 validation samples were tested using the PLSDA models and consequently the HCA models. External cluster evaluation criteria of purity and Rand index were calculated at different taxonomic levels to compare the performance of clustering using Raman spectra as well as the other datasets. Results showed that Raman spectra performed comparably, and in some cases better than, the other data types with Rand index and purity values up to 0.933 and 0.947, respectively. This study clearly demonstrates that the discrimination of bacterial species using Raman spectroscopic data and hierarchical cluster analysis is possible and has the potential to be a powerful point-of-care tool in clinical settings.

  6. Electrostatic behavior of the charge-regulated bacterial cell surface.

    Science.gov (United States)

    Hong, Yongsuk; Brown, Derick G

    2008-05-06

    The electrostatic behavior of the charge-regulated surfaces of Gram-negative Escherichia coli and Gram-positive Bacillus brevis was studied using numerical modeling in conjunction with potentiometric titration and electrophoretic mobility data as a function of solution pH and electrolyte composition. Assuming a polyelectrolytic polymeric bacterial cell surface, these experimental and numerical analyses were used to determine the effective site numbers of cell surface acid-base functional groups and Ca(2+) sorption coefficients. Using effective site concentrations determined from 1:1 electrolyte (NaCl) experimental data, the charge-regulation model was able to replicate the effects of 2:1 electrolyte (CaCl(2)), both alone and as a mixture with NaCl, on the measured zeta potential using a single Ca(2+) surface binding constant for each of the bacterial species. This knowledge is vital for understanding how cells respond to changes in solution pH and electrolyte composition as well as how they interact with other surfaces. The latter is especially important due to the widespread use of the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory in the interpretation of bacterial adhesion. As surface charge and surface potential both vary on a charge-regulated surface, accurate modeling of bacterial interactions with surfaces ultimately requires use of an electrostatic model that accounts for the charge-regulated nature of the cell surface.

  7. Exploring bacterial outer membrane barrier to combat bad bugs.

    Science.gov (United States)

    Ghai, Ishan; Ghai, Shashank

    2017-01-01

    One of the main fundamental mechanisms of antibiotic resistance in Gram-negative bacteria comprises an effective change in the membrane permeability to antibiotics. The Gram-negative bacterial complex cell envelope comprises an outer membrane that delimits the periplasm from the exterior environment. The outer membrane contains numerous protein channels, termed as porins or nanopores, which are mainly involved in the influx of hydrophilic compounds, including antibiotics. Bacterial adaptation to reduce influx through these outer membrane proteins (Omps) is one of the crucial mechanisms behind antibiotic resistance. Thus to interpret the molecular basis of the outer membrane permeability is the current challenge. This review attempts to develop a state of knowledge pertinent to Omps and their effective role in antibiotic influx. Further, it aims to study the bacterial response to antibiotic membrane permeability and hopefully provoke a discussion toward understanding and further exploration of prospects to improve our knowledge on physicochemical parameters that direct the translocation of antibiotics through the bacterial membrane protein channels.

  8. Exploring bacterial outer membrane barrier to combat bad bugs

    Directory of Open Access Journals (Sweden)

    Ghai I

    2017-08-01

    Full Text Available Ishan Ghai,1 Shashank Ghai2 1School of Engineering and Life Sciences, Jacobs University, Bremen, 2Leibniz University, Hannover, Germany Abstract: One of the main fundamental mechanisms of antibiotic resistance in Gram-negative bacteria comprises an effective change in the membrane permeability to antibiotics. The Gram-negative bacterial complex cell envelope comprises an outer membrane that delimits the periplasm from the exterior environment. The outer membrane contains numerous protein channels, termed as porins or nanopores, which are mainly involved in the influx of hydrophilic compounds, including antibiotics. Bacterial adaptation to reduce influx through these outer membrane proteins (Omps is one of the crucial mechanisms behind antibiotic resistance. Thus to interpret the molecular basis of the outer membrane permeability is the current challenge. This review attempts to develop a state of knowledge pertinent to Omps and their effective role in antibiotic influx. Further, it aims to study the bacterial response to antibiotic membrane permeability and hopefully provoke a discussion toward understanding and further exploration of prospects to improve our knowledge on physicochemical parameters that direct the translocation of antibiotics through the bacterial membrane protein channels. Keywords: antibiotics, Gram-negative bacteria, cell envelope, protein channels, nanopores, influx, antibiotic resistance

  9. Bacterial Biosensors for Measuring Availability of Environmental Pollutants

    Directory of Open Access Journals (Sweden)

    Jan Roelof van der Meer

    2008-07-01

    Full Text Available Traditionally, pollution risk assessment is based on the measurement of a pollutant’s total concentration in a sample. The toxicity of a given pollutant in the environment, however, is tightly linked to its bioavailability, which may differ significantly from the total amount. Physico-chemical and biological parameters strongly influence pollutant fate in terms of leaching, sequestration and biodegradation. Bacterial sensorreporters, which consist of living micro-organisms genetically engineered to produce specific output in response to target chemicals, offer an interesting alternative to monitoring approaches. Bacterial sensor-reporters detect bioavailable and/or bioaccessible compound fractions in samples. Currently, a variety of environmental pollutants can be targeted by specific biosensor-reporters. Although most of such strains are still confined to the lab, several recent reports have demonstrated utility of bacterial sensing-reporting in the field, with method detection limits in the nanomolar range. This review illustrates the general design principles for bacterial sensor-reporters, presents an overview of the existing biosensor-reporter strains with emphasis on organic compound detection. A specific focus throughout is on the concepts of bioavailability and bioaccessibility, and how bacteria-based sensing-reporting systems can help to improve our basic understanding of the different processes at work.

  10. Focal Targeting of the Bacterial Envelope by Antimicrobial Peptides

    Directory of Open Access Journals (Sweden)

    Rafi eRashid

    2016-06-01

    Full Text Available Antimicrobial peptides (AMPs are utilized by both eukaryotic and prokaryotic organisms. AMPs such as the human beta defensins, human neutrophil peptides, human cathelicidin, and many bacterial bacteriocins are cationic and capable of binding to anionic regions of the bacterial surface. Cationic AMPs (CAMPs target anionic lipids (e.g. phosphatidylglycerol (PG and cardiolipins (CL in the cell membrane and anionic components (e.g. lipopolysaccharide (LPS and lipoteichoic acid (LTA of the cell envelope. Bacteria have evolved mechanisms to modify these same targets in order to resist CAMP killing, e.g. lysinylation of PG to yield cationic lysyl-PG and alanylation of LTA. Since CAMPs offer a promising therapeutic alternative to conventional antibiotics, which are becoming less effective due to rapidly emerging antibiotic resistance, there is a strong need to improve our understanding about the AMP mechanism of action. Recent literature suggests that AMPs often interact with the bacterial cell envelope at discrete foci. Here we review recent AMP literature, with an emphasis on focal interactions with bacteria, including (1 CAMP disruption mechanisms, (2 delocalization of membrane proteins and lipids by CAMPs, and (3 CAMP sensing systems and resistance mechanisms. We conclude with new approaches for studying the bacterial membrane, e.g., lipidomics, high resolution imaging and non-detergent-based membrane domain extraction.

  11. The evolution of modularity in bacterial metabolic networks.

    Science.gov (United States)

    Kreimer, Anat; Borenstein, Elhanan; Gophna, Uri; Ruppin, Eytan

    2008-05-13

    Deciphering the modular organization of metabolic networks and understanding how modularity evolves have attracted tremendous interest in recent years. Here, we present a comprehensive large scale characterization of modularity across the bacterial tree of life, systematically quantifying the modularity of the metabolic networks of >300 bacterial species. Three main determinants of metabolic network modularity are identified. First, network size is an important topological determinant of network modularity. Second, several environmental factors influence network modularity, with endosymbionts and mammal-specific pathogens having lower modularity scores than bacterial species that occupy a wider range of niches. Moreover, even among the pathogens, those that alternate between two distinct niches, such as insect and mammal, tend to have relatively high metabolic network modularity. Third, horizontal gene transfer is an important force that contributes significantly to metabolic modularity. We additionally reconstruct the metabolic network of ancestral bacterial species and examine the evolution of modularity across the tree of life. This reveals a trend of modularity decrease from ancestors to descendants that is likely the outcome of niche specialization and the incorporation of peripheral metabolic reactions.

  12. Surface display of proteins by Gram-negative bacterial autotransporters

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    Mourez Michael

    2006-06-01

    Full Text Available Abstract Expressing proteins of interest as fusions to proteins of the bacterial envelope is a powerful technique with many biotechnological and medical applications. Autotransporters have recently emerged as a good tool for bacterial surface display. These proteins are composed of an N-terminal signal peptide, followed by a passenger domain and a translocator domain that mediates the outer membrane translocation of the passenger. The natural passenger domain of autotransporters can be replaced by heterologous proteins that become displayed at the bacterial surface by the translocator domain. The simplicity and versatility of this system has made it very attractive and it has been used to display functional enzymes, vaccine antigens as well as polypeptides libraries. The recent advances in the study of the translocation mechanism of autotransporters have raised several controversial issues with implications for their use as display systems. These issues include the requirement for the displayed polypeptides to remain in a translocation-competent state in the periplasm, the requirement for specific signal sequences and "autochaperone" domains, and the influence of the genetic background of the expression host strain. It is therefore important to better understand the mechanism of translocation of autotransporters in order to employ them to their full potential. This review will focus on the recent advances in the study of the translocation mechanism of autotransporters and describe practical considerations regarding their use for bacterial surface display.

  13. Ecophysiological characterization of rhizosphere bacterial communities at different root locations and plant developmental stages of cucumber grown on rockwool

    NARCIS (Netherlands)

    Folman, L.B.; Postma, J.; Veen, van J.A.

    2001-01-01

    Bacterial communities from the rhizosphere of cucumber were characterized with respect to growth rates and carbon source utilization, in order to develop a selection strategy for biocontrol agents against Pythium aphanidermatum. Rhizosphere samples were collected from different root regions (root

  14. Exploring the links between groundwater quality and bacterial communities near oil and gas extraction activities.

    Science.gov (United States)

    Santos, Inês C; Martin, Misty S; Reyes, Michelle L; Carlton, Doug D; Stigler-Granados, Paula; Valerio, Melissa A; Whitworth, Kristina W; Hildenbrand, Zacariah L; Schug, Kevin A

    2018-03-15

    Bacterial communities in groundwater are very important as they maintain a balanced biogeochemical environment. When subjected to stressful environments, for example, due to anthropogenic contamination, bacterial communities and their dynamics change. Studying the responses of the groundwater microbiome in the face of environmental changes can add to our growing knowledge of microbial ecology, which can be utilized for the development of novel bioremediation strategies. High-throughput and simpler techniques that allow the real-time study of different microbiomes and their dynamics are necessary, especially when examining larger data sets. Matrix-assisted laser desorption-ionization (MALDI) time-of-flight mass spectrometry (TOF-MS) is a workhorse for the high-throughput identification of bacteria. In this work, groundwater samples were collected from a rural area in southern Texas, where agricultural activities and unconventional oil and gas development are the most prevalent anthropogenic activities. Bacterial communities were assessed using MALDI-TOF MS, with bacterial diversity and abundance being analyzed with the contexts of numerous organic and inorganic groundwater constituents. Mainly denitrifying and heterotrophic bacteria from the Phylum Proteobacteria were isolated. These microorganisms are able to either transform nitrate into gaseous forms of nitrogen or degrade organic compounds such as hydrocarbons. Overall, the bacterial communities varied significantly with respect to the compositional differences that were observed from the collected groundwater samples. Collectively, these data provide a baseline measurement of bacterial diversity in groundwater located near anthropogenic surface and subsurface activities. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Bioactivity and phylogeny of the marine bacterial genus Pseudoalteromonas

    DEFF Research Database (Denmark)

    Vynne, Nikolaj Grønnegaard

    -associated strains were significantly more likely to possess stable antibacterial activity and be pigmented. Pseudoalteromonas strains are known as prolific producers of bioactive secondary metabolites; hence screening the global strain collection for production of novel antibiotics was initiated. Novel quinolone...... collection, in part because of its production of an intense black pigment in contrast to its phylogenetic placement within the non-pigmented clade. This strain was subsequently shown to represent a new bacterial species named Pseudoalteromonas galatheae. Initial studies revealed the potential production......The purpose of this Ph.D. project was to evaluate a global collection of marine Pseudoalteromonas bacteria as a source of novel bioactive compounds, and to investigate the distribution and production of such compounds among different species within the Pseudoalteromonas genus. The strain collection...

  16. Iron bacterial phylogeny and their execution towards iron availability in Equatorial Indian Ocean and Coastal Arabian Sea

    Digital Repository Service at National Institute of Oceanography (India)

    Rajasabapathy, R.; Mohandass, C.; VijayRaj, A.S.; Madival, V.V.; Meena, R.M.

    Based on distinct colony morphology, color, size, shape and certain other traits, 92 bacterial isolates were investigated to understand their managerial ability on iron from the Arabian Sea and Equatorial Indian Ocean samples. The ARDRA (amplified r...

  17. Collective Social Entrepreneurship: Arenas for Gendering Social Innovation and Marginalized Women’s Collective Action

    DEFF Research Database (Denmark)

    Andersen, Linda Lundgaard; Banerjee, Swati

    2018-01-01

    This chapter focuses on collective(s) and social entrepreneurship and explores how gendering social innovation through marginalized women’s collective actions might add depth and new insight to our understanding of social innovation. We explore different forms of organizations and collectives...

  18. Metaphor, skepticism, understanding Metaphor, skepticism, understanding

    Directory of Open Access Journals (Sweden)

    Helena Martins

    2010-05-01

    Full Text Available

    This paper examines the idea that metaphor is a basic cognitive tool from a Wittgensteinian point of view. One specific aspect of Wittgenstein’s legacy is explored, namely his account of verbal understanding. Two interconnected and notoriously difficult features of this account are highlighted and discussed: the idea that linguistic understanding is not an event or a process, but an “abiding condition” (Philosophical Investigations, §143-84; and the idea that neither the meaning of a linguistic expression nor our understanding of it can ever go beyond our capacity of explaining it (Philosophical Investigations, §75. This perspective is shown to be particularly apt in reflecting upon the virtues of metaphor as a means of understanding, especially because it allows for the avoidance of both essentialist and skeptical accounts.

    This paper examines the idea that metaphor is a basic cognitive tool from a Wittgensteinian point of view. One specific aspect of Wittgenstein’s legacy is explored, namely his account of verbal understanding. Two interconnected and notoriously difficult features of this account are highlighted and discussed: the idea that linguistic understanding is not an event or a process, but an “abiding condition” (Philosophical Investigations, §143-84; and the idea that neither the meaning of a linguistic expression nor our understanding of it can ever go beyond our capacity of explaining it (Philosophical Investigations, §75. This perspective is shown to be particularly apt in reflecting upon the virtues of metaphor as a means of understanding, especially because it allows for the avoidance of both essentialist and skeptical accounts

  19. 76 FR 79648 - Agency Information Collection Activities: Proposed Collection; Comment Request-Understanding the...

    Science.gov (United States)

    2011-12-22

    ...-2576 or via email to Steve[email protected] . Comments will also be accepted through the Federal e... income and household circumstances. A new job, a reduction in work hours, the addition of a household...

  20. Understanding Identity and Organizations

    DEFF Research Database (Denmark)

    Christensen, Lars Thøger

    2013-01-01

    The article reviews the book "Understanding Identity and Organizations," by Kate Kenny, Andrea Whitle, and Hugh Wilmott.......The article reviews the book "Understanding Identity and Organizations," by Kate Kenny, Andrea Whitle, and Hugh Wilmott....