WorldWideScience

Sample records for bacterial biodiversity-ecosystem functioning

  1. Distributional (in)congruence of biodiversity-ecosystem functioning

    NARCIS (Netherlands)

    C. Mulder; A. Boit; S. Mori; J.A. Vonk; S.D. Dyer; L. Faggiano; S. Geisen; A.L. González; M. Kaspari; S. Lavorel; P.A. Marquet; A.G. Rossberg; R.W. Sterner; W. Voigt; D.H. Wall

    2012-01-01

    The majority of research on biodiversity-ecosystem functioning in laboratories has concentrated on a few traits, but there is increasing evidence from the field that functional diversity controls ecosystem functioning more often than does species number. Given the importance of traits as predictors

  2. Testing the stress-gradient hypothesis with aquatic detritivorous invertebrates : insights for biodiversity-ecosystem functioning research

    OpenAIRE

    Fugère, V.; Andino, P.; Espinosa, R; Anthelme, Fabien; D. Jacobsen; Dangles, Olivier

    2012-01-01

    1. The stress-gradient hypothesis (SGH) states that environmental stress modulates species interactions, causing a shift from negative interactions to net positive interactions with increasing stress. 2. Potentially, this modulation of species interactions could in turn influence biodiversity-ecosystem function (B-EF) relationships along stress gradients. Although the SGH has been extensively discussed in plant community ecology in the past two decades, it has received little attention from a...

  3. Using a multi-trait approach to manipulate plant functional diversity in a biodiversity-ecosystem function experiment.

    Directory of Open Access Journals (Sweden)

    Conrad Schittko

    Full Text Available A frequent pattern emerging from biodiversity-ecosystem function studies is that functional group richness enhances ecosystem functions such as primary productivity. However, the manipulation of functional group richness goes along with major disadvantages like the transformation of functional trait data into categories or the exclusion of functional differences between organisms in the same group. In a mesocosm study we manipulated plant functional diversity based on the multi-trait Functional Diversity (FD-approach of Petchey and Gaston by using database data of seven functional traits and information on the origin of the species in terms of being native or exotic. Along a gradient ranging from low to high FD we planted 40 randomly selected eight-species mixtures under controlled conditions. We found a significant positive linear correlation of FD with aboveground productivity and a negative correlation with invasibility of the plant communities. Based on community-weighted mean calculations for each functional trait, we figured out that the traits N-fixation and species origin, i.e. being native or exotic, played the most important role for community productivity. Our results suggest that the identification of the impact of functional trait diversity and the relative contributions of relevant traits is essential for a mechanistic understanding of the role of biodiversity for ecosystem functions such as aboveground biomass production and resistance against invasion.

  4. Using a multi-trait approach to manipulate plant functional diversity in a biodiversity-ecosystem function experiment.

    Science.gov (United States)

    Schittko, Conrad; Hawa, Mahmoud; Wurst, Susanne

    2014-01-01

    A frequent pattern emerging from biodiversity-ecosystem function studies is that functional group richness enhances ecosystem functions such as primary productivity. However, the manipulation of functional group richness goes along with major disadvantages like the transformation of functional trait data into categories or the exclusion of functional differences between organisms in the same group. In a mesocosm study we manipulated plant functional diversity based on the multi-trait Functional Diversity (FD)-approach of Petchey and Gaston by using database data of seven functional traits and information on the origin of the species in terms of being native or exotic. Along a gradient ranging from low to high FD we planted 40 randomly selected eight-species mixtures under controlled conditions. We found a significant positive linear correlation of FD with aboveground productivity and a negative correlation with invasibility of the plant communities. Based on community-weighted mean calculations for each functional trait, we figured out that the traits N-fixation and species origin, i.e. being native or exotic, played the most important role for community productivity. Our results suggest that the identification of the impact of functional trait diversity and the relative contributions of relevant traits is essential for a mechanistic understanding of the role of biodiversity for ecosystem functions such as aboveground biomass production and resistance against invasion.

  5. Seafloor heterogeneity influences the biodiversity-ecosystem functioning relationships in the deep sea

    Science.gov (United States)

    Zeppilli, Daniela; Pusceddu, Antonio; Trincardi, Fabio; Danovaro, Roberto

    2016-05-01

    Theoretical ecology predicts that heterogeneous habitats allow more species to co-exist in a given area. In the deep sea, biodiversity is positively linked with ecosystem functioning, suggesting that deep-seabed heterogeneity could influence ecosystem functions and the relationships between biodiversity and ecosystem functioning (BEF). To shed light on the BEF relationships in a heterogeneous deep seabed, we investigated variations in meiofaunal biodiversity, biomass and ecosystem efficiency within and among different seabed morphologies (e.g., furrows, erosional troughs, sediment waves and other depositional structures, landslide scars and deposits) in a narrow geo-morphologically articulated sector of the Adriatic Sea. We show that distinct seafloor morphologies are characterized by highly diverse nematode assemblages, whereas areas sharing similar seabed morphologies host similar nematode assemblages. BEF relationships are consistently positive across the entire region, but different seabed morphologies are characterised by different slope coefficients of the relationship. Our results suggest that seafloor heterogeneity, allowing diversified assemblages across different habitats, increases diversity and influence ecosystem processes at the regional scale, and BEF relationships at smaller spatial scales. We conclude that high-resolution seabed mapping and a detailed analysis of the species distribution at the habitat scale are crucial for improving management of goods and services delivered by deep-sea ecosystems.

  6. Biodiversity-ecosystem functioning relationships in long-term time series and palaeoecological records: deep sea as a test bed.

    Science.gov (United States)

    Yasuhara, Moriaki; Doi, Hideyuki; Wei, Chih-Lin; Danovaro, Roberto; Myhre, Sarah E

    2016-05-19

    The link between biodiversity and ecosystem functioning (BEF) over long temporal scales is poorly understood. Here, we investigate biological monitoring and palaeoecological records on decadal, centennial and millennial time scales from a BEF framework by using deep sea, soft-sediment environments as a test bed. Results generally show positive BEF relationships, in agreement with BEF studies based on present-day spatial analyses and short-term manipulative experiments. However, the deep-sea BEF relationship is much noisier across longer time scales compared with modern observational studies. We also demonstrate with palaeoecological time-series data that a larger species pool does not enhance ecosystem stability through time, whereas higher abundance as an indicator of higher ecosystem functioning may enhance ecosystem stability. These results suggest that BEF relationships are potentially time scale-dependent. Environmental impacts on biodiversity and ecosystem functioning may be much stronger than biodiversity impacts on ecosystem functioning at long, decadal-millennial, time scales. Longer time scale perspectives, including palaeoecological and ecosystem monitoring data, are critical for predicting future BEF relationships on a rapidly changing planet. PMID:27114583

  7. Responses of leaf processing to impacts in streams in Atlantic rain Forest, Rio de Janeiro, Brazil - a test of the biodiversity-ecosystem functioning relationship?

    OpenAIRE

    Moulton T. P.; Magalhães S. A. P.

    2003-01-01

    The relationship between biodiversity and ecosystem functioning has been intensely debated and researched in recent times. It is generally agreed that there is redundancy of species in ecosystems such that loss of species does not necessarily result in change in the functioning of the ecosystem in which they occur. However the state of our knowledge does not allow prediction of sensitivity or specificity of this relationship for any particular ecosystem. A widely-held opinion is that ecosyste...

  8. The quest for a mechanistic understanding of biodiversity-ecosystem services relationships.

    Science.gov (United States)

    Duncan, Clare; Thompson, Julian R; Pettorelli, Nathalie

    2015-10-22

    Ecosystem services (ES) approaches to biodiversity conservation are currently high on the ecological research and policy agendas. However, despite a wealth of studies into biodiversity's role in maintaining ES (B-ES relationships) across landscapes, we still lack generalities in the nature and strengths of these linkages. Reasons for this are manifold, but can largely be attributed to (i) a lack of adherence to definitions and thus a confusion between final ES and the ecosystem functions (EFs) underpinning them, (ii) a focus on uninformative biodiversity indices and singular hypotheses and (iii) top-down analyses across large spatial scales and overlooking of context-dependency. The biodiversity-ecosystem functioning (B-EF) field provides an alternate context for examining biodiversity's mechanistic role in shaping ES, focusing on species' characteristics that may drive EFs via multiple mechanisms across contexts. Despite acknowledgements of a need for B-ES research to look towards underlying B-EF linkages, the connections between these areas of research remains weak. With this review, we pull together recent B-EF findings to identify key areas for future developments in B-ES research. We highlight a means by which B-ES research may begin to identify how and when multiple underlying B-EF relationships may scale to final ES delivery and trade-offs.

  9. Collective Functionality through Bacterial Individuality

    Science.gov (United States)

    Ackermann, Martin

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

  10. Impacts of climate change on biodiversity, ecosystems, and ecosystem services: technical input to the 2013 National Climate Assessment

    Science.gov (United States)

    Staudinger, Michelle D.; Grimm, Nancy B.; Staudt, Amanda; Carter, Shawn L.; Stuart, F. Stuart; Kareiva, Peter; Ruckelshaus, Mary; Stein, Bruce A.

    2012-01-01

    Ecosystems, and the biodiversity and services they support, are intrinsically dependent on climate. During the twentieth century, climate change has had documented impacts on ecological systems, and impacts are expected to increase as climate change continues and perhaps even accelerates. This technical input to the National Climate Assessment synthesizes our scientific understanding of the way climate change is affecting biodiversity, ecosystems, ecosystem services, and what strategies might be employed to decrease current and future risks. Building on past assessments of how climate change and other stressors are affecting ecosystems in the United States and around the world, we approach the subject from several different perspectives. First, we review the observed and projected impacts on biodiversity, with a focus on genes, species, and assemblages of species. Next, we examine how climate change is affecting ecosystem structural elements—such as biomass, architecture, and heterogeneity—and functions—specifically, as related to the fluxes of energy and matter. People experience climate change impacts on biodiversity and ecosystems as changes in ecosystem services; people depend on ecosystems for resources that are harvested, their role in regulating the movement of materials and disturbances, and their recreational, cultural, and aesthetic value. Thus, we review newly emerging research to determine how human activities and a changing climate are likely to alter the delivery of these ecosystem services. This technical input also examines two cross-cutting topics. First, we recognize that climate change is happening against the backdrop of a wide range of other environmental and anthropogenic stressors, many of which have caused dramatic ecosystem degradation already. This broader range of stressors interacts with climate change, and complicates our abilities to predict and manage the impacts on biodiversity, ecosystems, and the services they support. The

  11. Socioeconomic influences on biodiversity, ecosystem services and human well-being: a quantitative application of the DPSIR model in Jiangsu, China.

    Science.gov (United States)

    Hou, Ying; Zhou, Shudong; Burkhard, Benjamin; Müller, Felix

    2014-08-15

    One focus of ecosystem service research is the connection between biodiversity, ecosystem services and human well-being as well as the socioeconomic influences on them. Despite existing investigations, exact impacts from the human system on the dynamics of biodiversity, ecosystem services and human well-being are still uncertain because of the insufficiency of the respective quantitative analyses. Our research aims are discerning the socioeconomic influences on biodiversity, ecosystem services and human well-being and demonstrating mutual impacts between these items. We propose a DPSIR framework coupling ecological integrity, ecosystem services as well as human well-being and suggest DPSIR indicators for the case study area Jiangsu, China. Based on available statistical and surveying data, we revealed the factors significantly impacting biodiversity, ecosystem services and human well-being in the research area through factor analysis and correlation analysis, using the 13 prefecture-level cities of Jiangsu as samples. The results show that urbanization and industrialization in the urban areas have predominant positive influences on regional biodiversity, agricultural productivity and tourism services as well as rural residents' living standards. Additionally, the knowledge, technology and finance inputs for agriculture also have generally positive impacts on these system components. Concerning regional carbon storage, non-cropland vegetation cover obviously plays a significant positive role. Contrarily, the expansion of farming land and the increase of total food production are two important negative influential factors of biodiversity, ecosystem's food provisioning service capacity, regional tourism income and the well-being of the rural population. Our study provides a promising approach based on the DPSIR model to quantitatively capture the socioeconomic influential factors of biodiversity, ecosystem services and human well-being for human-environmental systems

  12. Socioeconomic influences on biodiversity, ecosystem services and human well-being: a quantitative application of the DPSIR model in Jiangsu, China.

    Science.gov (United States)

    Hou, Ying; Zhou, Shudong; Burkhard, Benjamin; Müller, Felix

    2014-08-15

    One focus of ecosystem service research is the connection between biodiversity, ecosystem services and human well-being as well as the socioeconomic influences on them. Despite existing investigations, exact impacts from the human system on the dynamics of biodiversity, ecosystem services and human well-being are still uncertain because of the insufficiency of the respective quantitative analyses. Our research aims are discerning the socioeconomic influences on biodiversity, ecosystem services and human well-being and demonstrating mutual impacts between these items. We propose a DPSIR framework coupling ecological integrity, ecosystem services as well as human well-being and suggest DPSIR indicators for the case study area Jiangsu, China. Based on available statistical and surveying data, we revealed the factors significantly impacting biodiversity, ecosystem services and human well-being in the research area through factor analysis and correlation analysis, using the 13 prefecture-level cities of Jiangsu as samples. The results show that urbanization and industrialization in the urban areas have predominant positive influences on regional biodiversity, agricultural productivity and tourism services as well as rural residents' living standards. Additionally, the knowledge, technology and finance inputs for agriculture also have generally positive impacts on these system components. Concerning regional carbon storage, non-cropland vegetation cover obviously plays a significant positive role. Contrarily, the expansion of farming land and the increase of total food production are two important negative influential factors of biodiversity, ecosystem's food provisioning service capacity, regional tourism income and the well-being of the rural population. Our study provides a promising approach based on the DPSIR model to quantitatively capture the socioeconomic influential factors of biodiversity, ecosystem services and human well-being for human-environmental systems

  13. From bacterial genome to functionality; case bifidobacteria.

    Science.gov (United States)

    Ventura, Marco; O'Connell-Motherway, Mary; Leahy, Sinead; Moreno-Munoz, Jose Antonio; Fitzgerald, Gerald F; van Sinderen, Douwe

    2007-11-30

    The availability of complete bacterial genome sequences has significantly furthered our understanding of the genetics, physiology and biochemistry of the microorganisms in question, particularly those that have commercially important applications. Bifidobacteria are among such microorganisms, as they constitute mammalian commensals of biotechnological significance due to their perceived role in maintaining a balanced gastrointestinal (GIT) microflora. Bifidobacteria are therefore frequently used as health-promoting or probiotic components in functional food products. A fundamental understanding of the metabolic activities employed by these commensal bacteria, in particular their capability to utilize a wide range of complex oligosaccharides, can reveal ways to provide in vivo growth advantages relative to other competing gut bacteria or pathogens. Furthermore, an in depth analysis of adaptive responses to nutritional or environmental stresses may provide methodologies to retain viability and improve functionality during commercial preparation, storage and delivery of the probiotic organism. PMID:17629975

  14. Exploring connections in social-ecological systems : The links between biodiversity, ecosystem services, and human well-being in South Africa

    OpenAIRE

    Hamann, Maike

    2016-01-01

    A key challenge of the Anthropocene is to advance human development without undermining critical ecosystem services. Central to this challenge is a better understanding of the interactions and feedbacks between biodiversity, ecosystem services and human well-being, which interact in dynamic and complex social-ecological systems. These relationships have been the focus of much work in the past decades, however more remains to be done to comprehensively identify and quantify them, especially at...

  15. Jack-of-all-trades effects drive biodiversity-ecosystem multifunctionality relationships in European forests.

    Science.gov (United States)

    van der Plas, Fons; Manning, Peter; Allan, Eric; Scherer-Lorenzen, Michael; Verheyen, Kris; Wirth, Christian; Zavala, Miguel A; Hector, Andy; Ampoorter, Evy; Baeten, Lander; Barbaro, Luc; Bauhus, Jürgen; Benavides, Raquel; Benneter, Adam; Berthold, Felix; Bonal, Damien; Bouriaud, Olivier; Bruelheide, Helge; Bussotti, Filippo; Carnol, Monique; Castagneyrol, Bastien; Charbonnier, Yohan; Coomes, David; Coppi, Andrea; Bastias, Cristina C; Muhie Dawud, Seid; De Wandeler, Hans; Domisch, Timo; Finér, Leena; Gessler, Arthur; Granier, André; Grossiord, Charlotte; Guyot, Virginie; Hättenschwiler, Stephan; Jactel, Hervé; Jaroszewicz, Bogdan; Joly, François-Xavier; Jucker, Tommaso; Koricheva, Julia; Milligan, Harriet; Müller, Sandra; Muys, Bart; Nguyen, Diem; Pollastrini, Martina; Raulund-Rasmussen, Karsten; Selvi, Federico; Stenlid, Jan; Valladares, Fernando; Vesterdal, Lars; Zielínski, Dawid; Fischer, Markus

    2016-03-24

    There is considerable evidence that biodiversity promotes multiple ecosystem functions (multifunctionality), thus ensuring the delivery of ecosystem services important for human well-being. However, the mechanisms underlying this relationship are poorly understood, especially in natural ecosystems. We develop a novel approach to partition biodiversity effects on multifunctionality into three mechanisms and apply this to European forest data. We show that throughout Europe, tree diversity is positively related with multifunctionality when moderate levels of functioning are required, but negatively when very high function levels are desired. For two well-known mechanisms, 'complementarity' and 'selection', we detect only minor effects on multifunctionality. Instead a third, so far overlooked mechanism, the 'jack-of-all-trades' effect, caused by the averaging of individual species effects on function, drives observed patterns. Simulations demonstrate that jack-of-all-trades effects occur whenever species effects on different functions are not perfectly correlated, meaning they may contribute to diversity-multifunctionality relationships in many of the world's ecosystems.

  16. Fold modulating function: Bacterial toxins to functional amyloids

    Directory of Open Access Journals (Sweden)

    Adnan Khawaja Syed

    2014-08-01

    Full Text Available Many bacteria produce cytolytic toxins that target host cells or other competing microbes. It is well known that environmental factors control toxin expression, however recent work suggests that some bacteria manipulate the fold of these protein toxins to control their function. The β-sheet rich amyloid fold is a highly stable ordered aggregate that many toxins form in response to specific environmental conditions. When in the amyloid state, toxins become inert, losing the cytolytic activity they display in the soluble form. Emerging evidence suggest that some amyloids function as toxin storage systems until they are again needed, while other bacteria utilize amyloids as a structural matrix component of biofilms. This amyloid matrix component facilitates resistance to biofilm disruptive challenges. The bacterial amyloids discussed in this review reveal an elegant system where changes in protein fold and solubility dictate the function of proteins in response to the environment.

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

    Lifescience Database Archive (English)

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

  18. Hijacking of eukaryotic functions by intracellular bacterial pathogens

    OpenAIRE

    Alonso, Ana; García del Portillo, Francisco

    2004-01-01

    Intracellular bacterial pathogens have evolved as a group of microorganisms endowed with weapons to hijack many biological processes of eukaryotic cells. This review discusses how these pathogens perturb diverse host cell functions, such as cytoskeleton dynamics and organelle vesicular trafficking. Alteration of the cytoskeleton is discussed in the context of the bacterial entry process (invasion), which occurs either by activation of membrane-located host receptors ("zipper" mechani...

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

    Science.gov (United States)

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

    2013-07-01

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

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

    Science.gov (United States)

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

    2013-07-01

    Emerging and reemerging bacterial infectious diseases are a major public health concern worldwide. The role of bacteriophages in the emergence of novel bacterial pathogens by horizontal gene transfer was highlighted by the May 2011 Escherichia coli O104:H4 outbreaks that originated in Germany and spread to other European countries. This outbreak also highlighted the pivotal role played by recent advances in functional genomics in rapidly deciphering the virulence mechanism elicited by this novel pathogen and developing rapid diagnostics and therapeutics. However, despite a steady increase in the number of phage sequences in the public databases, boosted by the next-generation sequencing technologies, few functional genomics studies of bacteriophages have been conducted. Our definition of 'functional genomics' encompasses a range of aspects: phage genome sequencing, annotation and ascribing functions to phage genes, prophage identification in bacterial sequences, elucidating the events in various stages of phage life cycle using genomic, transcriptomic and proteomic approaches, defining the mechanisms of host takeover including specific bacterial-phage protein interactions and identifying virulence and other adaptive features encoded by phages and finally, using prophage genomic information for bacterial detection/diagnostics. Given the breadth and depth of this definition and the fact that some of these aspects (especially phage-encoded virulence/adaptive features) have been treated extensively in other reviews, we restrict our focus only on certain aspects. These include phage genome sequencing and annotation, identification of prophages in bacterial sequences and genetic characterization of phages, functional genomics of the infection process and finally, bacterial identification using genomic information. PMID:23520178

  1. Hijacking mitochondria: bacterial toxins that modulate mitochondrial function.

    Science.gov (United States)

    Jiang, Jhih-Hang; Tong, Janette; Gabriel, Kipros

    2012-05-01

    Bacterial infection has enormous global social and economic impacts stemming from effects on human health and agriculture. Although there are still many unanswered questions, decades of research has uncovered many of the pathogenic mechanisms at play. It is now clear that bacterial pathogens produce a plethora of proteins known as "toxins" and "effectors" that target a variety of physiological host processes during the course of infection. One of the targets of host targeted bacterial toxins and effectors are the mitochondria. The mitochondrial organelles are major players in many biological functions, including energy conversion to ATP and cell death pathways, which inherently makes them targets for bacterial proteins. We present a summary of the toxins targeted to mitochondria and for those that have been studied in finer detail, we also summarize what we know about the mechanisms of targeting and finally their action at the organelle.

  2. Functional recovery of biofilm bacterial communities after copper exposure

    Energy Technology Data Exchange (ETDEWEB)

    Boivin, Marie-Elene Y. [National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven (Netherlands) and Vrije Universiteit, Department of Animal Ecology, De Boelelaan 1085, 1081 HV Amsterdam (Netherlands)]. E-mail: marie-elene.boivin@rivm.nl; Massieux, Boris [Netherlands Institutes of Ecology, Centre for Limnology, Rijkstraatweg 6, 3631 AC Nieuwersluis (Netherlands); Breure, Anton M. [National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven (Netherlands); Greve, Gerdit D. [National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven (Netherlands); Vrije Universiteit, Department of Animal Ecology, De Boelelaan 1085, 1081 HV Amsterdam (Netherlands); Rutgers, Michiel [National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA Bilthoven (Netherlands); Admiraal, Wim [University of Amsterdam, Department of Aquatic Ecology and Ecotoxicology, Kruislaan 320, 1098 SM Amsterdam (Netherlands)

    2006-03-15

    Potential of bacterial communities in biofilms to recover after copper exposure was investigated. Biofilms grown outdoor in shallow water on glass dishes were exposed in the laboratory to 0.6, 2.1, 6.8 {mu}mol/l copper amended surface water and a reference and subsequently to un-amended surface water. Transitions of bacterial communities were characterised with denaturing gradient gel electrophoresis (DGGE) and community-level physiological profiles (CLPP). Exposure to 6.8 {mu}mol/l copper provoked distinct changes in DGGE profiles of bacterial consortia, which did not reverse upon copper depuration. Exposure to 2.1 and 6.8 {mu}mol/l copper was found to induce marked changes in CLPP of bacterial communities that proved to be reversible during copper depuration. Furthermore, copper exposure induced the development of copper-tolerance, which was partially lost during depuration. It is concluded that bacterial communities exposed to copper contaminated water for a period of 26 days are capable to restore their metabolic attributes after introduction of unpolluted water in aquaria for 28 days. - Genetically different bacterial communities can have similar functions and tolerance to copper.

  3. Hopanoids as functional analogues of cholesterol in bacterial membranes.

    Science.gov (United States)

    Sáenz, James P; Grosser, Daniel; Bradley, Alexander S; Lagny, Thibaut J; Lavrynenko, Oksana; Broda, Martyna; Simons, Kai

    2015-09-22

    The functionality of cellular membranes relies on the molecular order imparted by lipids. In eukaryotes, sterols such as cholesterol modulate membrane order, yet they are not typically found in prokaryotes. The structurally similar bacterial hopanoids exhibit similar ordering properties as sterols in vitro, but their exact physiological role in living bacteria is relatively uncharted. We present evidence that hopanoids interact with glycolipids in bacterial outer membranes to form a highly ordered bilayer in a manner analogous to the interaction of sterols with sphingolipids in eukaryotic plasma membranes. Furthermore, multidrug transport is impaired in a hopanoid-deficient mutant of the gram-negative Methylobacterium extorquens, which introduces a link between membrane order and an energy-dependent, membrane-associated function in prokaryotes. Thus, we reveal a convergence in the architecture of bacterial and eukaryotic membranes and implicate the biosynthetic pathways of hopanoids and other order-modulating lipids as potential targets to fight pathogenic multidrug resistance.

  4. Capsule shields the function of short bacterial adhesins

    DEFF Research Database (Denmark)

    Schembri, Mark; Dalsgaard, D.; Klemm, Per

    2004-01-01

    Bacterial surface structures such as capsules and adhesins are generally regarded as important virulence factors. Here we demonstrate that capsules block the function of the self-recognizing protein antigen 43 through physical shielding. The phenomenon is not restricted to Escherichia coli but can...

  5. The structure and function of bacterial light-harvesting complexes.

    Science.gov (United States)

    Law, Christopher J; Roszak, Aleksander W; Southall, June; Gardiner, Alastair T; Isaacs, Neil W; Cogdell, Richard J

    2004-01-01

    The harvesting of solar radiation by purple photosynthetic bacteria is achieved by circular, integral membrane pigment-protein complexes. There are two main types of light-harvesting complex, termed LH2 and LH1, that function to absorb light energy and to transfer that energy rapidly and efficiently to the photochemical reaction centres where it is trapped. This mini-review describes our present understanding of the structure and function of the purple bacterial light-harvesting complexes.

  6. Exchange of rotor components in functioning bacterial flagellar motor

    International Nuclear Information System (INIS)

    The bacterial flagellar motor is a rotary motor driven by the electrochemical potential of a coupling ion. The interaction between a rotor and stator units is thought to generate torque. The overall structure of flagellar motor has been thought to be static, however, it was recently proved that stators are exchanged in a rotating motor. Understanding the dynamics of rotor components in functioning motor is important for the clarifying of working mechanism of bacterial flagellar motor. In this study, we focused on the dynamics and the turnover of rotor components in a functioning flagellar motor. Expression systems for GFP-FliN, FliM-GFP, and GFP-FliG were constructed, and each GFP-fusion was functionally incorporated into the flagellar motor. To investigate whether the rotor components are exchanged in a rotating motor, we performed fluorescence recovery after photobleaching experiments using total internal reflection fluorescence microscopy. After photobleaching, in a tethered cell producing GFP-FliN or FliM-GFP, the recovery of fluorescence at the rotational center was observed. However, in a cell producing GFP-FliG, no recovery of fluorescence was observed. The transition phase of fluorescence intensity after full or partially photobleaching allowed the turnover of FliN subunits to be calculated as 0.0007 s-1, meaning that FliN would be exchanged in tens of minutes. These novel findings indicate that a bacterial flagellar motor is not a static structure even in functioning state. This is the first report for the exchange of rotor components in a functioning bacterial flagellar motor.

  7. Bacterial cellulose biosynthesis: diversity of operons, subunits, products and functions

    OpenAIRE

    Römling, Ute; Galperin, Michael Y

    2015-01-01

    Recent studies of bacterial cellulose biosynthesis, including structural characterization of a functional cellulose synthase complex, provided the first mechanistic insight into this fascinating process. In most studied bacteria, just two subunits, BcsA and BcsB, are necessary and sufficient for the formation of the polysaccharide chain in vitro. Other subunits – which differ among various taxa – affect the enzymatic activity and product yield in vivo by modulating expression of biosynthesis ...

  8. Bacterial cellulose biosynthesis: diversity of operons, subunits, products and functions

    Science.gov (United States)

    Römling, Ute; Galperin, Michael Y.

    2015-01-01

    Summary Recent studies of bacterial cellulose biosynthesis, including structural characterization of a functional cellulose synthase complex, provided the first mechanistic insight into this fascinating process. In most studied bacteria, just two subunits, BcsA and BcsB, are necessary and sufficient for the formation of the polysaccharide chain in vitro. Other subunits – which differ among various taxa – affect the enzymatic activity and product yield in vivo by modulating expression of biosynthesis apparatus, export of the nascent β-D-glucan polymer to the cell surface, and the organization of cellulose fibers into a higher-order structure. These auxiliary subunits play key roles in determining the quantity and structure of the resulting biofilm, which is particularly important for interactions of bacteria with higher organisms that lead to rhizosphere colonization and modulate virulence of cellulose-producing bacterial pathogens inside and outside of host cells. Here we review the organization of four principal types of cellulose synthase operons found in various bacterial genomes, identify additional bcs genes that encode likely components of the cellulose biosynthesis and secretion machinery, and propose a unified nomenclature for these genes and subunits. We also discuss the role of cellulose as a key component of biofilms formed by a variety of free-living and pathogenic bacteria and, for the latter, in the choice between acute infection and persistence in the host. PMID:26077867

  9. Role of functionally dominant species in varying environmental regimes: evidence for the performance-enhancing effect of biodiversity

    Directory of Open Access Journals (Sweden)

    Langenheder Silke

    2012-07-01

    Full Text Available Abstract Background Theory suggests that biodiversity can act as a buffer against disturbances and environmental variability via two major mechanisms: Firstly, a stabilising effect by decreasing the temporal variance in ecosystem functioning due to compensatory processes; and secondly, a performance enhancing effect by raising the level of community response through the selection of better performing species. Empirical evidence for the stabilizing effect of biodiversity is readily available, whereas experimental confirmation of the performance-enhancing effect of biodiversity is sparse. Results Here, we test the effect of different environmental regimes (constant versus fluctuating temperature on bacterial biodiversity-ecosystem functioning relations. We show that positive effects of species richness on ecosystem functioning are enhanced by stronger temperature fluctuations due to the increased performance of individual species. Conclusions Our results provide evidence for the performance enhancing effect and suggest that selection towards functionally dominant species is likely to benefit the maintenance of ecosystem functioning under more variable conditions.

  10. Beyond growth: novel functions for bacterial cell wall hydrolases.

    Science.gov (United States)

    Wyckoff, Timna J; Taylor, Jennifer A; Salama, Nina R

    2012-11-01

    The peptidoglycan cell wall maintains turgor pressure and cell shape of most bacteria. Cell wall hydrolases are essential, together with synthases, for growth and daughter cell separation. Recent work in diverse organisms has uncovered new cell wall hydrolases that act autonomously or on neighboring cells to modulate invasion of prey cells, cell shape, innate immune detection, intercellular communication, and competitor lysis. The hydrolases involved in these processes catalyze the cleavage of bonds throughout the sugar and peptide moities of peptidoglycan. Phenotypes associated with these diverse hydrolases reveal new functions of the bacterial cell wall beyond growth and division.

  11. Bacterial dynamics in steady-state biofilters: beyond functional stability.

    Science.gov (United States)

    Cabrol, Léa; Malhautier, Luc; Poly, Franck; Lepeuple, Anne-Sophie; Fanlo, Jean-Louis

    2012-01-01

    The spatial and temporal dynamics of microbial community structure and function were surveyed in duplicated woodchip-biofilters operated under constant conditions for 231 days. The contaminated gaseous stream for treatment was representative of composting emissions, included ammonia, dimethyl disulfide and a mixture of five oxygenated volatile organic compounds. The community structure and diversity were investigated by denaturing gradient gel electrophoresis on 16S rRNA gene fragments. During the first 42 days, microbial acclimatization revealed the influence of operating conditions and contaminant loading on the biofiltration community structure and diversity, as well as the limited impact of inoculum compared to the greater persistence of the endogenous woodchip community. During long-term operation, a high and stable removal efficiency was maintained despite a highly dynamic microbial community, suggesting the probable functional redundancy of the community. Most of the contaminant removal occurred in the first compartment, near the gas inlet, where the microbial diversity was the highest. The stratification of the microbial structures along the filter bed was statistically correlated to the longitudinal distribution of environmental conditions (selective pressure imposed by contaminant concentrations) and function (contaminant elimination capacity), highlighting the central role of the bacterial community. The reproducibility of microbial succession in replicates suggests that the community changes were presumably driven by a deterministic process.

  12. Structure-function investigations of bacterial photosynthetic reaction centers.

    Science.gov (United States)

    Leonova, M M; Fufina, T Yu; Vasilieva, L G; Shuvalov, V A

    2011-12-01

    During photosynthesis light energy is converted into energy of chemical bonds through a series of electron and proton transfer reactions. Over the first ultrafast steps of photosynthesis that take place in the reaction center (RC) the quantum efficiency of the light energy transduction is nearly 100%. Compared to the plant and cyanobacterial photosystems, bacterial RCs are well studied and have relatively simple structure. Therefore they represent a useful model system both for manipulating of the electron transfer parameters to study detailed mechanisms of its separate steps as well as to investigate the common principles of the photosynthetic RC structure, function, and evolution. This review is focused on the research papers devoted to chemical and genetic modifications of the RCs of purple bacteria in order to study principles and mechanisms of their functioning. Investigations of the last two decades show that the maximal rates of the electron transfer reactions in the RC depend on a number of parameters. Chemical structure of the cofactors, distances between them, their relative orientation, and interactions to each other are of great importance for this process. By means of genetic and spectral methods, it was demonstrated that RC protein is also an essential factor affecting the efficiency of the photochemical charge separation. Finally, some of conservative water molecules found in RC not only contribute to stability of the protein structure, but are directly involved in the functioning of the complex.

  13. Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest.

    Science.gov (United States)

    Kembel, Steven W; O'Connor, Timothy K; Arnold, Holly K; Hubbell, Stephen P; Wright, S Joseph; Green, Jessica L

    2014-09-23

    The phyllosphere--the aerial surfaces of plants, including leaves--is a ubiquitous global habitat that harbors diverse bacterial communities. Phyllosphere bacterial communities have the potential to influence plant biogeography and ecosystem function through their influence on the fitness and function of their hosts, but the host attributes that drive community assembly in the phyllosphere are poorly understood. In this study we used high-throughput sequencing to quantify bacterial community structure on the leaves of 57 tree species in a neotropical forest in Panama. We tested for relationships between bacterial communities on tree leaves and the functional traits, taxonomy, and phylogeny of their plant hosts. Bacterial communities on tropical tree leaves were diverse; leaves from individual trees were host to more than 400 bacterial taxa. Bacterial communities in the phyllosphere were dominated by a core microbiome of taxa including Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria, and Sphingobacteria. Host attributes including plant taxonomic identity, phylogeny, growth and mortality rates, wood density, leaf mass per area, and leaf nitrogen and phosphorous concentrations were correlated with bacterial community structure on leaves. The relative abundances of several bacterial taxa were correlated with suites of host plant traits related to major axes of plant trait variation, including the leaf economics spectrum and the wood density-growth/mortality tradeoff. These correlations between phyllosphere bacterial diversity and host growth, mortality, and function suggest that incorporating information on plant-microbe associations will improve our ability to understand plant functional biogeography and the drivers of variation in plant and ecosystem function.

  14. Metabolomic Functional Analysis of Bacterial Genomes: Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Arp, Daniel J; Sayavedra-Soto, Luis A

    2008-01-01

    The availability of the complete DNA sequence of the bacterial genome of Nitrosomonas europaea offered the opportunity for unprecedented and detailed investigations of function. We studied the function of genes involved in carbohydrate and Fe metabolism. N. europaea has genes for the synthesis and degradation of glycogen and sucrose but cannot grow on substrates other than ammonia and CO2. Granules of glycogen were detected in whole cells by electron microscopy and quantified in cell-free extracts by enzymatic methods. The cellular glycogen and sucrose content varied depending on the composition of the growth medium and cellular growth stage. N. europaea also depends heavily on iron for metabolism of ammonia, is particularly interesting since it lacks genes for siderophore production, and has genes with only low similarity to known iron reductases, yet grows relatively well in medium containing low Fe. By comparing the transcriptomes of cells grown in iron-replete medium versus iron-limited medium, 247 genes were identified as differentially expressed. Mutant strains deficient in genes for sucrose, glycogen and iron metabolism were created and are being used to further our understanding of ammonia oxidizing bacteria.

  15. Function and modulation of bacterial porins: insights from electrophysiology.

    Science.gov (United States)

    Delcour, A H

    1997-06-15

    Electrophysiological techniques provide a wealth of information regarding the molecular mechanisms that underlie the function and modulation of ion channels. They have revealed that bacterial porins do not behave as static, permanently open pores but display a much more complex and dynamic behavior than anticipated from non-electrophysiological studies. The channels switch between short-lived open and closed conformations (gating activity), and can also remain in an inactivated, non-ion conducting state for prolonged periods of time. Thus the role of porins is not limited to that of a molecular filter, but is extended to the control of outer membrane permeability through the regulation of their activity. Electrophysiological studies have indeed demonstrated that both gating and inactivation are modulated by a variety of physical and chemical parameters and are highly cooperative phenomena, often involving numerous channels working in concert. Cooperativity acts as an amplification mechanism that grants a large population of porins, such as found in the outer membrane, with sensitivity to modulation by external or internal factors. By conferring permeability properties to the outer membrane, porins play a crucial role in the bacterium's antibiotic susceptibility and survival in various environmental conditions. The detailed information that electrophysiology only can provide on porin function and modulation promises to yield a more accurate description of how porin properties can be used by cells to adapt to a changing environment, and to offer mechanisms that might optimize the drug sensitivity of the microorganism. PMID:9228742

  16. Bacterial Cellulose (BC) as a Functional Nanocomposite Biomaterial

    Science.gov (United States)

    Nandgaonkar, Avinav Ghanashyam

    Cellulosic is the most abundant biopolymer in the landscape and can be found in many different organisms. It has been already seen use in the medical field, for example cotton for wound dressings and sutures. Although cellulose is naturally occurring and has found a number of applications inside and outside of the medical field, it is not typically produced in its pure state. A lengthy process is required to separate the lignin, hemicelluloses and other molecules from the cellulose in most renewables (wood, agricultural fibers such as cotton, monocots, grasses, etc.). Although bacterial cellulose has a similar chemical structure to plant cellulose, it is easier to process because of the absence of lignin and hemicelluloses which require a lot of energy and chemicals for removal. Bacterial cellulose (BC) is produced from various species of bacteria such as Gluconacetobacter xylinus. Due to its high water uptake, it has the tendency to form gels. It displays high tensile strength, biocompatibility, and purity compared to wood cellulose. It has found applications in fields such as paper, paper products, audio components (e.g., speaker diaphragms), flexible electronics, supercapacitors, electronics, and soft tissue engineering. In my dissertation, we have functionalized and studied BC-based materials for three specific applications: cartilage tissue engineering, bioelectronics, and dye degradation. In our first study, we prepared a highly organized porous material based on BC by unidirectional freezing followed by a freeze-drying process. Chitosan was added to impart additional properties to the resulting BC-based scaffolds that were evaluated in terms of their morphological, chemical, and physical properties for cartilage tissue engineering. The properties of the resulting scaffold were tailored by adjusting the concentration of chitosan over 1, 1.5, and 2 % (by wt-%). The scaffolds containing chitosan showed excellent shape recovery and structural stability after

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-09-01

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

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

    Science.gov (United States)

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

    2016-09-21

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

  20. Functional recovery of biofilm bacterial communities after copper exposure.

    NARCIS (Netherlands)

    Boivin, Marie-Elène Y; Massieux, Boris; Breure, Anton M; Greve, Gerdit D; Rutgers, Michiel; Admiraal, Wim

    2006-01-01

    Potential of bacterial communities in biofilms to recover after copper exposure was investigated. Biofilms grown outdoor in shallow water on glass dishes were exposed in the laboratory to 0.6, 2.1, 6.8 micromol/l copper amended surface water and a reference and subsequently to un-amended surface wat

  1. Ecosystem response of pasture soil communities to fumigation-induced microbial diversity reductions: an examination of the biodiversity-ecosystem function relationship

    NARCIS (Netherlands)

    Griffiths, B.S.; Ritz, K.; Bardgett, R.D.; Cook, R.; Christensen, S.; Ekelund, F.; Sorensen, S.J.; Bccth, E.; Bloem, J.; Ruiter, de P.C.; Dolfing, J.; Nicolardot, B.

    2000-01-01

    A technique based on progressive fumigation was used to reduce soil microbial biodiversity, and the effects of such reductions upon the stability of key soil processes were measured. Mineral soil samples from a grassland were fumigated with chloroform for up to 24 h and then incubated for 5 months t

  2. Soil bacterial endemism and potential functional redundancy in natural broadleaf forest along a latitudinal gradient.

    Science.gov (United States)

    Zhang, Yuguang; Cong, Jing; Lu, Hui; Deng, Ye; Liu, Xiao; Zhou, Jizhong; Li, Diqiang

    2016-01-01

    Microorganisms play key roles in ecosystem processes and biogeochemical cycling, however, the relationship between soil microbial taxa diversity and their function in natural ecosystems is largely unknown. To determine how soil bacteria community and function are linked from the local to regional scale, we studied soil bacteria community composition, potential function and environmental conditions in natural and mature broadleaf forests along a latitudinal gradient in China, using the Illumina 16S rRNA sequencing and GeoChip technologies. The results showed strong biogeographic endemism pattern in soil bacteria were existed, and the spatial distance and climatic variables were the key controlling factors for this pattern. Therefore, dispersal limitation and environmental selection may represent two key processes in generating and maintaining the soil bacterial biogeographic pattern. By contrast, the soil bacterial potential function is highly convergent along the latitudinal gradient and there were highly differing bacterial community compositions, and the soil chemistry may include the main factors active in shaping the soil bacterial potential function. Therefore, the soil bacterial potential function may be affected by local gradients in resource availability, and predicting soil bacterial potential function requires knowledge of abiotic and biotic environmental factors. PMID:27357005

  3. Soil bacterial endemism and potential functional redundancy in natural broadleaf forest along a latitudinal gradient

    Science.gov (United States)

    Zhang, Yuguang; Cong, Jing; Lu, Hui; Deng, Ye; Liu, Xiao; Zhou, Jizhong; Li, Diqiang

    2016-06-01

    Microorganisms play key roles in ecosystem processes and biogeochemical cycling, however, the relationship between soil microbial taxa diversity and their function in natural ecosystems is largely unknown. To determine how soil bacteria community and function are linked from the local to regional scale, we studied soil bacteria community composition, potential function and environmental conditions in natural and mature broadleaf forests along a latitudinal gradient in China, using the Illumina 16S rRNA sequencing and GeoChip technologies. The results showed strong biogeographic endemism pattern in soil bacteria were existed, and the spatial distance and climatic variables were the key controlling factors for this pattern. Therefore, dispersal limitation and environmental selection may represent two key processes in generating and maintaining the soil bacterial biogeographic pattern. By contrast, the soil bacterial potential function is highly convergent along the latitudinal gradient and there were highly differing bacterial community compositions, and the soil chemistry may include the main factors active in shaping the soil bacterial potential function. Therefore, the soil bacterial potential function may be affected by local gradients in resource availability, and predicting soil bacterial potential function requires knowledge of abiotic and biotic environmental factors.

  4. Genetic difference but functional similarity among fish gut bacterial communities through molecular and biochemical fingerprints

    OpenAIRE

    Mouchet, M.A.; Bouvier, C.; Bouvier, T.; Troussellier, Marc; Escalas, A.; Mouillot, D.

    2012-01-01

    Considering the major involvement of gut microflora in the digestive function of various macro-organisms, bacterial communities inhabiting fish guts may be the main actors of organic matter degradation by fish. Nevertheless, the extent and the sources of variability in the degradation potential of gut bacterial communities are largely overlooked. Using Biolog Ecoplate (TM) and denaturing gradient gel electrophoresis (DGGE), we explored functional (i.e. the ability to degrade organic matter) a...

  5. Bacterial community structure and function shift across a northern boreal forest fire chronosequence

    Science.gov (United States)

    Sun, Hui; Santalahti, Minna; Pumpanen, Jukka; Köster, Kajar; Berninger, Frank; Raffaello, Tommaso; Asiegbu, Fred O.; Heinonsalo, Jussi

    2016-01-01

    Soil microbial responses to fire are likely to change over the course of forest recovery. Investigations on long-term changes in bacterial dynamics following fire are rare. We characterized the soil bacterial communities across three different times post fire in a 2 to 152-year fire chronosequence by Illumina MiSeq sequencing, coupled with a functional gene array (GeoChip). The results showed that the bacterial diversity did not differ between the recently and older burned areas, suggesting a concomitant recovery in the bacterial diversity after fire. The differences in bacterial communities over time were mainly driven by the rare operational taxonomic units (OTUs analysis using gene signal intensity revealed that the sites with different fire histories formed separate clusters, suggesting potential differences in maintaining essential biogeochemical soil processes. Soil temperature, pH and water contents were the most important factors in shaping the bacterial community structures and function. This study provides functional insight on the impact of fire disturbance on soil bacterial community. PMID:27573440

  6. Bacterial community structure and function shift across a northern boreal forest fire chronosequence.

    Science.gov (United States)

    Sun, Hui; Santalahti, Minna; Pumpanen, Jukka; Köster, Kajar; Berninger, Frank; Raffaello, Tommaso; Asiegbu, Fred O; Heinonsalo, Jussi

    2016-01-01

    Soil microbial responses to fire are likely to change over the course of forest recovery. Investigations on long-term changes in bacterial dynamics following fire are rare. We characterized the soil bacterial communities across three different times post fire in a 2 to 152-year fire chronosequence by Illumina MiSeq sequencing, coupled with a functional gene array (GeoChip). The results showed that the bacterial diversity did not differ between the recently and older burned areas, suggesting a concomitant recovery in the bacterial diversity after fire. The differences in bacterial communities over time were mainly driven by the rare operational taxonomic units (OTUs cycling pathways were present in all sites showing high redundancy in the gene profiles. However, hierarchical cluster analysis using gene signal intensity revealed that the sites with different fire histories formed separate clusters, suggesting potential differences in maintaining essential biogeochemical soil processes. Soil temperature, pH and water contents were the most important factors in shaping the bacterial community structures and function. This study provides functional insight on the impact of fire disturbance on soil bacterial community. PMID:27573440

  7. Genome-scale co-evolutionary inference identifies functions and clients of bacterial Hsp90.

    Science.gov (United States)

    Press, Maximilian O; Li, Hui; Creanza, Nicole; Kramer, Günter; Queitsch, Christine; Sourjik, Victor; Borenstein, Elhanan

    2013-01-01

    The molecular chaperone Hsp90 is essential in eukaryotes, in which it facilitates the folding of developmental regulators and signal transduction proteins known as Hsp90 clients. In contrast, Hsp90 is not essential in bacteria, and a broad characterization of its molecular and organismal function is lacking. To enable such characterization, we used a genome-scale phylogenetic analysis to identify genes that co-evolve with bacterial Hsp90. We find that genes whose gain and loss were coordinated with Hsp90 throughout bacterial evolution tended to function in flagellar assembly, chemotaxis, and bacterial secretion, suggesting that Hsp90 may aid assembly of protein complexes. To add to the limited set of known bacterial Hsp90 clients, we further developed a statistical method to predict putative clients. We validated our predictions by demonstrating that the flagellar protein FliN and the chemotaxis kinase CheA behaved as Hsp90 clients in Escherichia coli, confirming the predicted role of Hsp90 in chemotaxis and flagellar assembly. Furthermore, normal Hsp90 function is important for wild-type motility and/or chemotaxis in E. coli. This novel function of bacterial Hsp90 agreed with our subsequent finding that Hsp90 is associated with a preference for multiple habitats and may therefore face a complex selection regime. Taken together, our results reveal previously unknown functions of bacterial Hsp90 and open avenues for future experimental exploration by implicating Hsp90 in the assembly of membrane protein complexes and adaptation to novel environments. PMID:23874229

  8. The structure and functions of bacterial communities in an agrocenosis

    Science.gov (United States)

    Dobrovol'skaya, T. G.; Khusnetdinova, K. A.; Manucharova, N. A.; Balabko, P. N.

    2016-01-01

    The most significant factor responsible for the specific taxonomic composition of the bacterial communities in the agrocenosis studied was found to be a part or organ of plants (leaves, flowers, roots, fruits). A stage of plant ontogeny also determines changes of taxa. In the course of the plant growth, eccrisotrophic bacteria are replaced by hydrolytic ones that belong to the group of cellulose-decomposing bacteria. Representatives of the proteobacteria genera that are difficult to identify by phenotypic methods were determined using molecular-biological methods. They were revealed only on oat leaves in the moist period. As the vetch-oat mixture was fertilized with BIOUD-1 (foliar application) in the phyllosphere of both oats and vetch, on all the plant organs, representatives of the Rhodococcus genus as dominants were isolated. This fact was related to the capability of bacteria to decompose the complex aromatic compounds that are ingredients of the fertilizers applied. Another positive effect for plants of the bacterial communities forming in agrocenoses is the presence of bacteria that are antagonists of phytopathogenic bacteria. Thus, in agrocenoses, some interrelationships promoting the growth and reproduction of plants are formed in crop plants and bacteria.

  9. Biodiversity loss in grasslands : consequences for ecosystem functioning and interactions with above- and belowground organisms

    NARCIS (Netherlands)

    Ruijven, van J.

    2005-01-01

    Considering the current rate of extinctions, it is crucial to understand the consequences of these losses of biodiversity for the functioning of ecosystems. Grasslands proved a very suitable ecosystem for biodiversity-ecosystem functioning research.In earlier experiments, nitrogen-

  10. GroE chaperonins assisted functional expression of bacterial enzymes in Saccharomyces cerevisiae.

    Science.gov (United States)

    Xia, Peng-Fei; Zhang, Guo-Chang; Liu, Jing-Jing; Kwak, Suryang; Tsai, Ching-Sung; Kong, In Iok; Sung, Bong Hyun; Sohn, Jung-Hoon; Wang, Shu-Guang; Jin, Yong-Su

    2016-10-01

    Rapid advances in the capabilities of reading and writing DNA along with increasing understanding of microbial metabolism at the systems-level have paved an incredible path for metabolic engineering. Despite these advances, post-translational tools facilitating functional expression of heterologous enzymes in model hosts have not been developed well. Some bacterial enzymes, such as Escherichia coli xylose isomerase (XI) and arabinose isomerase (AI) which are essential for utilizing cellulosic sugars, cannot be functionally expressed in Saccharomyces cerevisiae. We hypothesized and demonstrated that the mismatching of the HSP60 chaperone systems between bacterial and eukaryotic cells might be the reason these bacterial enzymes cannot be functionally expressed in yeast. The results showed that the co-expression of E. coli GroE can facilitate the functional expression of E. coli XI and AI, as well as the Agrobacterium tumefaciens D-psicose epimerase in S. cerevisiae. The co-expression of bacterial chaperonins in S. cerevisiae is a promising post-translational strategy for the functional expression of bacterial enzymes in yeast. Biotechnol. Bioeng. 2016;113: 2149-2155. © 2016 Wiley Periodicals, Inc. PMID:27003667

  11. Community niche predicts the functioning of denitrifying bacterial assemblages

    NARCIS (Netherlands)

    Salles, Joana F.; Poly, Franck; Schmid, Bernhard; Le Roux, Xavier

    2009-01-01

    Predicting biodiversity effects on ecosystem functioning requires adequate evaluation of the mechanisms explaining why more diverse systems could perform better than less diverse ones. In this context, tackling functional diversity has become an important issue. Even though the aggregation of specie

  12. Determining and comparing protein function in Bacterial genome sequences

    DEFF Research Database (Denmark)

    Vesth, Tammi Camilla

    predictions were made in about 60% of the cases. This project has highlighted the difficulties and challenges in functional annotation and computational analysis of sequence data. It has provided possible solutions for creating reproducible pipelines for comparative genomics as well as constructed a number......In November 2013, there was around 21.000 different prokaryotic genomes sequenced and publicly available, and the number is growing daily with another 20.000 or more genomes expected to be sequenced and deposited by the end of 2014. An important part of the analysis of this data is the functional...... annotation of genes – the descriptions assigned to genes that describe the likely function of the encoded proteins. This process is limited by several factors, including the definition of a function which can be more or less specific as well as how many genes can actually be assigned a function based...

  13. Smart phone based bacterial detection using bio functionalized fluorescent nanoparticles

    International Nuclear Information System (INIS)

    We are describing immunochromatographic test strips with smart phone-based fluorescence readout. They are intended for use in the detection of the foodborne bacterial pathogens Salmonella spp. and Escherichia coli O157. Silica nanoparticles (SiNPs) were doped with FITC and Ru(bpy), conjugated to the respective antibodies, and then used in a conventional lateral flow immunoassay (LFIA). Fluorescence was recorded by inserting the nitrocellulose strip into a smart phone-based fluorimeter consisting of a light weight (40 g) optical module containing an LED light source, a fluorescence filter set and a lens attached to the integrated camera of the cell phone in order to acquire high-resolution fluorescence images. The images were analysed by exploiting the quick image processing application of the cell phone and enable the detection of pathogens within few minutes. This LFIA is capable of detecting pathogens in concentrations as low as 105 cfu mL−1 directly from test samples without pre-enrichment. The detection is one order of magnitude better compared to gold nanoparticle-based LFIAs under similar condition. The successful combination of fluorescent nanoparticle-based pathogen detection by LFIAs with a smart phone-based detection platform has resulted in a portable device with improved diagnosis features and having potential application in diagnostics and environmental monitoring. (author)

  14. Primary role of electron work function for evaluation of nanostructured titania implant surface against bacterial infection.

    Science.gov (United States)

    Golda-Cepa, M; Syrek, K; Brzychczy-Wloch, M; Sulka, G D; Kotarba, A

    2016-09-01

    The electron work function as an essential descriptor for the evaluation of metal implant surfaces against bacterial infection is identified for the first time. Its validity is demonstrated on Staphylococcus aureus adhesion to nanostructured titania surfaces. The established correlation: work function-bacteria adhesion is of general importance since it can be used for direct evaluation of any electrically conductive implant surfaces. PMID:27207043

  15. Diversity of Dominant Bacterial Taxa in Activated Sludge Promotes Functional Resistance following Toxic Shock Loading

    KAUST Repository

    Saikaly, Pascal

    2010-12-14

    Examining the relationship between biodiversity and functional stability (resistance and resilience) of activated sludge bacterial communities following disturbance is an important first step towards developing strategies for the design of robust biological wastewater treatment systems. This study investigates the relationship between functional resistance and biodiversity of dominant bacterial taxa by subjecting activated sludge samples, with different levels of biodiversity, to toxic shock loading with cupric sulfate (Cu[II]), 3,5-dichlorophenol (3,5-DCP), or 4-nitrophenol (4-NP). Respirometric batch experiments were performed to determine the functional resistance of activated sludge bacterial community to the three toxicants. Functional resistance was estimated as the 30 min IC50 or the concentration of toxicant that results in a 50% reduction in oxygen utilization rate compared to a referential state represented by a control receiving no toxicant. Biodiversity of dominant bacterial taxa was assessed using polymerase chain reaction-terminal restriction fragment length polymorphism (PCR-T-RFLP) targeting the 16S ribosomal RNA (16S rRNA) gene. Statistical analysis of 30 min IC50 values and PCR-T-RFLP data showed a significant positive correlation (P<0.05) between functional resistance and microbial diversity for each of the three toxicants tested. To our knowledge, this is the first study showing a positive correlation between biodiversity of dominant bacterial taxa in activated sludge and functional resistance. In this system, activated sludge bacterial communities with higher biodiversity are functionally more resistant to disturbance caused by toxic shock loading. © 2010 Springer Science+Business Media, LLC.

  16. Radial Basis Function Networks Applied in Bacterial Classification Based on MALDI-TOF-MS

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The radial basis function networks were applied to bacterial classification based on the matrix-assisted laser desorption/ionization time-of-flight mass spectrometric (MALDI-TOF-MS) data. The classification of bacteria cultured at different time was discussed and the effect of the network parameters on the classification was investigated. The cross-validation method was used to test the trained networks. The correctness of the classification of different bacteria investigated changes in a wide range from 61.5% to 92.8%. Owing to the complexity of biological effects in bacterial growth, the more rigid control of bacterial culture conditions seems to be a critical factor for improving the rate of correctness for bacterial classification.

  17. Genome-scale co-evolutionary inference identifies functions and clients of bacterial Hsp90.

    Directory of Open Access Journals (Sweden)

    Maximilian O Press

    Full Text Available The molecular chaperone Hsp90 is essential in eukaryotes, in which it facilitates the folding of developmental regulators and signal transduction proteins known as Hsp90 clients. In contrast, Hsp90 is not essential in bacteria, and a broad characterization of its molecular and organismal function is lacking. To enable such characterization, we used a genome-scale phylogenetic analysis to identify genes that co-evolve with bacterial Hsp90. We find that genes whose gain and loss were coordinated with Hsp90 throughout bacterial evolution tended to function in flagellar assembly, chemotaxis, and bacterial secretion, suggesting that Hsp90 may aid assembly of protein complexes. To add to the limited set of known bacterial Hsp90 clients, we further developed a statistical method to predict putative clients. We validated our predictions by demonstrating that the flagellar protein FliN and the chemotaxis kinase CheA behaved as Hsp90 clients in Escherichia coli, confirming the predicted role of Hsp90 in chemotaxis and flagellar assembly. Furthermore, normal Hsp90 function is important for wild-type motility and/or chemotaxis in E. coli. This novel function of bacterial Hsp90 agreed with our subsequent finding that Hsp90 is associated with a preference for multiple habitats and may therefore face a complex selection regime. Taken together, our results reveal previously unknown functions of bacterial Hsp90 and open avenues for future experimental exploration by implicating Hsp90 in the assembly of membrane protein complexes and adaptation to novel environments.

  18. Regulation of bacterial RecA protein function.

    Science.gov (United States)

    Cox, Michael M

    2007-01-01

    The RecA protein is a recombinase functioning in recombinational DNA repair in bacteria. RecA is regulated at many levels. The expression of the recA gene is regulated within the SOS response. The activity of the RecA protein itself is autoregulated by its own C-terminus. RecA is also regulated by the action of other proteins. To date, these include the RecF, RecO, RecR, DinI, RecX, RdgC, PsiB, and UvrD proteins. The SSB protein also indirectly affects RecA function by competing for ssDNA binding sites. The RecO and RecR, and possibly the RecF proteins, all facilitate RecA loading onto SSB-coated ssDNA. The RecX protein blocks RecA filament extension, and may have other effects on RecA activity. The DinI protein stabilizes RecA filaments. The RdgC protein binds to dsDNA and blocks RecA access to dsDNA. The PsiB protein, encoded by F plasmids, is uncharacterized, but may inhibit RecA in some manner. The UvrD helicase removes RecA filaments from RecA. All of these proteins function in a network that determines where and how RecA functions. Additional regulatory proteins may remain to be discovered. The elaborate regulatory pattern is likely to be reprised for RecA homologues in archaeans and eukaryotes. PMID:17364684

  19. Cryptic diversity and ecosystem functioning: a complex tale of differential effects on decomposition.

    Science.gov (United States)

    De Meester, N; Gingold, R; Rigaux, A; Derycke, S; Moens, T

    2016-10-01

    Marine ecosystems are experiencing accelerating population and species loss. Some ecosystem functions are decreasing and there is growing interest in the link between biodiversity and ecosystem functioning. The role of cryptic (morphologically identical but genetically distinct) species in this biodiversity-ecosystem functioning link is unclear and has not yet been formally tested. We tested if there is a differential effect of four cryptic species of the bacterivorous nematode Litoditis marina on the decomposition process of macroalgae. Bacterivorous nematodes can stimulate or slow down bacterial activity and modify the bacterial assemblage composition. Moreover, we tested if interspecific interactions among the four cryptic species influence the decomposition process. A laboratory experiment with both mono- and multispecific nematode cultures was conducted, and loss of organic matter and the activity of two key extracellular enzymes for the degradation of phytodetritus were assessed. L. marina mainly influenced qualitative aspects of the decomposition process rather than its overall rate: an effect of the nematodes on the enzymatic activities became manifest, although no clear nematode effect on bulk organic matter weight loss was found. We also demonstrated that species-specific effects on the decomposition process existed. Combining the four cryptic species resulted in high competition, with one dominant species, but without complete exclusion of other species. These interspecific interactions translated into different effects on the decomposition process. The species-specific differences indicated that each cryptic species may play an important and distinct role in ecosystem functioning. Functional differences may result in coexistence among very similar species. PMID:27337962

  20. Variable effects of dispersal on productivity of bacterial communities due to changes in functional trait composition.

    Directory of Open Access Journals (Sweden)

    Ina Severin

    Full Text Available Previous studies have shown variable relationships between dispersal rate and ecosystem functioning, but the reasons for and mechanisms behind variable dispersal rate-functioning patterns are currently unknown. In this study we used six bacterial lake water communities in a laboratory experiment in order to investigate how dispersal among communities influences community productivity by evaluating three different mechanisms: 1 changes in taxonomic diversity, 2 changes in phylogenetic diversity or 3 changes in the composition of functional traits. The experiment was conducted in two phases; (A a dialysis bag experiment where the dispersal rate among six communities was manipulated and the subsequent change in bacterial diversity and growth rate was recorded, and (B a regrowth experiment where we manipulated available resources to study how well a taxon grows on certain organic carbon resources, i.e. their functional traits. From experiment (B we could thus estimate changes in functional traits in communities in experiment (A. Bacterial production was affected by dispersal, but not consistently among lakes. Neither change in taxonomic or phylogenetic diversity with dispersal could explain the observed dispersal-productivity relationships. Instead, changes in trait composition with dispersal, especially the communities' ability to use p-coumaric acid, an aromatic compound, could explain the observed dispersal-productivity relationships. Changes in this trait caused by dispersal seemed especially important for bacterial productivity in waters with a high aromaticity of the organic matter pool. We conclude that the effect of dispersal on bacterial communities can affect ecosystem functioning in different ways, through changes in functional key-traits which are important for the local environment.

  1. A functional gene array for detection of bacterial virulence elements.

    Directory of Open Access Journals (Sweden)

    Crystal Jaing

    Full Text Available Emerging known and unknown pathogens create profound threats to public health. Platforms for rapid detection and characterization of microbial agents are critically needed to prevent and respond to disease outbreaks. Available detection technologies cannot provide broad functional information about known or novel organisms. As a step toward developing such a system, we have produced and tested a series of high-density functional gene arrays to detect elements of virulence and antibiotic resistance mechanisms. Our first generation array targets genes from Escherichia coli strains K12 and CFT073, Enterococcus faecalis and Staphylococcus aureus. We determined optimal probe design parameters for gene family detection and discrimination. When tested with organisms at varying phylogenetic distances from the four target strains, the array detected orthologs for the majority of targeted gene families present in bacteria belonging to the same taxonomic family. In combination with whole-genome amplification, the array detects femtogram concentrations of purified DNA, either spiked in to an aerosol sample background, or in combinations from one or more of the four target organisms. This is the first report of a high density NimbleGen microarray system targeting microbial antibiotic resistance and virulence mechanisms. By targeting virulence gene families as well as genes unique to specific biothreat agents, these arrays will provide important data about the pathogenic potential and drug resistance profiles of unknown organisms in environmental samples.

  2. Understanding Sodium Channel Function and Modulation Using Atomistic Simulations of Bacterial Channel Structures.

    Science.gov (United States)

    Boiteux, C; Allen, T W

    2016-01-01

    Sodium channels are chief proteins involved in electrical signaling in the nervous system, enabling critical functions like heartbeat and brain activity. New high-resolution X-ray structures for bacterial sodium channels have created an opportunity to see how these proteins operate at the molecular level. An important challenge to overcome is establishing relationships between the structures and functions of mammalian and bacterial channels. Bacterial sodium channels are known to exhibit the main structural features of their mammalian counterparts, as well as several key functional characteristics, including selective ion conduction, voltage-dependent gating, pore-based inactivation and modulation by local anesthetic, antiarrhythmic and antiepileptic drugs. Simulations have begun to shed light on each of these features in the past few years. Despite deviations in selectivity signatures for bacterial and mammalian channels, simulations have uncovered the nature of the multiion conduction mechanism associated with Na(+) binding to a high-field strength site established by charged glutamate side chains. Simulations demonstrated a surprising level of flexibility of the protein, showing that these side chains are active participants in the permeation process. They have also uncovered changes in protein structure, leading to asymmetrical collapses of the activation gate that have been proposed to correspond to inactivated structures. These observations offer the potential to examine the mechanisms of state-dependent drug activity, focusing on pore-blocking and pore-based slow inactivation in bacterial channels, without the complexities of inactivation on multiple timescales seen in eukaryotic channels. Simulations have provided molecular views of the interactions of drugs, consistent with sites predicted in mammalian channels, as well as a wealth of other sites as potential new drug targets. In this chapter, we survey the new insights into sodium channel function that

  3. Functional Characterization of Bacterial Communities Responsible for Fermentation of Doenjang: A Traditional Korean Fermented Soybean Paste

    Science.gov (United States)

    Jung, Woo Yong; Jung, Ji Young; Lee, Hyo Jung; Jeon, Che Ok

    2016-01-01

    Doenjang samples were prepared in triplicate and their microbial abundance, bacterial communities, and metabolites throughout fermentation were analyzed to investigate the functional properties of microorganisms in doenjang. Viable bacterial cells were approximately three orders of magnitude higher than fungal cells, suggesting that bacteria are more responsible for doenjang fermentation. Pyrosequencing and proton nuclear magnetic resonance spectroscopy were applied for the analysis of bacterial communities and metabolites, respectively. Bacterial community analysis based on 16S rRNA gene sequences revealed that doenjang samples included Bacillus, Enterococcus, Lactobacillus, Clostridium, Staphylococcus, Corynebacterium, Oceanobacillus, and Tetragenococcus. These genera were found either in doenjang-meju or solar salts, but not in both, suggesting two separate sources of bacteria. Bacillus and Enterococcus were dominant genera during the fermentation, but their abundances were not associated with metabolite changes, suggesting that they may not be major players in doenjang fermentation. Tetragenococcus was dominant in 108 day-doenjang samples, when lactate, acetate, putrescine, and tyramine increased quickly as glucose and fructose decreased, indicating that Tetragenococcus might be primarily responsible for organic acid and biogenic amine production. Lactobacillus was identified as a dominant group from the 179-day samples, associated with the increase of γ-aminobutyric acid (GABA) and the decrease of galactose, indicating a potential role for this genus as a major GABA producer during fermentation. The results of this study clarified the functional properties of major bacterial communities in the doenjang fermentation process, contributing to the production of safe and high-quality doenjang. PMID:27303399

  4. Functional Characterization of Bacterial Communities Responsible for Fermentation of Doenjang: A Traditional Korean Fermented Soybean Paste.

    Science.gov (United States)

    Jung, Woo Yong; Jung, Ji Young; Lee, Hyo Jung; Jeon, Che Ok

    2016-01-01

    Doenjang samples were prepared in triplicate and their microbial abundance, bacterial communities, and metabolites throughout fermentation were analyzed to investigate the functional properties of microorganisms in doenjang. Viable bacterial cells were approximately three orders of magnitude higher than fungal cells, suggesting that bacteria are more responsible for doenjang fermentation. Pyrosequencing and proton nuclear magnetic resonance spectroscopy were applied for the analysis of bacterial communities and metabolites, respectively. Bacterial community analysis based on 16S rRNA gene sequences revealed that doenjang samples included Bacillus, Enterococcus, Lactobacillus, Clostridium, Staphylococcus, Corynebacterium, Oceanobacillus, and Tetragenococcus. These genera were found either in doenjang-meju or solar salts, but not in both, suggesting two separate sources of bacteria. Bacillus and Enterococcus were dominant genera during the fermentation, but their abundances were not associated with metabolite changes, suggesting that they may not be major players in doenjang fermentation. Tetragenococcus was dominant in 108 day-doenjang samples, when lactate, acetate, putrescine, and tyramine increased quickly as glucose and fructose decreased, indicating that Tetragenococcus might be primarily responsible for organic acid and biogenic amine production. Lactobacillus was identified as a dominant group from the 179-day samples, associated with the increase of γ-aminobutyric acid (GABA) and the decrease of galactose, indicating a potential role for this genus as a major GABA producer during fermentation. The results of this study clarified the functional properties of major bacterial communities in the doenjang fermentation process, contributing to the production of safe and high-quality doenjang. PMID:27303399

  5. Molecular assessment of bacterial community dynamics and functional endpoints during sediment bioaccumulation test

    NARCIS (Netherlands)

    Diepens, N.J.; Dimitrov, M.R.; Koelmans, A.A.; Smidt, H.

    2015-01-01

    Whole sediment toxicity tests play an important role in environmental risk assessment of organic chemicals. It is not clear, however, to what extent changing microbial community composition and associated functions affect sediment test results. We assessed the development of bacterial communities in

  6. A product of heme catabolism modulates bacterial function and survival.

    Directory of Open Access Journals (Sweden)

    Christopher L Nobles

    Full Text Available Bilirubin is the terminal metabolite in heme catabolism in mammals. After deposition into bile, bilirubin is released in large quantities into the mammalian gastrointestinal (GI tract. We hypothesized that intestinal bilirubin may modulate the function of enteric bacteria. To test this hypothesis, we investigated the effect of bilirubin on two enteric pathogens; enterohemorrhagic E. coli (EHEC, a Gram-negative that causes life-threatening intestinal infections, and E. faecalis, a Gram-positive human commensal bacterium known to be an opportunistic pathogen with broad-spectrum antibiotic resistance. We demonstrate that bilirubin can protect EHEC from exogenous and host-generated reactive oxygen species (ROS through the absorption of free radicals. In contrast, E. faecalis was highly susceptible to bilirubin, which causes significant membrane disruption and uncoupling of respiratory metabolism in this bacterium. Interestingly, similar results were observed for other Gram-positive bacteria, including B. cereus and S. aureus. A model is proposed whereby bilirubin places distinct selective pressure on enteric bacteria, with Gram-negative bacteria being protected from ROS (positive outcome and Gram-positive bacteria being susceptible to membrane disruption (negative outcome. This work suggests bilirubin has differential but biologically relevant effects on bacteria and justifies additional efforts to determine the role of this neglected waste catabolite in disease processes, including animal models.

  7. Bacterial mimetics of endocrine secretory granules as immobilized in vivo depots for functional protein drugs

    Science.gov (United States)

    Céspedes, María Virtudes; Fernández, Yolanda; Unzueta, Ugutz; Mendoza, Rosa; Seras-Franzoso, Joaquin; Sánchez-Chardi, Alejando; Álamo, Patricia; Toledo-Rubio, Verónica; Ferrer-Miralles, Neus; Vázquez, Esther; Schwartz, Simó; Abasolo, Ibane; Corchero, José Luis; Mangues, Ramon; Villaverde, Antonio

    2016-01-01

    In the human endocrine system many protein hormones including urotensin, glucagon, obestatin, bombesin and secretin, among others, are supplied from amyloidal secretory granules. These granules form part of the so called functional amyloids, which within the whole aggregome appear to be more abundant than formerly believed. Bacterial inclusion bodies (IBs) are non-toxic, nanostructured functional amyloids whose biological fabrication can be tailored to render materials with defined biophysical properties. Since under physiological conditions they steadily release their building block protein in a soluble and functional form, IBs are considered as mimetics of endocrine secretory granules. We have explored here if the in vivo implantation of functional IBs in a given tissue would represent a stable local source of functional protein. Upon intratumoral injection of bacterial IBs formed by a potent protein ligand of CXCR4 we have observed high stability and prevalence of the material in absence of toxicity, accompanied by apoptosis of CXCR4+ cells and tumor ablation. Then, the local immobilization of bacterial amyloids formed by therapeutic proteins in tumors or other tissues might represent a promising strategy for a sustained local delivery of protein drugs by mimicking the functional amyloidal architecture of the mammals’ endocrine system. PMID:27775083

  8. Effects of transient temperature conditions on the divergence of activated sludge bacterial community structure and function.

    Science.gov (United States)

    Nadarajah, Nalina; Allen, D Grant; Fulthorpe, Roberta R

    2007-06-01

    The effect of temperature fluctuations on bacterial community structure and function in lab-scale sequencing batch reactors treating bleached kraft mill effluent was investigated. An increase in temperature from 30 to 45 degrees C caused shifts in both bacterial community structure and function. Triplicate reactors were highly similar for 40 days following startup. After the temperature shift, their community structure and function started to diverge from each other and from the control. A multi-response permutation procedure confirmed that the variability in community structure between transient and control reactors were greater than that among the triplicate transient reactors. The fact that these disturbances manifest themselves in different ways in apparently identical reactors suggests a high degree of variability between replicate systems.

  9. Variable effects of dispersal on productivity of bacterial communities due to changes in functional trait composition

    DEFF Research Database (Denmark)

    Severin, Ina; Östman, Örjan; Lindström, Eva S.

    2013-01-01

    ) a dialysis bag experiment where the dispersal rate among six communities was manipulated and the subsequent change in bacterial diversity and growth rate was recorded, and (B) a regrowth experiment where we manipulated available resources to study how well a taxon grows on certain organic carbon resources, i......Previous studies have shown variable relationships between dispersal rate and ecosystem functioning, but the reasons for and mechanisms behind variable dispersal rate - functioning patterns are currently unknown. In this study we used six bacterial lake water communities in a laboratory experiment...... in order to investigate how dispersal among communities influences community productivity by evaluating three different mechanisms: 1) changes in taxonomic diversity, 2) changes in phylogenetic diversity or 3) changes in the composition of functional traits. The experiment was conducted in two phases; (A...

  10. Chronic filarial infection provides protection against bacterial sepsis by functionally reprogramming macrophages.

    Directory of Open Access Journals (Sweden)

    Fabian Gondorf

    2015-01-01

    Full Text Available Helminths immunomodulate their hosts and induce a regulatory, anti-inflammatory milieu that prevents allergies and autoimmune diseases. Helminth immunomodulation may benefit sepsis outcome by preventing exacerbated inflammation and severe pathology, but the influence on bacterial clearance remains unclear. To address this, mice were chronically infected with the filarial nematode Litomosoides sigmodontis (L.s. and the outcome of acute systemic inflammation caused by i.p. Escherichia coli injection was determined. L.s. infection significantly improved E. coli-induced hypothermia, bacterial clearance and sepsis survival and correlated with reduced concentrations of associated pro-inflammatory cytokines/chemokines and a less pronounced pro-inflammatory macrophage gene expression profile. Improved sepsis outcome in L.s.-infected animals was mediated by macrophages, but independent of the alternatively activated macrophage subset. Endosymbiotic Wolbachia bacteria that are present in most human pathogenic filariae, as well as L.s., signal via TLR2 and modulate macrophage function. Here, gene expression profiles of peritoneal macrophages from L.s.-infected mice revealed a downregulation of genes involved in TLR signaling, and pulsing of macrophages in vitro with L.s. extract reduced LPS-triggered activation. Subsequent transfer improved sepsis outcome in naïve mice in a Wolbachia- and TLR2-dependent manner. In vivo, phagocytosis was increased in macrophages from L.s.-infected wild type, but not TLR2-deficient animals. In association, L.s. infection neither improved bacterial clearance in TLR2-deficient animals nor ameliorated E. coli-induced hypothermia and sepsis survival. These results indicate that chronic L.s. infection has a dual beneficial effect on bacterial sepsis, reducing pro-inflammatory immune responses and improving bacterial control. Thus, helminths and their antigens may not only improve the outcome of autoimmune and allergic diseases

  11. Genome-scale Co-evolutionary Inference Identifies Functions and Clients of Bacterial Hsp90

    OpenAIRE

    Press, Maximilian O.; Li, Hui; Creanza, Nicole; Kramer, Günter; Queitsch, Christine; Sourjik, Victor; Borenstein, Elhanan

    2013-01-01

    The molecular chaperone Hsp90 is essential in eukaryotes, in which it facilitates the folding of developmental regulators and signal transduction proteins known as Hsp90 clients. In contrast, Hsp90 is not essential in bacteria, and a broad characterization of its molecular and organismal function is lacking. To enable such characterization, we used a genome-scale phylogenetic analysis to identify genes that co-evolve with bacterial Hsp90. We find that genes whose gain and loss were coordinate...

  12. Small Intestinal Bacterial Overgrowth in Patients with Refractory Functional Gastrointestinal Disorders

    OpenAIRE

    Shimura, Shino; Ishimura, Norihisa; Mikami, Hironobu; Okimoto, Eiko; Uno, Goichi; Tamagawa, Yuji; Aimi, Masahito; Oshima, Naoki; Sato, Shuichi; Ishihara, Shunji; Kinoshita, Yoshikazu

    2016-01-01

    Background/Aims Small intestinal bacterial overgrowth (SIBO) is considered to be involved in the pathogenesis of functional gastrointestinal disorders (FGID). However, the prevalence and clinical conditions of SIBO in patients with FGID remain to be fully elucidated. Here, we examined the frequency of SIBO in patients with refractory FGID. Methods We prospectively enrolled patients with refractory FGID based on Rome III criteria. A glucose hydrogen breath test (GHBT) was performed using a gas...

  13. Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley

    OpenAIRE

    Bulgarelli, D.; Garrido Oter, R.; Muench, P.; Weiman, A.; Droege, J.; Pan, Y.; McHardy, A; Schulze-Lefert, P.

    2015-01-01

    Summary The microbial communities inhabiting the root interior of healthy plants, as well as the rhizosphere, which consists of soil particles firmly attached to roots, engage in symbiotic associations with their host. To investigate the structural and functional diversification among these communities, we employed a combination of 16S rRNA gene profiling and shotgun metagenome analysis of the microbiota associated with wild and domesticated accessions of barley (Hordeum vulgare). Bacterial f...

  14. Effects of viruses on bacterial functions under contrasting nutritional conditions for four species of bacteria isolated from Hong Kong waters

    Science.gov (United States)

    Liu, Hao; Yuan, Xiangcheng; Xu, Jie; Harrison, Paul J.; He, Lei; Yin, Kedong

    2015-09-01

    Free living viruses are ubiquitous in marine waters and concentrations are usually several times higher than the bacterial abundance. These viruses are capable of lysing host bacteria and therefore, play an important role in the microbial loop in oligotrophic waters. However, few studies have been conducted to compare the role of viruses in regulating bacterial abundance and heterotrophic activities between natural oligotrophic waters and anthropogenic influenced eutrophic waters. In this study, we examined viral effects on bacterial functions of four single bacterial species incubated with natural viral assemblages in seawater samples from eutrophic and oligotrophic waters. The viral-lysis of bacteria was significantly higher in eutrophic than oligotrophic waters. This suggests that viruses were capable of controlling bacterial abundance, respiration and production in the eutrophic waters. Cellular bacterial respiration and production was higher with viruses than without viruses, which was more evident in the oligotrophic waters. These results indicate that viruses can slow down bacterial consumption of oxygen and reduce bacteria-induced eutrophication effects in anthropogenic eutrophic waters, but switch to the role of sustaining the bacterial population when nutrients are limiting. There were bacterial species differences in resisting viral attack, which can influence the dominance and biodiversity of bacterial species in coastal waters.

  15. Comparative structural and functional analysis of staphylococcus aureus glucokinase with other bacterial glucokinases

    Directory of Open Access Journals (Sweden)

    P S Kumar

    2014-01-01

    Full Text Available Glucokinase is classified in bacteria based upon having ATP binding site and ′repressor/open reading frames of unknown function/sugar kinases′ motif, the sequence of glucokinase gene (JN645812 of Staphylococcus aureus ATCC12600 showed presence of ATP binding site and ′repressor/open reading frames of unknown function/sugar kinases′ motif. We have earlier observed glucokinase of S. aureus has higher affinity towards the substrate compared to other bacterial glucokinase and under anaerobic condition with increased glucose concentration S. aureus exhibited higher rate of biofilm formation. To establish this, 3D structure of glucokinase was built using homology modeling method, the PROCHECK and ProSA-Web analysis indicated this built glucokinase structure was close to the crystal structure. This structure was superimposed with different bacterial glucokinase structures and from the root-mean-square deviation values, it is concluded that S. aureus glucokinase exhibited very close homology with Enterococcus faecalis and Clostridium difficle while with other bacteria it showed high degree of variations both in domain and nondomain regions. Glucose docking results indicated -12.3697 kcal/mol for S. aureus glucokinase compared with other bacterial glucokinase suggesting higher affinity of glucose which correlates with enzyme kinetics and higher rate of biofilm formation.

  16. Impacts of methamidophos, copper, and their combinations on bacterial community structure and function in black soil

    Institute of Scientific and Technical Information of China (English)

    ZHANG; Huiwen; ZHOU; Qixing; ZHANG; Qianru; ZHANG; Chengg

    2005-01-01

    The potential ecotoxicologial risks of methamidophos, copper, and their combinations on microbial community of black soil ecosystem in the Northeast China were assessed in species richness and structures by using 16S rDNA-PCR-DGGE analysis approach, and functional characteristics at community levels by using BIOLOGGN system analysis method as well as two conventional methods(DHA and SIR). All results of DGGE banding fingerprint patterns(amplified by bacterial specific 16S rDNA V3 high variable region universal primer) indicated that the species richness of bacterial community in tested soil was significantly decreased to different extents by using different concentrations of single methamidophos, copper, especially some of their combinations had worse effects than their corresponding single factors. In addition,the structures of soil bacterial community had been disturbed under all stresses applied in this study because of the enrichment of some species and the disappearance of other species from the bacterial community. The effects of the single factors with lower concentrations on the communiy structure were weaker than those with higher concentrations. Moreover, the bacterial community structures under the combined stresses of methamidophos and copper were significantly different from those of control and their corresponding single factors. The change of DHA and carbon source substrate utilizing fingerprint patterns based on BIOLOGGNsystem were two relatively sensitive directors corresponding to the stress presented in this study. Between methamodophos and copper, there happened the significant joint-toxic actions when they were used in combination on DHA and carbon source substrate utilizing fingerprint patterns of soil bacterial communities. The DHA of soil under the combined stresses was lower than that of the control and that under the single factors, and the BIOLOGGN substrate utilizing patterns of soil treated by combinations were distinctively

  17. Comparison of bacterial cells and amine-functionalized abiotic surfaces as support for Pd nanoparticle synthesis

    DEFF Research Database (Denmark)

    De Corte, Simon; Bechstein, Stefanie; Lokanathan, Arcot R.;

    2013-01-01

    An increasing demand for catalytic Pd nanoparticles has motivated the search for sustainable production methods. An innovative approach uses bacterial cells as support material for synthesizing Pd nanoparticles by reduction of Pd(II) with e.g. hydrogen or formate. Nevertheless, drawbacks of...... on these surfaces was higher than for Pd particles formed on Shewanella oneidensis cells. Smaller Pd nanoparticles generally have better catalytic properties, and previous studies have shown that the particle size can be lowered by increasing the amount of support material used during Pd particle...... materials were visualized by transmission electron microscopy, and their activity was evaluated by catalysis of p-nitrophenol reduction. Surfaces functionalized with 3-aminopropyltriethoxysilane and chitosan were interesting alternatives to bacterial cells, as the catalytic activity of Pd particles formed...

  18. Widespread abundance of functional bacterial amyloid in Mycolata and other Gram-positive bacteria

    DEFF Research Database (Denmark)

    Jordal, Peter Bruun; Dueholm, Morten Simonsen; Larsen, Poul;

    2009-01-01

    Until recently, extracellular functional bacterial amyloid (FuBA) has been detected and characterized in only a few bacterial species, including Escherichia coli, Salmonella and Gram-positive Streptomyces coelicolor. Here we have probed Gram-positive bacteria with conformationally specific...... antibodies to reveal the existence of FuBA in 12 out of 14 examined Mycolata species as well as six other examined distantly related species belonging to the phyla Actinobacteria and Firmicutes. Most of the bacteria produced extracellular fimbria, sometimes in copious amounts, and in two cases large...... extracellular fibrils were also produced. In three cases, FuBA was only revealed after extensive removal of extracellular material by saponification, indicating an integrated attachment within the cellular envelope. Spores from species within the genera Streptomyces, Bacillus and Nocardia were all coated with...

  19. Effect of Copper Treatment on the Composition and Function of the Bacterial Community in the Sponge Haliclona cymaeformis

    KAUST Repository

    Tian, R.-M.

    2014-11-04

    Marine sponges are the most primitive metazoan and host symbiotic microorganisms. They are crucial components of the marine ecological system and play an essential role in pelagic processes. Copper pollution is currently a widespread problem and poses a threat to marine organisms. Here, we examined the effects of copper treatment on the composition of the sponge-associated bacterial community and the genetic features that facilitate the survival of enriched bacteria under copper stress. The 16S rRNA gene sequencing results showed that the sponge Haliclona cymaeformis harbored symbiotic sulfur-oxidizing Ectothiorhodospiraceae and photosynthetic Cyanobacteria as dominant species. However, these autotrophic bacteria decreased substantially after treatment with a high copper concentration, which enriched for a heterotrophic-bacterium-dominated community. Metagenomic comparison revealed a varied profile of functional genes and enriched functions, including bacterial motility and chemotaxis, extracellular polysaccharide and capsule synthesis, virulence-associated genes, and genes involved in cell signaling and regulation, suggesting short-period mechanisms of the enriched bacterial community for surviving copper stress in the microenvironment of the sponge. Microscopic observation and comparison revealed dynamic bacterial aggregation within the matrix and lysis of sponge cells. The bacteriophage community was also enriched, and the complete genome of a dominant phage was determined, implying that a lytic phage cycle was stimulated by the high copper concentration. This study demonstrated a copper-induced shift in the composition of functional genes of the sponge-associated bacterial community, revealing the selective effect of copper treatment on the functions of the bacterial community in the microenvironment of the sponge. IMPORTANCE This study determined the bacterial community structure of the common sponge Haliclona cymaeformis and examined the effect of copper

  20. Shifts in diversity and function of lake bacterial communities upon glacier retreat.

    Science.gov (United States)

    Peter, Hannes; Sommaruga, Ruben

    2016-07-01

    Global climate change is causing a wastage of glaciers and threatening biodiversity in glacier-fed ecosystems. The high turbidity typically found in those ecosystems, which is caused by inorganic particles and result of the erosive activity of glaciers is a key environmental factor influencing temperature and light availability, as well as other factors in the water column. Once these lakes loose hydrological connectivity to glaciers and turn clear, the accompanying environmental changes could represent a potential bottleneck for the established local diversity with yet unknown functional consequences. Here, we study three lakes situated along a turbidity gradient as well as one clear unconnected lake and evaluate seasonal changes in their bacterial community composition and diversity. Further, we assess potential consequences for community functioning. Glacier runoff represented a diverse source community for the lakes and several taxa were able to colonize downstream turbid habitats, although they were not found in the clear lake. Operational taxonomic unit-based alpha diversity and phylogenetic diversity decreased along the turbidity gradient, but metabolic functional diversity was negatively related to turbidity. No evidence for multifunctional redundancy, which may allow communities to maintain functioning upon alterations in diversity, was found. Our study gives a first view on how glacier-fed lake bacterial communities are affected by the melting of glaciers and indicates that diversity and community composition significantly change when hydrological connectivity to the glacier is lost and lakes turn clear. PMID:26771929

  1. Effects of Dispersal and Initial Diversity on the Composition and Functional Performance of Bacterial Communities.

    Science.gov (United States)

    Zha, Yinghua; Berga, Mercè; Comte, Jérôme; Langenheder, Silke

    2016-01-01

    Natural communities are open systems and consequently dispersal can play an important role for the diversity, composition and functioning of communities at the local scale. It is, however, still unclear how effects of dispersal differ depending on the initial diversity of local communities. Here we implemented an experiment where we manipulated the initial diversity of natural freshwater bacterioplankton communities using a dilution-to-extinction approach as well as dispersal from a regional species pool. The aim was further to test whether dispersal effects on bacterial abundance and functional parameters (average community growth rates, respiration rates, substrate utilisation ability) differ in dependence of the initial diversity of the communities. First of all, we found that both initial diversity and dispersal rates had an effect on the recruitment of taxa from a regional source, which was higher in communities with low initial diversity and at higher rates of dispersal. Higher initial diversity and dispersal also promoted higher levels of richness and evenness in local communities and affected, both, separately or interactively, the functional performance of communities. Our study therefore suggests that dispersal can influence the diversity, composition and functioning of bacterial communities and that this effect may be enhanced if the initial diversity of communities is depleted. PMID:27182596

  2. Structure and Function of the Bi-Directional Bacterial Flagellar Motor

    Directory of Open Access Journals (Sweden)

    Yusuke V. Morimoto

    2014-02-01

    Full Text Available The bacterial flagellum is a locomotive organelle that propels the bacterial cell body in liquid environments. The flagellum is a supramolecular complex composed of about 30 different proteins and consists of at least three parts: a rotary motor, a universal joint, and a helical filament. The flagellar motor of Escherichia coli and Salmonella enterica is powered by an inward-directed electrochemical potential difference of protons across the cytoplasmic membrane. The flagellar motor consists of a rotor made of FliF, FliG, FliM and FliN and a dozen stators consisting of MotA and MotB. FliG, FliM and FliN also act as a molecular switch, enabling the motor to spin in both counterclockwise and clockwise directions. Each stator is anchored to the peptidoglycan layer through the C-terminal periplasmic domain of MotB and acts as a proton channel to couple the proton flow through the channel with torque generation. Highly conserved charged residues at the rotor–stator interface are required not only for torque generation but also for stator assembly around the rotor. In this review, we will summarize our current understanding of the structure and function of the proton-driven bacterial flagellar motor.

  3. Proinflammatory effects of bacterial lipoprotein on human neutrophil activation status, function and cytotoxic potential in vitro.

    LENUS (Irish Health Repository)

    Power, C

    2012-02-03

    Bacterial lipoprotein (BLP) is the most abundant protein in gram-negative bacterial cell walls, heavily outweighing lipopolysaccharide (LPS). Herein we present findings demonstrating the potent in vitro effects of BLP on neutrophil (PMN) activation status, function, and capacity to transmigrate an endothelial monolayer. PMNs are the principal effectors of the initial host response to injury or infection and constitute a significant threat to invading bacterial pathogens. The systemic inflammatory response syndrome (SIRS) is characterised by significant host tissue injury mediated, in part, by uncontrolled regulation of PMN cytotoxic activity. We found that BLP-activated human PMN as evidenced by increased CD11b\\/CD18 (Mac-1) expression. Up-regulation of PMN Mac-1 in response to BLP occurred independently of membrane-bound CD14 (mCD14). A similar up-regulation of intercellular adhesion molecule-1 (ICAM-1) on endothelial cells was observed whilst E-Selectin expression was unaffected. PMN transmigration across a human umbilical vein endothelial cell (HUVEC) monolayer was markedly increased after treating either PMN\\'s or HUVEC independently with BLP. This increased transmigration did not occur as a result of any direct effect of BLP on HUVEC monolayer permeability, assessed objectively using the passage of FITC-labeled Dextran-70. BLP primed PMN for enhanced respiratory burst and superoxide anion production in response to PMA, but did not influence phagocytosis of opsonized Escherichia coli. BLP far exceeds LPS as a gram-negative bacterial wall component, these findings therefore implicate BLP as an additional putative mediator of SIRS arising from gram-negative infection.

  4. Functions of the MMR system and special roles of mutL in bacterial evolution

    Institute of Scientific and Technical Information of China (English)

    JUN GONG; RU JING JIA

    2006-01-01

    DNA mismatch repair guards the integrity of the genome of almost all organisms by correcting DNA biosynthetic errors and by ensuring the fidelity of homologous genetic recombination. MutL is one of the important proteins involved in mismatch repair system. It has been suggested to function as a master coordinator or molecular matchmaker because it interacts physically with MutS, the endonuclease MutH, and DNA helicase UvrD. It also binds to DNA and has an ATPase activity. MutL defective bacteria strains have elevated mutation rates and it has been reported recently that MutL defect may have an important impact on bacterial evolution.

  5. Are fire, soil fertility and toxicity, water availability, plant functional diversity, and litter decomposition related in a Neotropical savanna?

    OpenAIRE

    Carvalho, Gustavo Henrique; Batalha, Marco Antônio; Silva, Igor Aurélio; Cianciaruso, Marcus Vinicius; Petchey, Owen L

    2014-01-01

    Understanding how biodiversity and ecosystem functioning respond to changes in the environment is fundamental to the maintenance of ecosystem function. In realistic scenarios, the biodiversity-ecosystem functioning path may account for only a small share of all factors determining ecosystem function. Here, we investigated the strength to which variations in environmental characteristics in a Neotropical savanna affected functional diversity and decomposition. We sought an integrative approach...

  6. Soil Respiration and Bacterial Structure and Function after 17 Years of a Reciprocal Soil Transplant Experiment.

    Science.gov (United States)

    Bond-Lamberty, Ben; Bolton, Harvey; Fansler, Sarah; Heredia-Langner, Alejandro; Liu, Chongxuan; McCue, Lee Ann; Smith, Jeffrey; Bailey, Vanessa

    2016-01-01

    The effects of climate change on soil organic matter-its structure, microbial community, carbon storage, and respiration response-remain uncertain and widely debated. In addition, the effects of climate changes on ecosystem structure and function are often modulated or delayed, meaning that short-term experiments are not sufficient to characterize ecosystem responses. This study capitalized on a long-term reciprocal soil transplant experiment to examine the response of dryland soils to climate change. The two transplant sites were separated by 500 m of elevation on the same mountain slope in eastern Washington state, USA, and had similar plant species and soil types. We resampled the original 1994 soil transplants and controls, measuring CO2 production, temperature response, enzyme activity, and bacterial community structure after 17 years. Over a laboratory incubation of 100 days, reciprocally transplanted soils respired roughly equal cumulative amounts of carbon as non-transplanted controls from the same site. Soils transplanted from the hot, dry, lower site to the cooler and wetter (difference of -5°C monthly maximum air temperature, +50 mm yr-1 precipitation) upper site exhibited almost no respiratory response to temperature (Q10 of 1.1), but soils originally from the upper, cooler site had generally higher respiration rates. The bacterial community structure of transplants did not differ significantly from that of untransplanted controls, however. Slight differences in local climate between the upper and lower Rattlesnake locations, simulated with environmental control chambers during the incubation, thus prompted significant differences in microbial activity, with no observed change to bacterial structure. These results support the idea that environmental shifts can influence soil C through metabolic changes, and suggest that microbial populations responsible for soil heterotrophic respiration may be constrained in surprising ways, even as shorter- and

  7. Soil respiration and bacterial structure and function after 17 years of a reciprocal soil transplant experiment

    Energy Technology Data Exchange (ETDEWEB)

    Bond-Lamberty, Benjamin; Bolton, Harvey; Fansler, Sarah J.; Heredia-Langner, Alejandro; Liu, Chongxuan; McCue, Lee Ann; Smith, Jeff L.; Bailey, Vanessa L.

    2016-03-02

    The effects of climate change on soil organic matter—its structure, microbial community, carbon storage, and respiration response—remain uncertain and widely debated. In addition, the effects of climate changes on ecosystem structure and function are often modulated or delayed, meaning that short-term experiments are not sufficient to characterize ecosystem responses. This study capitalized on a long-term reciprocal soil transplant experiment to examine the response of dryland soils to climate change. The two transplant sites were separated by 500 m of elevation on the same mountain slope in eastern Washington state, USA, and had similar plant species and soil types. We resampled the original 1994 soil transplants and controls, measuring CO2 production, temperature response, enzyme activity, and bacterial community structure after 17 years. Over a laboratory incubation of 100 days, reciprocally transplanted soils respired roughly equal cumulative amounts of carbon as non-transplanted controls from the same site. Soils transplanted from the hot, dry, lower site to the cooler and wetter (difference of -5 °C monthly maximum air temperature, +50 mm yr-1 precipitation) upper site exhibited almost no respiratory response to temperature (Q10 of 1.1), but soils originally from the upper, cooler site had generally higher respiration rates. The bacterial community structure of transplants did not differ significantly from that of untransplanted controls, however. Slight differences in local climate between the upper and lower Rattlesnake locations, simulated with environmental control chambers during the incubation, thus prompted significant differences in microbial activity, with no observed change to bacterial structure. These results support the idea that environmental shifts can influence soil C through metabolic changes, and suggest that microbial populations responsible for soil heterotrophic respiration may be constrained in surprising ways, even as shorter- and

  8. Enhanced Disease Susceptibility1 Mediates Pathogen Resistance and Virulence Function of a Bacterial Effector in Soybean.

    Science.gov (United States)

    Wang, Jialin; Shine, M B; Gao, Qing-Ming; Navarre, Duroy; Jiang, Wei; Liu, Chunyan; Chen, Qingshan; Hu, Guohua; Kachroo, Aardra

    2014-05-28

    Enhanced disease susceptibility1 (EDS1) and phytoalexin deficient4 (PAD4) are well-known regulators of both basal and resistance (R) protein-mediated plant defense. We identified two EDS1-like (GmEDS1a/GmEDS1b) proteins and one PAD4-like (GmPAD4) protein that are required for resistance signaling in soybean (Glycine max). Consistent with their significant structural conservation to Arabidopsis (Arabidopsis thaliana) counterparts, constitutive expression of GmEDS1 or GmPAD4 complemented the pathogen resistance defects of Arabidopsis eds1 and pad4 mutants, respectively. Interestingly, however, the GmEDS1 and GmPAD4 did not complement pathogen-inducible salicylic acid accumulation in the eds1/pad4 mutants. Furthermore, the GmEDS1a/GmEDS1b proteins were unable to complement the turnip crinkle virus coat protein-mediated activation of the Arabidopsis R protein Hypersensitive reaction to Turnip crinkle virus (HRT), even though both interacted with HRT. Silencing GmEDS1a/GmEDS1b or GmPAD4 reduced basal and pathogen-inducible salicylic acid accumulation and enhanced soybean susceptibility to virulent pathogens. The GmEDS1a/GmEDS1b and GmPAD4 genes were also required for Resistance to Pseudomonas syringae pv glycinea2 (Rpg2)-mediated resistance to Pseudomonas syringae. Notably, the GmEDS1a/GmEDS1b proteins interacted with the cognate bacterial effector AvrA1 and were required for its virulence function in rpg2 plants. Together, these results show that despite significant structural similarities, conserved defense signaling components from diverse plants can differ in their functionalities. In addition, we demonstrate a role for GmEDS1 in regulating the virulence function of a bacterial effector.

  9. Genetic and functional diversities of bacterial communities in the rhizosphere of Arachis hypogaea.

    Science.gov (United States)

    Haldar, Shyamalina; Choudhury, Susanta Roy; Sengupta, Sanghamitra

    2011-06-01

    Bioinoculants are environmentally friendly, energy efficient and economically viable resources in sustainable agriculture. Knowledge of the structure and activities of microbial population in the rhizosphere of a plant is essential to formulate an effective bioinoculant. In this study, the bacterial community present in the rhizosphere of an important oilseed legume, Arachis hypogaea (L.) was described with respect to adjoining bulk soil as a baseline control using a 16S rDNA based metagenomic approach. Significantly higher abundance of Gamma-proteobacteria, a prevalence of Bacillus and the Cytophaga-Flavobacteria group of Bacteroidetes and absence of the Rhizobiaceae family of Alpha-proteobacteria were the major features observed in the matured Arachis-rhizosphere. The functional characterization of the rhizosphere-competent bacteria was performed using culture-dependent determination of phenotypes. Most bacterial isolates from the groundnut-rhizosphere exhibited multiple biochemical activities associated with plant growth and disease control. Validation of the beneficial traits in candidate bioinoculants in pot-cultures and field trials is necessary before their targeted application in the groundnut production system. PMID:21380504

  10. Structure and function of the bacterial root microbiota in wild and domesticated barley.

    Science.gov (United States)

    Bulgarelli, Davide; Garrido-Oter, Ruben; Münch, Philipp C; Weiman, Aaron; Dröge, Johannes; Pan, Yao; McHardy, Alice C; Schulze-Lefert, Paul

    2015-03-11

    The microbial communities inhabiting the root interior of healthy plants, as well as the rhizosphere, which consists of soil particles firmly attached to roots, engage in symbiotic associations with their host. To investigate the structural and functional diversification among these communities, we employed a combination of 16S rRNA gene profiling and shotgun metagenome analysis of the microbiota associated with wild and domesticated accessions of barley (Hordeum vulgare). Bacterial families Comamonadaceae, Flavobacteriaceae, and Rhizobiaceae dominate the barley root-enriched microbiota. Host genotype has a small, but significant, effect on the diversity of root-associated bacterial communities, possibly representing a footprint of barley domestication. Traits related to pathogenesis, secretion, phage interactions, and nutrient mobilization are enriched in the barley root-associated microbiota. Strikingly, protein families assigned to these same traits showed evidence of positive selection. Our results indicate that the combined action of microbe-microbe and host-microbe interactions drives microbiota differentiation at the root-soil interface. PMID:25732064

  11. Particle Swarm and Bacterial Foraging Inspired Hybrid Artificial Bee Colony Algorithm for Numerical Function Optimization

    Directory of Open Access Journals (Sweden)

    Li Mao

    2016-01-01

    Full Text Available Artificial bee colony (ABC algorithm has good performance in discovering the optimal solutions to difficult optimization problems, but it has weak local search ability and easily plunges into local optimum. In this paper, we introduce the chemotactic behavior of Bacterial Foraging Optimization into employed bees and adopt the principle of moving the particles toward the best solutions in the particle swarm optimization to improve the global search ability of onlooker bees and gain a hybrid artificial bee colony (HABC algorithm. To obtain a global optimal solution efficiently, we make HABC algorithm converge rapidly in the early stages of the search process, and the search range contracts dynamically during the late stages. Our experimental results on 16 benchmark functions of CEC 2014 show that HABC achieves significant improvement at accuracy and convergence rate, compared with the standard ABC, best-so-far ABC, directed ABC, Gaussian ABC, improved ABC, and memetic ABC algorithms.

  12. Functionalization of a Rigid Divalent Ligand for LecA, a Bacterial Adhesion Lectin**

    Science.gov (United States)

    Fu, Ou; Pukin, Aliaksei V; Quarles van Ufford, H C; Kemmink, Johan; de Mol, Nico J; Pieters, Roland J

    2015-01-01

    The bacterial adhesion lectin LecA is an attractive target for interference with the infectivity of its producer P. aeruginosa. Divalent ligands with two terminal galactoside moieties connected by an alternating glucose-triazole spacer were previously shown to be very potent inhibitors. In this study, we chose to prepare a series of derivatives with various new substituents in the spacer in hopes of further enhancing the LecA inhibitory potency of the molecules. Based on the binding mode, modifications were made to the spacer to enable additional spacer–protein interactions. The introduction of positively charged, negatively charged, and also lipophilic functional groups was successful. The compounds were good LecA ligands, but no improved binding was seen, even though altered thermodynamic parameters were observed by isothermal titration calorimetry (ITC). PMID:26478841

  13. Long acting β2-agonist and corticosteroid restore airway glandular cell function altered by bacterial supernatant

    Directory of Open Access Journals (Sweden)

    Nawrocki-Raby Béatrice

    2010-01-01

    Full Text Available Abstract Background Staphylococcus aureus releases virulence factors (VF that may impair the innate protective functions of airway cells. The aim of this study was to determine whether a long-acting β2 adrenergic receptor agonist (salmeterol hydroxynaphthoate, Sal combined with a corticosteroid (fluticasone propionate, FP was able to regulate ion content and cytokine expression by airway glandular cells after exposure to S. aureus supernatant. Methods A human airway glandular cell line was incubated with S. aureus supernatant for 1 h and then treated with the combination Sal/FP for 4 h. The expression of actin and CFTR proteins was analyzed by immunofluorescence. Videomicroscopy was used to evaluate chloride secretion and X-ray microanalysis to measure the intracellular ion and water content. The pro-inflammatory cytokine expression was assessed by RT-PCR and ELISA. Results When the cells were incubated with S. aureus supernatant and then with Sal/FP, the cellular localisation of CFTR was apical compared to the cytoplasmic localisation in cells incubated with S. aureus supernatant alone. The incubation of airway epithelial cells with S. aureus supernatant reduced by 66% the chloride efflux that was fully restored by Sal/FP treatment. We also observed that Sal/FP treatment induced the restoration of ion (Cl and S and water content within the intracellular secretory granules of airway glandular cells and reduced the bacterial supernatant-dependent increase of pro-inflammatory cytokines IL8 and TNFα. Conclusions Our results demonstrate that treatment with the combination of a corticosteroid and a long-acting β2 adrenergic receptor agonist after bacterial infection restores the airway glandular cell function. Abnormal mucus induced by defective ion transport during pulmonary infection could benefit from treatment with a combination of β2 adrenergic receptor agonist and glucocorticoid.

  14. Prophylactic treatment with growth hormone improves intestinal barrier function and alleviates bacterial translocation in stressed rats

    Institute of Scientific and Technical Information of China (English)

    丁连安; 黎介寿; 李幼生; 刘放南; 谭力

    2004-01-01

    Background Damage to the gut barrier often occurs during critical illnesses. In such cases, it is very important to alleviate impairment of the intestinal barrier and protect intestinal barrier function. This study investigated the protective effect of growth hormone on intestinal barrier function in rats under stress.Methods This study consisted of prospective, randomized, and controlled animal experiments. Twenty-five Sprague-Dawley rats served as total parenteral nutrition (TPN) models and were divided into three groups: TPN group, sepsis (Sep) group, and growth hormone (GH) group. Another 8 rats served as normal controls. Each group received different stress stimuli. Rats were fed for 7 days, and samples were taken for examination 24 hours after garaging with dual saccharides. Results The architecture of the small intestinal mucosa in the Sep group showed the most severe damage among all groups. Nitric oxide levels in blood plasma and immunoglobulin A levels in the intestinal mucosa of the GH group were significantly lower than in the Sep group (P<0.02). There were no significant changes in CD3 counts and in the CD4/CD8 ratio between the four groups. Dual sugar tests and bacteriological examinations revealed that intestinal permeability and rate of bacterial translocation in the GH group were lower than in the Sep group (P<0.01, respectively).Conclusion Prophylactic treatment with growth hormone can alleviate damage to intestinal barrier function caused by trauma and endotoxemia in rats under stress.

  15. A computational approach to discovering the functions of bacterial phytochromes by analysis of homolog distributions

    Directory of Open Access Journals (Sweden)

    Lamparter Tilman

    2006-03-01

    bacterial phytochromes in ammonium assimilation and amino acid metabolism. Conclusion It was possible to identify several proteins that might share common functions with bacterial phytochromes by the co-distribution approach. This computational approach might also be helpful in other cases.

  16. Effects of mercury contamination on the culturable heterotrophic, functional and genetic diversity of the bacterial community in soil

    DEFF Research Database (Denmark)

    Rasmussen, Lasse Dam; Sørensen, S. J.

    2001-01-01

    This study investigates the effect of mercury contamination on the culturable heterotrophic, functional and genetic diversity of the bacterial community in soil. The changes in diversity were monitored in soil microcosms, enriched with 25 mug Hg(II) g(-1) soil, over a period of 3 months...... by purification of total soil DNA and amplification of bacterial 16S rDNA fragments by polymerase chain reaction. Concentrations of bioavailable and total mercury were measured throughout the experiment. The effect on the culturable heterotrophic and genetic diversity was very similar, showing an immediate...... analysed by Shannon-Weaver indices, functional diversity was found to increase almost immediately after mercury addition and to remain at a level higher than the control soil for the rest of the experiment. The fraction of culturable heterotrophic bacteria increased from 1% to 10% of the total bacterial...

  17. Impaired neutrophil function in 24p3 null mice contributes to enhanced susceptibility to bacterial infections

    OpenAIRE

    Liu, Zhuoming; Petersen, Robert; Devireddy, L.

    2013-01-01

    Lipocalin 24p3 (24p3) is a neutrophil secondary granule protein. 24p3 is also a siderocalin, which binds several bacterial siderophores. It was therefore proposed that synthesis and secretion of 24p3 by stimulated macrophages or release of 24p3 upon neutrophil degranulation sequesters iron-laden siderophores to attenuate bacterial growth. Accordingly, 24p3-deficient mice are susceptible to bacterial pathogens whose siderophores would normally be chelated by 24p3. Specific granule deficiency (...

  18. An improved method for oriT-directed cloning and functionalization of large bacterial genomic regions.

    Science.gov (United States)

    Kvitko, Brian H; McMillan, Ian A; Schweizer, Herbert P

    2013-08-01

    We have made significant improvements to a broad-host-range system for the cloning and manipulation of large bacterial genomic regions based on site-specific recombination between directly repeated oriT sites during conjugation. Using two suicide capture vectors carrying flanking homology regions, oriT sites are recombined on either side of the target region. Using a broad-host-range conjugation helper plasmid, the region between the oriT sites is conjugated into an Escherichia coli recipient strain, where it is circularized and maintained as a chimeric mini-F vector. The cloned target region is functionalized in multiple ways to accommodate downstream manipulation. The target region is flanked with Gateway attB sites for recombination into other vectors and by rare 18-bp I-SceI restriction sites for subcloning. The Tn7-functionalized target can also be inserted at a naturally occurring chromosomal attTn7 site(s) or maintained as a broad-host-range plasmid for complementation or heterologous expression studies. We have used the oriTn7 capture technique to clone and complement Burkholderia pseudomallei genomic regions up to 140 kb in size and have created isogenic Burkholderia strains with various combinations of genomic islands. We believe this system will greatly aid the cloning and genetic analysis of genomic islands, biosynthetic gene clusters, and large open reading frames. PMID:23747708

  19. A functional interaction between ribosomal proteins S7 and S11 within the bacterial ribosome.

    Science.gov (United States)

    Robert, Francis; Brakier-Gingras, Léa

    2003-11-01

    In this study, we used site-directed mutagenesis to disrupt an interaction that had been detected between ribosomal proteins S7 and S11 in the crystal structure of the bacterial 30 S subunit. This interaction, which is located in the E site, connects the head of the 30 S subunit to the platform and is involved in the formation of the exit channel through which passes the 30 S-bound messenger RNA. Neither mutations in S7 nor mutations in S11 prevented the incorporation of the proteins into the 30 S subunits but they perturbed the function of the ribosome. In vivo assays showed that ribosomes with either mutated S7 or S11 were altered in the control of translational fidelity, having an increased capacity for frameshifting, readthrough of a nonsense codon and codon misreading. Toeprinting and filter-binding assays showed that 30 S subunits with either mutated S7 or S11 have an enhanced capacity to bind mRNA. The effects of the S7 and S11 mutations can be related to an increased flexibility of the head of the 30 S, to an opening of the mRNA exit channel and to a perturbation of the proposed allosteric coupling between the A and E sites. Altogether, our results demonstrate that S7 and S11 interact in a functional manner and support the notion that protein-protein interactions contribute to the dynamics of the ribosome.

  20. Small Intestinal Bacterial Overgrowth in Patients with Refractory Functional Gastrointestinal Disorders

    Science.gov (United States)

    Shimura, Shino; Ishimura, Norihisa; Mikami, Hironobu; Okimoto, Eiko; Uno, Goichi; Tamagawa, Yuji; Aimi, Masahito; Oshima, Naoki; Sato, Shuichi; Ishihara, Shunji; Kinoshita, Yoshikazu

    2016-01-01

    Background/Aims Small intestinal bacterial overgrowth (SIBO) is considered to be involved in the pathogenesis of functional gastrointestinal disorders (FGID). However, the prevalence and clinical conditions of SIBO in patients with FGID remain to be fully elucidated. Here, we examined the frequency of SIBO in patients with refractory FGID. Methods We prospectively enrolled patients with refractory FGID based on Rome III criteria. A glucose hydrogen breath test (GHBT) was performed using a gas analyzer after an overnight fast, with breath hydrogen concentration measured at baseline and every 15 minutes after administration of glucose for a total of 3 hours. A peak hydrogen value ≥ 10 ppm above the basal value between 60 and 120 minutes after administration of glucose was diagnosed as SIBO. Results A total of 38 FGID patients, including 11 with functional dyspepsia (FD), 10 with irritable bowel syndrome (IBS), and 17 with overlapping with FD and IBS, were enrolled. Of those, 2 (5.3%) were diagnosed with SIBO (one patient diagnosed with FD; the other with overlapping FD and IBS). Their symptoms were clearly improved and breath hydrogen levels decreased to normal following levofloxacin administration for 7 days. Conclusions Two patients initially diagnosed with FD and IBS were also diagnosed with SIBO as assessed by GHBT. Although the frequency of SIBO is low among patients with FGID, it may be important to be aware of SIBO as differential diagnosis when examining patients with refractory gastrointestinal symptoms, especially bloating, as a part of routine clinical care. PMID:26554916

  1. Enzymatic modification of bacterial exopolysaccharides; xanthan lyase as a tool for structural and functional modification of xanthan

    NARCIS (Netherlands)

    Ruijssenaars, H.J.

    2001-01-01

    Bacterial extracellular polysaccharides (EPSs) can be applied, e.g., in foods, as a thickener or stabilizer. The functional properties that make a polysaccharide suitable for such applications are largely determined by the primary structure, i.e., the sugar composition, the linkage types between the

  2. BACTERIAL BIOFILM FORMATION VERSUS MAMMALIAN CELL GROWTH ON TITANIUM-BASED MONO- AND BI-FUNCTIONAL COATINGS

    NARCIS (Netherlands)

    Subbiahdoss, Guruprakash; Pidhatika, Bidhari; Coullerez, Geraldine; Charnley, Mirren; Kuijer, Roel; van der Mei, Henny C.; Textor, Marcus; Busscher, Henk J.

    2010-01-01

    Biomaterials-associated-infections (BAI) are serious complications in modern medicine. Although non-adhesive coatings, like polymer-brush coatings, have been shown to prevent bacterial adhesion, they do not support cell growth. Bi-functional coatings are supposed to prevent biofilm formation while s

  3. Bacterial reaction centers purified with styrene maleic acid copolymer retain native membrane functional properties and display enhanced stability

    NARCIS (Netherlands)

    Swainsbury, David J K; Scheidelaar, Stefan; Van Grondelle, Rienk; Killian, J. Antoinette; Jones, Michael R.

    2014-01-01

    Integral membrane proteins often present daunting challenges for biophysical characterization, a fundamental issue being how to select a surfactant that will optimally preserve the individual structure and functional properties of a given membrane protein. Bacterial reaction centers offer a rare opp

  4. Fabrication of Functional Wrinkled Interfaces from Polymer Blends: Role of the Surface Functionality on the Bacterial Adhesion

    Directory of Open Access Journals (Sweden)

    Marta Palacios-Cuesta

    2014-11-01

    Full Text Available The generation of nano-microstructured surfaces is a current challenge in polymer science. The fabrication of such surfaces has been accomplished mainly following two different alternatives i.e., by adapting techniques, such as molding (embossing or nano/microimprinting, or by developing novel techniques including laser ablation, soft lithography or laser scanning. Surface instabilities have been recently highlighted as a promising alternative to induce surface features. In particular, wrinkles have been extensively explored for this purpose. Herein, we describe the preparation of wrinkled interfaces by confining a photosensitive monomeric mixture composed of monofunctional monomer and a crosslinking agent within a substrate and a cover. The wrinkle characteristics can be controlled by the monomer mixture and the experimental conditions employed for the photopolymerization. More interestingly, incorporation within the material of a functional copolymer allowed us to vary the surface chemical composition while maintaining the surface structure. For that purpose we incorporated either a fluorinated copolymer that enhanced the surface hydrophobicity of the wrinkled interface or an acrylic acid containing copolymer that increased the hydrophilicity of the wrinkled surface. Finally, the role of the hydrophobicity on the bacterial surface adhesion will be tested by using Staphylococcus aureus.

  5. Structural and functional studies of MinD ATPase: implications for the molecular recognition of the bacterial cell division apparatus

    OpenAIRE

    Hayashi, Ikuko; Oyama, Takuji; Morikawa, Kosuke

    2001-01-01

    Proper placement of the bacterial cell division site requires the site-specific inactivation of other potential division sites. In Escherichia coli, selection of the correct mid-cell site is mediated by the MinC, MinD and MinE proteins. To clarify the functional role of the bacterial cell division inhibitor MinD, which is a membrane-associated ATPase that works as an activator of MinC, we determined the crystal structure of a Pyrococcus furiosus MinD homologue complexed with a substrate analo...

  6. Nucleotide and partner-protein control of bacterial replicative helicase structure and function.

    Science.gov (United States)

    Strycharska, Melania S; Arias-Palomo, Ernesto; Lyubimov, Artem Y; Erzberger, Jan P; O'Shea, Valerie L; Bustamante, Carlos J; Berger, James M

    2013-12-26

    Cellular replication forks are powered by ring-shaped, hexameric helicases that encircle and unwind DNA. To better understand the molecular mechanisms and control of these enzymes, we used multiple methods to investigate the bacterial replicative helicase, DnaB. A 3.3 Å crystal structure of Aquifex aeolicus DnaB, complexed with nucleotide, reveals a newly discovered conformational state for this motor protein. Electron microscopy and small angle X-ray scattering studies confirm the state seen crystallographically, showing that the DnaB ATPase domains and an associated N-terminal collar transition between two physical states in a nucleotide-dependent manner. Mutant helicases locked in either collar state are active but display different capacities to support critical activities such as duplex translocation and primase-dependent RNA synthesis. Our findings establish the DnaB collar as an autoregulatory hub that controls the ability of the helicase to transition between different functional states in response to both nucleotide and replication initiation/elongation factors. PMID:24373746

  7. Forward selection radial basis function networks applied to bacterial classification based on MALDI-TOF-MS.

    Science.gov (United States)

    Zhang, Zhuoyong; Wang, Dan; Harrington, Peter de B; Voorhees, Kent J; Rees, Jon

    2004-06-17

    Forward selection improved radial basis function (RBF) network was applied to bacterial classification based on the data obtained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The classification of each bacterium cultured at different time was discussed and the effect of parameters of the RBF network was investigated. The new method involves forward selection to prevent overfitting and generalized cross-validation (GCV) was used as model selection criterion (MSC). The original data was compressed by using wavelet transformation to speed up the network training and reduce the number of variables of the original MS data. The data was normalized prior training and testing a network to define the area the neural network to be trained in, accelerate the training rate, and reduce the range the parameters to be selected in. The one-out-of-n method was used to split the data set of p samples into a training set of size p-1 and a test set of size 1. With the improved method, the classification correctness for the five bacteria discussed in the present paper are 87.5, 69.2, 80, 92.3, and 92.8%, respectively.

  8. Antimicrobial functionalization of bacterial nanocellulose by loading with polihexanide and povidone-iodine.

    Science.gov (United States)

    Wiegand, Cornelia; Moritz, Sebastian; Hessler, Nadine; Kralisch, Dana; Wesarg, Falko; Müller, Frank A; Fischer, Dagmar; Hipler, Uta-Christina

    2015-10-01

    Bacterial nanocellulose (BNC) is chemically identical with plant cellulose but free of byproducts like lignin, pectin, and hemicelluloses, featuring a unique reticulate network of fine fibers. BNC sheets are mostly obtained by static cultivation. Now, a Horizontal Lift Reactor may provide a cost efficient method for mass production. This is of particular interest as BNC features several properties of an ideal wound dressing although it exhibits no bactericidal activity. Therefore, BNC was functionalized with the antiseptics povidone-iodine (PI) and polihexanide (PHMB). Drug loading and release, mechanical characteristics, biocompatibility, and antimicrobial efficacy were investigated. Antiseptics release was based on diffusion and swelling according to Ritger-Peppas equation. PI-loaded BNC demonstrated a delayed release compared to PHMB due to a high molar drug mass and structural changes induced by PI insertion into BNC that also increased the compressive strength of BNC samples. Biological assays demonstrated high biocompatibility of PI-loaded BNC in human keratinocytes but a distinctly lower antimicrobial activity against Staphylococcus aureus compared to PHMB-loaded BNC. Overall, BNC loaded with PHMB demonstrated a better therapeutic window. Moreover, compressive and tensile strength were not changed by incorporation of PHMB into BNC, and solidity during loading and release could be confirmed. PMID:26411441

  9. Bacterial and archaeal dynamics in phylogeny and function in the North Atlantic deep waters

    Science.gov (United States)

    Herndl, G. J.; Brink, M.; Agogue, H.

    2009-04-01

    The diversity and specific functional aspects linked to the N cycle of the bacterio- and archaeoplankton were investigated in the major deep water masses of the North Atlantic following the main driver of the thermohaline circulation, the North Atlantic Deep Water, from 65°N to 5°S. The phylogenetic composition of Bacteria and Archaea is not only depth-dependent but, specific water masses harbor specific prokaryotic communities. The specific composition of these communities in a particular water mass is maintained even over large distances. The distribution of archaeal and bacterial amoA genes were also determined. Archaeal amoA copy numbers decreased drastically with depth especially in the eastern subtropical Atlantic. This coincides with the lower nutrient concentration of the deep waters in the southern parts of the North Atlantic and the older age of the deep-water masses there. These data demonstrate that the diversity and potential nitrification activity are closely linked to the hydrology and chemical characteristics of the major water masses in the North Atlantic.

  10. Functional heterogeneity in CD4+ T cell responses against a bacterial pathogen

    Directory of Open Access Journals (Sweden)

    Ashley eViehmann Milam

    2015-12-01

    Full Text Available To investigate how CD4+ T cells function against a bacterial pathogen, we generated a Listeria monocytogenes-specific CD4+ T cell model. In this system, two TCRtg mouse lines, LLO56 and LLO118 recognize the same immunodominant epitope (LLO190-205 of Listeria monocytogenes and have identical in vitro responses. However, in vivo LLO56 and LLO118 display vastly different responses during both primary and secondary infection. LLO118 dominates in the primary response and in providing CD8 T cell help. LLO56 predominates in the secondary response. We have also shown that both specific (TCR-mediated and nonspecific stimuli (bypassing the TCR elicit distinct responses from the two transgenics, leading us to conclude that the strength of self-pMHC signaling during development tightly dictates the cell’s future response in the periphery. Herein, we review our findings in this transfer system, focusing on the contribution of the immunomodulatory molecule CD5 and the importance of self-interaction in peripheral maintenance of the cell. We also discuss the manner in which individual TCR affinities to foreign and self-pMHC contribute to the outcome of an immune response; our assertion is that there exists a spectrum of possible T cell responses to recognition of cognate antigen during infection, adding immense diversity to the immune system’s response to pathogens.

  11. The rhizosphere and PAH amendment mediate impacts on functional and structural bacterial diversity in sandy peat soil

    Energy Technology Data Exchange (ETDEWEB)

    Yrjaelae, Kim, E-mail: kim.yrjala@helsinki.f [Department of Biological and Environmental Sciences, General Microbiology, University of Helsinki, P.O. Box 56, (Biocenter 1C), 00014 Helsinki (Finland); Keskinen, Anna-Kaisa; Akerman, Marja-Leena; Fortelius, Carola [METROPOLIA University of Applied Science, Vantaa (Finland); Sipilae, Timo P. [Department of Biological and Environmental Sciences, General Microbiology, University of Helsinki, P.O. Box 56, (Biocenter 1C), 00014 Helsinki (Finland)

    2010-05-15

    To reveal the degradation capacity of bacteria in PAH polluted soil and rhizosphere we combined bacterial extradiol ring-cleavage dioxygenase and 16S rRNA analysis in Betula pubescens rhizoremediation. Characterisation of the functional bacterial community by RFLP revealed novel environmental dioxygenases, and their putative hosts were studied by 16S rRNA amplification. Plant rhizosphere and PAH amendment effects were detected by the RFLP/T-RFLP analysis. Functional species richness increased in the birch rhizosphere and PAH amendment impacted the compositional diversity of the dioxygenases and the structural 16S rRNA community. A shift from an Acidobacteria and Verrucomicrobia dominated to an Alpha- and Betaproteobacteria dominated community structure was detected in polluted soil. Clone sequence analysis indicated catabolic significance of Burkholderia in PAH polluted soil. These results advance our understanding of rhizoremediation and unveil the extent of uncharacterized functional bacteria to benefit bioremediation by facilitating the development of the molecular tool box to monitor bacterial populations in biodegradation. - The bacterial community analysis using 16S rRNA and extradiol dioxygenase marker genes in rhizoremediation revealed both a rhizosphere and a PAH-pollution effect.

  12. The rhizosphere and PAH amendment mediate impacts on functional and structural bacterial diversity in sandy peat soil

    International Nuclear Information System (INIS)

    To reveal the degradation capacity of bacteria in PAH polluted soil and rhizosphere we combined bacterial extradiol ring-cleavage dioxygenase and 16S rRNA analysis in Betula pubescens rhizoremediation. Characterisation of the functional bacterial community by RFLP revealed novel environmental dioxygenases, and their putative hosts were studied by 16S rRNA amplification. Plant rhizosphere and PAH amendment effects were detected by the RFLP/T-RFLP analysis. Functional species richness increased in the birch rhizosphere and PAH amendment impacted the compositional diversity of the dioxygenases and the structural 16S rRNA community. A shift from an Acidobacteria and Verrucomicrobia dominated to an Alpha- and Betaproteobacteria dominated community structure was detected in polluted soil. Clone sequence analysis indicated catabolic significance of Burkholderia in PAH polluted soil. These results advance our understanding of rhizoremediation and unveil the extent of uncharacterized functional bacteria to benefit bioremediation by facilitating the development of the molecular tool box to monitor bacterial populations in biodegradation. - The bacterial community analysis using 16S rRNA and extradiol dioxygenase marker genes in rhizoremediation revealed both a rhizosphere and a PAH-pollution effect.

  13. Bacterial Cellulose: A Robust Platform for Design of Three Dimensional Carbon-Based Functional Nanomaterials.

    Science.gov (United States)

    Wu, Zhen-Yu; Liang, Hai-Wei; Chen, Li-Feng; Hu, Bi-Cheng; Yu, Shu-Hong

    2016-01-19

    Three dimensional (3D) carbon nanomaterials exhibit great application potential in environmental protection, electrochemical energy storage and conversion, catalysis, polymer science, and advanced sensors fields. Current methods for preparing 3D carbon nanomaterials, for example, carbonization of organogels, chemical vapor deposition, and self-assembly of nanocarbon building blocks, inevitably involve some drawbacks, such as expensive and toxic precursors, complex equipment and technological requirements, and low production ability. From the viewpoint of practical application, it is highly desirable to develop a simple, cheap, and environmentally friendly way for fabricating 3D carbon nanomaterials in large scale. On the other hand, in order to extend the application scope and improve the performance of 3D carbon nanomaterials, we should explore efficient strategies to prepare diverse functional nanomaterials based on their 3D carbon structure. Recently, many researchers tend to fabricate high-performance 3D carbon-based nanomaterials from biomass, which is low cost, easy to obtain, and nontoxic to humans. Bacterial cellulose (BC), a typical biomass material, has long been used as the raw material of nata-de-coco (an indigenous dessert food of the Philippines). It consists of a polysaccharide with a β-1,4-glycosidic linkage and has a interconnected 3D porous network structure. Interestingly, the network is made up of a random assembly of cellulose nanofibers, which have a high aspect ratio with a diameter of 20-100 nm. As a result, BC has a high specific surface area. Additionally, BC hydrogels can be produced on an industrial scale via a microbial fermentation process at a very low price. Thus, it can be an ideal platform for design of 3D carbon-based functional nanomaterials. Before our work, no systematic work and summary on this topic had been reported. This Account presents the concepts and strategies of our studies on BC in the past few years, that is

  14. Bacterial Cellulose: A Robust Platform for Design of Three Dimensional Carbon-Based Functional Nanomaterials.

    Science.gov (United States)

    Wu, Zhen-Yu; Liang, Hai-Wei; Chen, Li-Feng; Hu, Bi-Cheng; Yu, Shu-Hong

    2016-01-19

    Three dimensional (3D) carbon nanomaterials exhibit great application potential in environmental protection, electrochemical energy storage and conversion, catalysis, polymer science, and advanced sensors fields. Current methods for preparing 3D carbon nanomaterials, for example, carbonization of organogels, chemical vapor deposition, and self-assembly of nanocarbon building blocks, inevitably involve some drawbacks, such as expensive and toxic precursors, complex equipment and technological requirements, and low production ability. From the viewpoint of practical application, it is highly desirable to develop a simple, cheap, and environmentally friendly way for fabricating 3D carbon nanomaterials in large scale. On the other hand, in order to extend the application scope and improve the performance of 3D carbon nanomaterials, we should explore efficient strategies to prepare diverse functional nanomaterials based on their 3D carbon structure. Recently, many researchers tend to fabricate high-performance 3D carbon-based nanomaterials from biomass, which is low cost, easy to obtain, and nontoxic to humans. Bacterial cellulose (BC), a typical biomass material, has long been used as the raw material of nata-de-coco (an indigenous dessert food of the Philippines). It consists of a polysaccharide with a β-1,4-glycosidic linkage and has a interconnected 3D porous network structure. Interestingly, the network is made up of a random assembly of cellulose nanofibers, which have a high aspect ratio with a diameter of 20-100 nm. As a result, BC has a high specific surface area. Additionally, BC hydrogels can be produced on an industrial scale via a microbial fermentation process at a very low price. Thus, it can be an ideal platform for design of 3D carbon-based functional nanomaterials. Before our work, no systematic work and summary on this topic had been reported. This Account presents the concepts and strategies of our studies on BC in the past few years, that is

  15. A survey of biofilms on wastewater aeration diffusers suggests bacterial community composition and function vary by substrate type and time.

    Science.gov (United States)

    Noble, Peter A; Park, Hee-Deung; Olson, Betty H; Asvapathanagul, Pitiporn; Hunter, M Colby; Garrido-Baserba, Manel; Lee, Sang-Hoon; Rosso, Diego

    2016-07-01

    Aeration diffusers in wastewater treatment plants generate air bubbles that promote mixing, distribution of dissolved oxygen, and microbial processing of dissolved and suspended matter in bulk solution. Biofouling of diffusers represents a significant problem to wastewater treatment plants because biofilms decrease oxygen transfer efficiency and increase backpressure on the blower. To better understand biofouling, we conducted a pilot study to survey the bacterial community composition and function of biofilms on different diffuser substrates and compare them to those in the bulk solution. DNA was extracted from the surface of ethylene-propylene-diene monomer (EPDM), polyurethane, and silicone diffusers operated for 15 months in a municipal treatment plant and sampled at 3 and 9 months. The bacterial community composition and function of the biofilms and bulk solution were determined by amplifying the 16S rRNA genes and pyrosequencing the amplicons and raw metagenomic DNA. The ordination plots and dendrograms of the 16S rRNA and functional genes showed that while the bacterial community composition and function of the bulk solution was independent of sampling time, the composition and function of the biofilms differed by diffuser type and testing time. For the EPDM and silicone diffusers, the biofilm communities were more similar in composition to the bulk solution at 3 months than 9 months. In contrast, the bacteria on the polyurethane diffusers were more dissimilar to the bulk solution at 3 months than 9 months. Taken together, the survey showed that the community composition and function of bacterial biofilms depend on the diffuser substrate and testing time, which warrants further elucidation. PMID:27294381

  16. Response of bacterial community structure and function to experimental rainwater additions in a coastal eutrophic embayment

    Science.gov (United States)

    Teira, Eva; Hernando-Morales, Víctor; Martínez-García, Sandra; Figueiras, Francisco G.; Arbones, Belén; Álvarez-Salgado, Xosé Antón

    2013-03-01

    Although recognized as a potentially important source of both inorganic and organic nutrients, the impact of rainwater on microbial populations from marine planktonic systems has been poorly assessed. The effect of rainwater additions on bacterioplankton metabolism and community composition was evaluated in microcosm experiments enclosing natural marine plankton populations from the Ría de Vigo (NW Spain). The experiments were conducted during three different seasons (spring, autumn and winter) using rainwater collected at three different locations: marine, urban and rural sites. Bacterial abundance and production significantly increased up to 1.3 and 1.8-fold, respectively, after urban rainwater additions in spring, when ambient nutrient concentration was very low. Overall, the increments in bacterial production were higher than those in bacterial respiration, which implies that a higher proportion of carbon consumed by bacteria would be available to higher trophic levels. The response of the different bacterial groups to distinct rainwater types differed between seasons. The most responsive bacterial groups were Betaproteobacteria which significantly increased their abundance after urban (in spring and winter) and marine (in spring) rainwater additions, and Bacteroidetes which positively responded to all rainwater treatments in spring and to urban rainwater in autumn. Gammaproteobacteria and Roseobacter responded only to urban (in spring) and marine (in winter) rainwater treatment, respectively. The responses to rainwater additions were moderate and transient, and the resulting bacterial community structure was not importantly altered.

  17. Bacterial effector binding to ribosomal protein s3 subverts NF-kappaB function.

    Directory of Open Access Journals (Sweden)

    Xiaofei Gao

    2009-12-01

    Full Text Available Enteric bacterial pathogens cause food borne disease, which constitutes an enormous economic and health burden. Enterohemorrhagic Escherichia coli (EHEC causes a severe bloody diarrhea following transmission to humans through various means, including contaminated beef and vegetable products, water, or through contact with animals. EHEC also causes a potentially fatal kidney disease (hemolytic uremic syndrome for which there is no effective treatment or prophylaxis. EHEC and other enteric pathogens (e.g., enteropathogenic E. coli (EPEC, Salmonella, Shigella, Yersinia utilize a type III secretion system (T3SS to inject virulence proteins (effectors into host cells. While it is known that T3SS effectors subvert host cell function to promote diarrheal disease and bacterial transmission, in many cases, the mechanisms by which these effectors bind to host proteins and disrupt the normal function of intestinal epithelial cells have not been completely characterized. In this study, we present evidence that the E. coli O157:H7 nleH1 and nleH2 genes encode T3SS effectors that bind to the human ribosomal protein S3 (RPS3, a subunit of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kappaB transcriptional complexes. NleH1 and NleH2 co-localized with RPS3 in the cytoplasm, but not in cell nuclei. The N-terminal region of both NleH1 and NleH2 was required for binding to the N-terminus of RPS3. NleH1 and NleH2 are autophosphorylated Ser/Thr protein kinases, but their binding to RPS3 is independent of kinase activity. NleH1, but not NleH2, reduced the nuclear abundance of RPS3 without altering the p50 or p65 NF-kappaB subunits or affecting the phosphorylation state or abundance of the inhibitory NF-kappaB chaperone IkappaBalpha NleH1 repressed the transcription of a RPS3/NF-kappaB-dependent reporter plasmid, but did not inhibit the transcription of RPS3-independent reporters. In contrast, NleH2 stimulated RPS3-dependent transcription, as well

  18. The transport mechanism of bacterial Cu+-ATPases: distinct efflux rates adapted to different function.

    Science.gov (United States)

    Raimunda, Daniel; González-Guerrero, Manuel; Leeber, Blaise W; Argüello, José M

    2011-06-01

    Cu(+)-ATPases play a key role in bacterial Cu(+) homeostasis by participating in Cu(+) detoxification and cuproprotein assembly. Characterization of Archaeoglobus fulgidus CopA, a model protein within the subfamily of P(1B-1) type ATPases, has provided structural and mechanistic details on this group of transporters. Atomic resolution structures of cytoplasmic regulatory metal binding domains (MBDs) and catalytic actuator, phosphorylation, and nucleotide binding domains are available. These, in combination with whole protein structures resulting from cryo-electron microscopy analyses, have enabled the initial modeling of these transporters. Invariant residues in helixes 6, 7 and 8 form two transmembrane metal binding sites (TM-MBSs). These bind Cu(+) with high affinity in a trigonal planar geometry. The cytoplasmic Cu(+) chaperone CopZ transfers the metal directly to the TM-MBSs; however, loading both of the TM-MBSs requires binding of nucleotides to the enzyme. In agreement with the classical transport mechanism of P-type ATPases, occupancy of both transmembrane sites by cytoplasmic Cu(+) is a requirement for enzyme phosphorylation and subsequent transport into the periplasmic or extracellular milieus. Recent transport studies have shown that all Cu(+)-ATPases drive cytoplasmic Cu(+) efflux, albeit with quite different transport rates in tune with their various physiological roles. Archetypical Cu(+)-efflux pumps responsible for Cu(+) tolerance, like the Escherichia coli CopA, have turnover rates ten times higher than those involved in cuproprotein assembly (or alternative functions). This explains the incapability of the latter group to significantly contribute to the metal efflux required for survival in high copper environments. PMID:21210186

  19. Bacterial Artificial Chromosomes: A Functional Genomics Tool for the Study of Positive-strand RNA Viruses.

    Science.gov (United States)

    Yun, Sang-Im; Song, Byung-Hak; Kim, Jin-Kyoung; Lee, Young-Min

    2015-01-01

    Reverse genetics, an approach to rescue infectious virus entirely from a cloned cDNA, has revolutionized the field of positive-strand RNA viruses, whose genomes have the same polarity as cellular mRNA. The cDNA-based reverse genetics system is a seminal method that enables direct manipulation of the viral genomic RNA, thereby generating recombinant viruses for molecular and genetic studies of both viral RNA elements and gene products in viral replication and pathogenesis. It also provides a valuable platform that allows the development of genetically defined vaccines and viral vectors for the delivery of foreign genes. For many positive-strand RNA viruses such as Japanese encephalitis virus (JEV), however, the cloned cDNAs are unstable, posing a major obstacle to the construction and propagation of the functional cDNA. Here, the present report describes the strategic considerations in creating and amplifying a genetically stable full-length infectious JEV cDNA as a bacterial artificial chromosome (BAC) using the following general experimental procedures: viral RNA isolation, cDNA synthesis, cDNA subcloning and modification, assembly of a full-length cDNA, cDNA linearization, in vitro RNA synthesis, and virus recovery. This protocol provides a general methodology applicable to cloning full-length cDNA for a range of positive-strand RNA viruses, particularly those with a genome of >10 kb in length, into a BAC vector, from which infectious RNAs can be transcribed in vitro with a bacteriophage RNA polymerase. PMID:26780115

  20. Surfactant improves lung function and mitigates bacterial growth in immature ventilated rabbits with experimentally induced neonatal group B streptococcal pneumonia

    OpenAIRE

    Herting, E.; Sun, B.; Jarstrand, C; Curstedt, T; Robertson, B.

    1997-01-01

    Aims—To study the influence of surfactant on lung function and bacterial proliferation in immature newborn rabbits with experimental group B streptococcal (GBS) pneumonia.
METHODS—Preterm rabbit fetuses (gest-ational age 28 days) underwent tracheotomy and were mechanically ventilated in a warmed body plethysmograph that permitted measurement of lung-thorax compliance. Fifteen minutes after the onset of ventilation the animals received either GBS or saline intratracheally; at 30 minutes, a bol...

  1. Enzymatic modification of bacterial exopolysaccharides; xanthan lyase as a tool for structural and functional modification of xanthan

    OpenAIRE

    Ruijssenaars, H.J.

    2001-01-01

    Bacterial extracellular polysaccharides (EPSs) can be applied, e.g., in foods, as a thickener or stabilizer. The functional properties that make a polysaccharide suitable for such applications are largely determined by the primary structure, i.e., the sugar composition, the linkage types between the sugar units, and the presence of side chains and non-sugar substituents. The aim of this research was to obtain EPS-modifying enzymes that could be used as tools both for studying structure-functi...

  2. Soil bacterial community and functional shifts in response to altered snowpack in moist acidic tundra of northern Alaska

    Science.gov (United States)

    Ricketts, Michael P.; Poretsky, Rachel S.; Welker, Jeffrey M.; Gonzalez-Meler, Miquel A.

    2016-09-01

    Soil microbial communities play a central role in the cycling of carbon (C) in Arctic tundra ecosystems, which contain a large portion of the global C pool. Climate change predictions for Arctic regions include increased temperature and precipitation (i.e. more snow), resulting in increased winter soil insulation, increased soil temperature and moisture, and shifting plant community composition. We utilized an 18-year snow fence study site designed to examine the effects of increased winter precipitation on Arctic tundra soil bacterial communities within the context of expected ecosystem response to climate change. Soil was collected from three pre-established treatment zones representing varying degrees of snow accumulation, where deep snow ˜ 100 % and intermediate snow ˜ 50 % increased snowpack relative to the control, and low snow ˜ 25 % decreased snowpack relative to the control. Soil physical properties (temperature, moisture, active layer thaw depth) were measured, and samples were analysed for C concentration, nitrogen (N) concentration, and pH. Soil microbial community DNA was extracted and the 16S rRNA gene was sequenced to reveal phylogenetic community differences between samples and determine how soil bacterial communities might respond (structurally and functionally) to changes in winter precipitation and soil chemistry. We analysed relative abundance changes of the six most abundant phyla (ranging from 82 to 96 % of total detected phyla per sample) and found four (Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi) responded to deepened snow. All six phyla correlated with at least one of the soil chemical properties (% C, % N, C : N, pH); however, a single predictor was not identified, suggesting that each bacterial phylum responds differently to soil characteristics. Overall, bacterial community structure (beta diversity) was found to be associated with snow accumulation treatment and all soil chemical properties. Bacterial

  3. Associations between soil bacterial community structure and nutrient cycling functions in long-term organic farm soils following cover crop and organic fertilizer amendment.

    Science.gov (United States)

    Fernandez, Adria L; Sheaffer, Craig C; Wyse, Donald L; Staley, Christopher; Gould, Trevor J; Sadowsky, Michael J

    2016-10-01

    Agricultural management practices can produce changes in soil microbial populations whose functions are crucial to crop production and may be detectable using high-throughput sequencing of bacterial 16S rRNA. To apply sequencing-derived bacterial community structure data to on-farm decision-making will require a better understanding of the complex associations between soil microbial community structure and soil function. Here 16S rRNA sequencing was used to profile soil bacterial communities following application of cover crops and organic fertilizer treatments in certified organic field cropping systems. Amendment treatments were hairy vetch (Vicia villosa), winter rye (Secale cereale), oilseed radish (Raphanus sativus), buckwheat (Fagopyrum esculentum), beef manure, pelleted poultry manure, Sustane(®) 8-2-4, and a no-amendment control. Enzyme activities, net N mineralization, soil respiration, and soil physicochemical properties including nutrient levels, organic matter (OM) and pH were measured. Relationships between these functional and physicochemical parameters and soil bacterial community structure were assessed using multivariate methods including redundancy analysis, discriminant analysis, and Bayesian inference. Several cover crops and fertilizers affected soil functions including N-acetyl-β-d-glucosaminidase and β-glucosidase activity. Effects, however, were not consistent across locations and sampling timepoints. Correlations were observed among functional parameters and relative abundances of individual bacterial families and phyla. Bayesian analysis inferred no directional relationships between functional activities, bacterial families, and physicochemical parameters. Soil functional profiles were more strongly predicted by location than by treatment, and differences were largely explained by soil physicochemical parameters. Composition of soil bacterial communities was predictive of soil functional profiles. Differences in soil function were

  4. Associations between soil bacterial community structure and nutrient cycling functions in long-term organic farm soils following cover crop and organic fertilizer amendment.

    Science.gov (United States)

    Fernandez, Adria L; Sheaffer, Craig C; Wyse, Donald L; Staley, Christopher; Gould, Trevor J; Sadowsky, Michael J

    2016-10-01

    Agricultural management practices can produce changes in soil microbial populations whose functions are crucial to crop production and may be detectable using high-throughput sequencing of bacterial 16S rRNA. To apply sequencing-derived bacterial community structure data to on-farm decision-making will require a better understanding of the complex associations between soil microbial community structure and soil function. Here 16S rRNA sequencing was used to profile soil bacterial communities following application of cover crops and organic fertilizer treatments in certified organic field cropping systems. Amendment treatments were hairy vetch (Vicia villosa), winter rye (Secale cereale), oilseed radish (Raphanus sativus), buckwheat (Fagopyrum esculentum), beef manure, pelleted poultry manure, Sustane(®) 8-2-4, and a no-amendment control. Enzyme activities, net N mineralization, soil respiration, and soil physicochemical properties including nutrient levels, organic matter (OM) and pH were measured. Relationships between these functional and physicochemical parameters and soil bacterial community structure were assessed using multivariate methods including redundancy analysis, discriminant analysis, and Bayesian inference. Several cover crops and fertilizers affected soil functions including N-acetyl-β-d-glucosaminidase and β-glucosidase activity. Effects, however, were not consistent across locations and sampling timepoints. Correlations were observed among functional parameters and relative abundances of individual bacterial families and phyla. Bayesian analysis inferred no directional relationships between functional activities, bacterial families, and physicochemical parameters. Soil functional profiles were more strongly predicted by location than by treatment, and differences were largely explained by soil physicochemical parameters. Composition of soil bacterial communities was predictive of soil functional profiles. Differences in soil function were

  5. Structural and functional diversity of soil bacterial and fungal communities following woody plant encroachment in the southern Great Plains

    Energy Technology Data Exchange (ETDEWEB)

    Hollister, Emily B [ORNL; Schadt, Christopher Warren [ORNL; Palumbo, Anthony Vito [ORNL; Ansley, R J [Texas A& M University; Boutton, Thomas W [Texas A& M University

    2010-01-01

    In the southern Great Plains (USA), encroachment of grassland ecosystems by Prosopis glandulosa (honey mesquite) is widespread. Mesquite encroachment alters net primary productivity, enhances stores of C and N in plants and soil, and leads to increased levels of soil microbial biomass and activity. While mesquite's impact on the biogeochemistry of the region is well established, it effects on soil microbial diversity and function are unknown. In this study, soils associated with four plant types (C{sub 3} perennial grasses, C{sub 4} midgrasses, C{sub 4} shortgrasses, and mesquite) from a mesquite-encroached mixed grass prairie were surveyed to in an attempt to characterize the structure, diversity, and functional capacity of their soil microbial communities. rRNA gene cloning and sequencing were used in conjunction with the GeoChip functional gene array to evaluate these potential differences. Mesquite soil supported increased bacterial and fungal diversity and harbored a distinct fungal community relative to other plant types. Despite differences in composition and diversity, few significant differences were detected with respect to the potential functional capacity of the soil microbial communities. These results may suggest that a high level of functional redundancy exists within the bacterial portion of the soil communities; however, given the bias of the GeoChip toward bacterial functional genes, potential functional differences among soil fungi could not be addressed. The results of this study illustrate the linkages shared between above- and belowground communities and demonstrate that soil microbial communities, and in particular soil fungi, may be altered by the process of woody plant encroachment.

  6. Efficient mineral weathering is a distinctive functional trait of the bacterial genus Collimonas

    NARCIS (Netherlands)

    Uroz, S.; Calvaruso, C.; Turpault, M.P.; Sarniguet, A.; De Boer, W.; Leveau, J.H.J.; Frey-Klett, P.

    2009-01-01

    The mineral weathering ability of 45 bacterial strains belonging to the genus Collimonas and coming from various terrestrial environments was compared to that of 5 representatives from the closely related genera Herbaspirillum and Janthinobacterium. Using glucose as the sole carbon source in a micro

  7. Probiotic yogurt in the elderly with intestinal bacterial overgrowth: endotoxaemia and innate immune functions

    DEFF Research Database (Denmark)

    Schiffrin, E.J.; Parlesak, Alexandr; Bode, C.;

    2009-01-01

    A study was conducted in healthy elderly living independently in senior housing to assess the impact of a probiotic yoghurt supplement on small intestinal bacterial overgrowth. Twenty-three participants with positive and thirteen participants with negative hydrogen breath test were studied before...

  8. Physical soil architectural traits are functionally linked to carbon decomposition and bacterial diversity

    Science.gov (United States)

    Rabbi, S. M. F.; Daniel, H.; Lockwood, P. V.; MacDonald, C.; Pereg, L.; Tighe, M.; Wilson, B. R.; Young, I. M.

    2016-09-01

    Aggregates play a key role in protecting soil organic carbon (SOC) from microbial decomposition. The objectives of this study were to investigate the influence of pore geometry on the organic carbon decomposition rate and bacterial diversity in both macro- (250-2000 μm) and micro-aggregates (53-250 μm) using field samples. Four sites of contrasting land use on Alfisols (i.e. native pasture, crop/pasture rotation, woodland) were investigated. 3D Pore geometry of the micro-aggregates and macro-aggregates were examined by X-ray computed tomography (μCT). The occluded particulate organic carbon (oPOC) of aggregates was measured by size and density fractionation methods. Micro-aggregates had 54% less μCT observed porosity but 64% more oPOC compared with macro-aggregates. In addition, the pore connectivity in micro-aggregates was lower than macro-aggregates. Despite both lower μCT observed porosity and pore connectivity in micro-aggregates, the organic carbon decomposition rate constant (Ksoc) was similar in both aggregate size ranges. Structural equation modelling showed a strong positive relationship of the concentration of oPOC with bacterial diversity in aggregates. We use these findings to propose a conceptual model that illustrates the dynamic links between substrate, bacterial diversity, and pore geometry that suggests a structural explanation for differences in bacterial diversity across aggregate sizes.

  9. Physical soil architectural traits are functionally linked to carbon decomposition and bacterial diversity.

    Science.gov (United States)

    Rabbi, S M F; Daniel, H; Lockwood, P V; Macdonald, C; Pereg, L; Tighe, M; Wilson, B R; Young, I M

    2016-01-01

    Aggregates play a key role in protecting soil organic carbon (SOC) from microbial decomposition. The objectives of this study were to investigate the influence of pore geometry on the organic carbon decomposition rate and bacterial diversity in both macro- (250-2000 μm) and micro-aggregates (53-250 μm) using field samples. Four sites of contrasting land use on Alfisols (i.e. native pasture, crop/pasture rotation, woodland) were investigated. 3D Pore geometry of the micro-aggregates and macro-aggregates were examined by X-ray computed tomography (μCT). The occluded particulate organic carbon (oPOC) of aggregates was measured by size and density fractionation methods. Micro-aggregates had 54% less μCT observed porosity but 64% more oPOC compared with macro-aggregates. In addition, the pore connectivity in micro-aggregates was lower than macro-aggregates. Despite both lower μCT observed porosity and pore connectivity in micro-aggregates, the organic carbon decomposition rate constant (Ksoc) was similar in both aggregate size ranges. Structural equation modelling showed a strong positive relationship of the concentration of oPOC with bacterial diversity in aggregates. We use these findings to propose a conceptual model that illustrates the dynamic links between substrate, bacterial diversity, and pore geometry that suggests a structural explanation for differences in bacterial diversity across aggregate sizes. PMID:27615807

  10. A nanobody:GFP bacterial platform that enables functional enzyme display and easy quantification of display capacity

    DEFF Research Database (Denmark)

    Wendel, Sofie; Christian Fischer, Emil; Martinez, Virginia;

    2016-01-01

    Background: Bacterial surface display is an attractive technique for the production of cell-anchored, functional proteins and engineering of whole-cell catalysts. Although various outer membrane proteins have been used for surface display, an easy and versatile high-throughput-compatible assay...... protein LppOmpA and the autotransporter C-IgAP exposed the nanobody on the surface of Escherichia coli with very different efficiency. Both anchors were capable of functionally displaying the enzyme Chitinase A as a fusion with the nanobody, and this considerably increased expression levels compared...

  11. Establishment of rumen-mimic bacterial consortia: A functional union for bio-hydrogen production from cellulosic bioresource

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Jui-Jen [Genomics Research Center, Academia Sinica, Nankang, Taipei 115 (China); Lin, Jia-Jen; Ho, Cheng-Yu.; Chin, Wei-Chih; Huang, Chieh-Chen [Department of Life Sciences, National Chung Hsing University,Taichung (China)

    2010-12-15

    The study aimed to establish stable rumen-mimic bacterial consortia as a functional union for simultaneous saccharification and fermentation from cellulosic bioresource. The consortia was constructed by repeated-batch culture with ruminal microflora and napiergrass at 38 C. The major bacterial composition of batch culture was monitored by 16S rRNA gene-targeted denaturing gradient gel electrophoresis (DGGE). The result showed that a stable consortia constituted by ruminal microflora was formed, and the consortia includes bacterial strains such as Clostridium xylanolyticum, Clostridium papyrosolvens, Clostridium beijerinckii, Ruminococcus sp., Ethanoligenens harbinense, and Desulfovibrio desulfuricans. The Clostridium genus was showed as the dominant population in the system and contributed to the biohydrogen production. During each eight days incubation period, the functional consortia could degrade an average of 27% hemicellulose and 2% cellulose from napiergrass biomass. While the increasing of the reducing sugars and their converting to biohydrogen gas productivity were also observed. The time course profile for cellulytic enzymes showed that the hydrolysis of complex lignocellulosic material may occur through the ordered actions of xylenase and cellulase activities. (author)

  12. Impact of CO2 leakage from sub-seabed carbon dioxide capture and storage (CCS) reservoirs on benthic virus-prokaryote interactions and functions

    OpenAIRE

    Eugenio eRastelli; Cinzia eCorinaldesi; Antonio eDell'Anno; Teresa eAmaro; Ana M Queiros; Stephen eWiddicombe; Roberto eDanovaro

    2015-01-01

    Atmospheric CO2 emissions are a global concern due to their predicted impact on biodiversity, ecosystems functioning and human life. Among the proposed mitigation strategies, CO2 capture and storage (CCS), primarily the injection of CO2 into marine deep geological formations has been suggested as a technically practical option for reducing emissions. However, concerns have been raised that possible leakage from such storage sites, and the associated elevated levels of pCO2 could locally impac...

  13. Impact of CO2 leakage from sub-seabed carbon dioxide capture and storage (CCS) reservoirs on benthic virus–prokaryote interactions and functions

    OpenAIRE

    Rastelli, Eugenio; Corinaldesi, Cinzia; Dell’Anno, Antonio; Amaro, Teresa; Queirós, Ana M.; Widdicombe, Stephen; Danovaro, Roberto

    2015-01-01

    Atmospheric CO2 emissions are a global concern due to their predicted impact on biodiversity, ecosystems functioning, and human life. Among the proposed mitigation strategies, CO2 capture and storage, primarily the injection of CO2 into marine deep geological formations has been suggested as a technically practical option for reducing emissions. However, concerns have been raised that possible leakage from such storage sites, and the associated elevated levels of pCO2 could locally impact the...

  14. Surface Treatments and Functional Coatings for Biocompatibility Improvement and Bacterial Adhesion Reduction in Dental Implantology

    Directory of Open Access Journals (Sweden)

    Pietro Mandracci

    2016-01-01

    Full Text Available Surface modification of dental implants is a key process in the production of these medical devices, and especially titanium implants used in the dental practice are commonly subjected to surface modification processes before their clinical use. A wide range of treatments, such as sand blasting, acid etching, plasma etching, plasma spray deposition, sputtering deposition and cathodic arc deposition, have been studied over the years in order to improve the performance of dental implants. Improving or accelerating the osseointegration process is usually the main goal of these surface processes, but the improvement of biocompatibility and the prevention of bacterial adhesion are also of considerable importance. In this review, we report on the research of the recent years in the field of surface treatments and coatings deposition for the improvement of dental implants performance, with a main focus on the osseointegration acceleration, the reduction of bacterial adhesion and the improvement of biocompatibility.

  15. An Improved Method for oriT-Directed Cloning and Functionalization of Large Bacterial Genomic Regions

    OpenAIRE

    Kvitko, Brian H.; McMillan, Ian A.; Schweizer, Herbert P.

    2013-01-01

    We have made significant improvements to a broad-host-range system for the cloning and manipulation of large bacterial genomic regions based on site-specific recombination between directly repeated oriT sites during conjugation. Using two suicide capture vectors carrying flanking homology regions, oriT sites are recombined on either side of the target region. Using a broad-host-range conjugation helper plasmid, the region between the oriT sites is conjugated into an Escherichia coli recipient...

  16. Particle Swarm and Bacterial Foraging Inspired Hybrid Artificial Bee Colony Algorithm for Numerical Function Optimization

    OpenAIRE

    Li Mao; Yu Mao; Changxi Zhou; Chaofeng Li; Xiao Wei; Hong Yang

    2016-01-01

    Artificial bee colony (ABC) algorithm has good performance in discovering the optimal solutions to difficult optimization problems, but it has weak local search ability and easily plunges into local optimum. In this paper, we introduce the chemotactic behavior of Bacterial Foraging Optimization into employed bees and adopt the principle of moving the particles toward the best solutions in the particle swarm optimization to improve the global search ability of onlooker bees and gain a hybrid a...

  17. Riemerella anatipestifer M949_1360 Gene Functions on the Lipopolysaccharide Biosynthesis and Bacterial Virulence.

    Science.gov (United States)

    Yu, Guijing; Wang, Xiaolan; Dou, Yafeng; Wang, Shaohui; Tian, Mingxing; Qi, Jingjing; Li, Tao; Ding, Chan; Wu, Yantao; Yu, Shengqing

    2016-01-01

    Riemerella anatipestifer causes septicemic and exudative diseases in poultry, resulting in major economic losses to the duck industry. Lipopolysaccharide (LPS), as an important virulence factor in Gram-negative bacteria, can be recognized by the immune system and plays a crucial role in many interactions between bacteria and animal hosts. In this study, we screened out one LPS defective mutant strain RAΔ604 from a random transposon mutant library of R. anatipestifer serotype 1 strain CH3, which did not react with the anti-CH3 LPS monoclonal antibody 1C1 in an indirect enzyme-linked immunosorbent assay. Southern blot analysis confirmed that the genome of RAΔ604 contained a single Tn4351 insert. Then, we found that the M949_1360 gene was inactivated by insertion of the transposon. Using silver staining and western blot analyses, we found that the LPS pattern of RAΔ604 was defective, as compared with that of the wild-type (WT) strain CH3. The mutant strain RAΔ604 showed no significant influence on bacterial growth, while bacterial counting and Live/dead BacLight Bacterial Viability staining revealed that bacterial viability was decreased, as compared with the WT strain CH3. In addition, the abilities of the mutant strain RAΔ604 to adhere and invade Vero cells were significantly decreased. Animal studies revealed that the virulence of the mutant strain RAΔ604 was decreased by more than 200-fold in a duck infection model, as compared with the WT strain CH3. Furthermore, immunization with live bacteria of the mutant strain RAΔ604 protected 87.5% ducks from challenge with R. anatipestifer serotype 1 strain WJ4, indicating that the mutant strain RAΔ604 could be used as a potential vaccine candidate in the future. PMID:27500736

  18. The transport mechanism of bacterial Cu+-ATPases: distinct efflux rates adapted to different function

    OpenAIRE

    Raimunda, Daniel; González-Guerrero, Manuel; Leeber, Blaise W.; Argüello, José M.

    2011-01-01

    Cu+-ATPases play a key role in bacterial Cu+ homeostasis by participating in Cu+ detoxification and cuproprotein assembly. Characterization of Archaeoglobus fulgidus CopA, a model protein within the subfamily of P1B-1 type ATPases, has provided structural and mechanistic details on this group of transporters. Atomic resolution structures of cytoplasmic regulatory metal binding domains (MBDs) and catalytic actuator, phosphorylation, and nucleotide binding domains are available. These, in combi...

  19. Fabrication of a Functionalized Magnetic Bacterial Nanocellulose with Iron Oxide Nanoparticles.

    Science.gov (United States)

    Arias, Sandra L; Shetty, Akshath R; Senpan, Angana; Echeverry-Rendón, Mónica; Reece, Lisa M; Allain, Jean Paul

    2016-01-01

    In this study, bacterial nanocellulose (BNC) produced by the bacteria Gluconacetobacter xylinus is synthesized and impregnated in situ with iron oxide nanoparticles (IONP) (Fe3O4) to yield a magnetic bacterial nanocellulose (MBNC). The synthesis of MBNC is a precise and specifically designed multi-step process. Briefly, bacterial nanocellulose (BNC) pellicles are formed from preserved G. xylinus strain according to our experimental requirements of size and morphology. A solution of iron(III) chloride hexahydrate (FeCl3·6H2O) and iron(II) chloride tetrahydrate (FeCl2·4H2O) with a 2:1 molar ratio is prepared and diluted in deoxygenated high purity water. A BNC pellicle is then introduced in the vessel with the reactants. This mixture is stirred and heated at 80 °C in a silicon oil bath and ammonium hydroxide (14%) is then added by dropping to precipitate the ferrous ions into the BNC mesh. This last step allows forming in situ magnetite nanoparticles (Fe3O4) inside the bacterial nanocellulose mesh to confer magnetic properties to BNC pellicle. A toxicological assay was used to evaluate the biocompatibility of the BNC-IONP pellicle. Polyethylene glycol (PEG) was used to cover the IONPs in order to improve their biocompatibility. Scanning electron microscopy (SEM) images showed that the IONP were located preferentially in the fibril interlacing spaces of the BNC matrix, but some of them were also found along the BNC ribbons. Magnetic force microscope measurements performed on the MBNC detected the presence magnetic domains with high and weak intensity magnetic field, confirming the magnetic nature of the MBNC pellicle. Young's modulus values obtained in this work are also in a reasonable agreement with those reported for several blood vessels in previous studies. PMID:27285589

  20. Phylogeny and Functions of Bacterial Communities Associated with Field-Grown Rice Shoots

    OpenAIRE

    Okubo, Takashi; Ikeda, Seishi; Sasaki, Kazuhiro; Ohshima, Kenshiro; Hattori, Masahira; Sato, Tadashi; Minamisawa, Kiwamu

    2014-01-01

    Metagenomic analysis was applied to bacterial communities associated with the shoots of two field-grown rice cultivars, Nipponbare and Kasalath. In both cultivars, shoot microbiomes were dominated by Alphaproteobacteria (51–52%), Actinobacteria (11–15%), Gammaproteobacteria (9–10%), and Betaproteobacteria (4–10%). Compared with other rice microbiomes (root, rhizosphere, and phyllosphere) in public databases, the shoot microbiomes harbored abundant genes for C1 compound metabolism and 1-aminoc...

  1. 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 ...

  2. Persistence of uterine bacterial infection, and its associations with endometritis and ovarian function in postpartum dairy cows.

    Science.gov (United States)

    Ghanem, Mohamed Elshabrawy; Tezuka, Erisa; Devkota, Bhuminand; Izaike, Yoshiaki; Osawa, Takeshi

    2015-01-01

    We investigated the relationship between the persistence of uterine bacterial infections with cytologically determined endometritis and ovarian function in 65 postpartum Holstein cows. Vaginal mucus discharges were collected, and endometrial smear samples (n = 130) were collected for cytological and bacteriological examinations from the cows at weeks 5 and 7 postpartum (pp). Blood samples were collected at weeks 3, 5 and 7 pp to determine plasma progesterone concentrations to monitor ovarian activity. According to the bacteriological examination, cows were classified into four groups. The first group (n = 32; 49%) comprised cows negative for bacteria at weeks 5 and 7 pp. The second group (n = 11; 17%) comprised cows with bacterial infections at week 5 pp but that were clear of infection at week 7 pp. The third group (n = 12; 19%) comprised cows without bacteria at week 5 pp but that acquired an infection by week 7 pp. The fourth group (n = 10; 15%) comprised cows with bacterial infections at weeks 5 and 7 pp (persistence of infection). A positive correlation (P < 0.001) was noted between the severity of cytologically determined endometritis, purulent vaginal discharge and the persistence of infection. Cows with persistent infections had a significantly (P < 0.01) prolonged luteal phase compared with cows without infection. In conclusion, the prevalence of cytologically determined endometritis and prolonged luteal phase were significantly increased in cows with persistent infections. PMID:25482111

  3. Core Functional Traits of Bacterial Communities in the Upper Mississippi River Show Limited Variation in Response to Land Cover

    Directory of Open Access Journals (Sweden)

    Christopher eStaley

    2014-08-01

    Full Text Available Taxonomic characterization of environmental microbial communities via high-throughput DNA sequencing has revealed that patterns in microbial biogeography affect community structure. However, shifts in functional diversity related to variation in taxonomic composition are poorly understood. To overcome limitations due to the prohibitive cost of high-depth metagenomic sequencing, tools to infer functional diversity based on phylogenetic distributions of functional traits have been developed. In this study we characterized functional microbial diversity at 11 sites along the Mississippi River in Minnesota using both metagenomic sequencing and functional-inference-based (PICRUSt approaches. This allowed us to determine how distance and variation in land cover throughout the river influenced the distribution of functional traits, as well as to validate PICRUSt inferences. The distribution and abundance of functional traits, by metagenomic analysis, were similar among sites, with a median standard deviation of 0.0002% among tier 3 functions in KEGG. Overall inferred functional variation was significantly different (P ≤ 0.035 between two water basins surrounded by agricultural versus developed land cover, and abundances of bacterial orders that correlated with functional traits by metagenomic analysis were greater where abundances of the trait were inferred to be higher. PICRUSt inferences were significantly correlated (r = 0.147, P = 1.80 × 10-30 with metagenomic annotations. Discrepancies between metagenomic and PICRUSt taxonomic-functional relationships, however, suggested potential functional redundancy among abundant and rare taxa that impeded the ability to accurately assess unique functional traits among rare taxa at this sequencing depth. Results of this study suggest that a suite of ‘core functional traits’ is conserved throughout the river and distributions of functional traits, rather than specific taxa, may shift in response to

  4. Extracellular Lipase and Protease Production from a Model Drinking Water Bacterial Community Is Functionally Robust to Absence of Individual Members.

    Directory of Open Access Journals (Sweden)

    Graham G Willsey

    Full Text Available Bacteria secrete enzymes into the extracellular space to hydrolyze macromolecules into constituents that can be imported for microbial nutrition. In bacterial communities, these enzymes and their resultant products can be modeled as community property. Our goal was to investigate the impact of individual community member absence on the resulting community production of exoenzymes (extracellular enzymes involved in lipid and protein hydrolysis. Our model community contained nine bacteria isolated from the potable water system of the International Space Station. Bacteria were grown in static conditions individually, all together, or in all combinations of eight species and exoproduct production was measured by colorimetric or fluorometric reagents to assess short chain and long chain lipases, choline-specific phospholipases C, and proteases. The exoenzyme production of each species grown alone varied widely, however, the enzyme activity levels of the mixed communities were functionally robust to absence of any single species, with the exception of phospholipase C production in one community. For phospholipase C, absence of Chryseobacterium gleum led to increased choline-specific phospholipase C production, correlated with increased growth of Burkholderia cepacia and Sphingomonas sanguinis. Because each individual species produced different enzyme activity levels in isolation, we calculated an expected activity value for each bacterial mixture using input levels or known final composition. This analysis suggested that robustness of each exoenzyme activity is not solely mediated by community composition, but possibly influenced by bacterial communication, which is known to regulate such pathways in many bacteria. We conclude that in this simplified model of a drinking water bacterial community, community structure imposes constraints on production and/or secretion of exoenzymes to generate a level appropriate to exploit a given nutrient environment.

  5. Amphiphilic block copolymers as flexible membrane materials generating structural and functional mimics of green bacterial antenna complexes.

    Science.gov (United States)

    Collins, A M; Timlin, J A; Anthony, S M; Montaño, G A

    2016-08-11

    We describe the ability of a short-chain amphiphilic block copolymer to self-assemble to form an artificial supramolecular light-harvesting system. Specifically, we demonstrate that the 2.5 kDa, poly(ethylene oxide)-block-poly(butadiene) (PEO-b-PBD), exhibits sufficient morphological flexibility as a membrane material and enables generation of mimics of three-dimensional chlorosomes as well as supported membrane bilayers containing energy acceptors. This overall architecture replicates green bacterial light-harvesting function whereby these assemblies exhibit long-range order and three-dimensional morphology similar to native chlorosomes and are capable of energy transfer internally and to external acceptors, located in a supporting biomimetic polymer membrane. Unlike native green bacterial systems that use multiple lipids as a matrix to generate the appropriate environment for chlorosome assembly and function, the described system matrix is comprised entirely of a single polymer amphiphile. This work demonstrates the potential of short-chain amphiphilic block copolymers in generating self-assembled, bio-mimetic membrane architectures, and in doing so, generates scalable, spatial-energetic landscapes for photonic applications. Finally, the results presented provide evidence of minimal requirements to induce chlorosome-like organization and function. PMID:27481550

  6. Bacterial molecular networks: bridging the gap between functional genomics and dynamical modelling.

    Science.gov (United States)

    van Helden, Jacques; Toussaint, Ariane; Thieffry, Denis

    2012-01-01

    This introductory review synthesizes the contents of the volume Bacterial Molecular Networks of the series Methods in Molecular Biology. This volume gathers 9 reviews and 16 method chapters describing computational protocols for the analysis of metabolic pathways, protein interaction networks, and regulatory networks. Each protocol is documented by concrete case studies dedicated to model bacteria or interacting populations. Altogether, the chapters provide a representative overview of state-of-the-art methods for data integration and retrieval, network visualization, graph analysis, and dynamical modelling.

  7. Survival of bacterial indicators and the functional diversity of native microbial communities in the Floridan aquifer system, south Florida

    Science.gov (United States)

    Lisle, John T.

    2014-01-01

    model than when exposed to groundwater from the APPZ (range: 0.540–0.684 h-1). The inactivation rates for the first phase of the models for P. aeruginosa were not significantly different between the UFA (range: 0.144–0.770 h-1) and APPZ (range: 0.159–0.772 h-1) aquifer zones. The inactivation rates for the second phase of the model for this P. aeruginosa were also similar between UFA (range: 0.003–0.008 h-1) and APPZ (0.004–0.005 h-1) zones, although significantly slower than the model’s first phase rates for this bacterial species. Geochemical data were used to determine which dissimilatory biogeochemical reactions were most likely to occur under the native conditions in the UFA and APPZ zones using thermodynamics principles to calculate free energy yields and other cell-related energetics data. The biogeochemical processes of acetotrophic and hydrogenotrophic sulfate reduction, methanogenesis and anaerobic oxidation of methane dominated in all six groundwater sites. A high throughput DNA microarray sequencing technology was used to characterize the diversity in the native aquifer bacterial communities (bacteria and archaea) and assign putative physiological capabilities to the members of those communities. The bacterial communities in both zones of the aquifer were shown to possess the capabilities for primary and secondary fermentation, acetogenesis, methanogenesis, anaerobic methane oxidation, syntrophy with methanogens, ammonification, and sulfate reduction. The data from this study provide the first determination of bacterial indicator survival during exposure to native geochemical conditions of the Floridan aquifer in south Florida. Additionally, the energetics and functional bacterial diversity characterizations are the first descriptions of native bacterial communities in this region of the Floridan aquifer and reveal how these communities persist under such extreme conditions. Collectively, these types of data can be used to develop and refine

  8. Structure, biosynthesis, and function of bacterial capsular polysaccharides synthesized by ABC transporter-dependent pathways.

    Science.gov (United States)

    Willis, Lisa M; Whitfield, Chris

    2013-08-30

    Bacterial capsules are formed primarily from long-chain polysaccharides with repeat-unit structures. A given bacterial species can produce a range of capsular polysaccharides (CPSs) with different structures and these help distinguish isolates by serotyping, as is the case with Escherichia coli K antigens. Capsules are important virulence factors for many pathogens and this review focuses on CPSs synthesized via ATP-binding cassette (ABC) transporter-dependent processes in Gram-negative bacteria. Bacteria utilizing this pathway are often associated with urinary tract infections, septicemia, and meningitis, and E. coli and Neisseria meningitidis provide well-studied examples. CPSs from ABC transporter-dependent pathways are synthesized at the cytoplasmic face of the inner membrane through the concerted action of glycosyltransferases before being exported across the inner membrane and translocated to the cell surface. A hallmark of these CPSs is a conserved reducing terminal glycolipid composed of phosphatidylglycerol and a poly-3-deoxy-d-manno-oct-2-ulosonic acid (Kdo) linker. Recent discovery of the structure of this conserved lipid terminus provides new insights into the early steps in CPS biosynthesis.

  9. Structure and function of a spectrin-like regulator of bacterial cytokinesis

    Science.gov (United States)

    Cleverley, Robert M.; Barrett, Jeffrey R.; Baslé, Arnaud; Bui, Nhat Khai; Hewitt, Lorraine; Solovyova, Alexandra; Xu, Zhi-Qiang; Daniel, Richard A.; Dixon, Nicholas E.; Harry, Elizabeth J.; Oakley, Aaron J.; Vollmer, Waldemar; Lewis, Richard J.

    2014-11-01

    Bacterial cell division is facilitated by a molecular machine—the divisome—that assembles at mid-cell in dividing cells. The formation of the cytokinetic Z-ring by the tubulin homologue FtsZ is regulated by several factors, including the divisome component EzrA. Here we describe the structure of the 60-kDa cytoplasmic domain of EzrA, which comprises five linear repeats of an unusual triple helical bundle. The EzrA structure is bent into a semicircle, providing the protein with the potential to interact at both N- and C-termini with adjacent membrane-bound divisome components. We also identify at least two binding sites for FtsZ on EzrA and map regions of EzrA that are responsible for regulating FtsZ assembly. The individual repeats, and their linear organization, are homologous to the spectrin proteins that connect actin filaments to the membrane in eukaryotes, and we thus propose that EzrA is the founding member of the bacterial spectrin family.

  10. Structure-function analysis of a bacterial deoxyadenosine kinase reveals the basis for substrate specificity.

    Science.gov (United States)

    Welin, Martin; Wang, Liya; Eriksson, Staffan; Eklund, Hans

    2007-03-01

    Deoxyribonucleoside kinases (dNKs) catalyze the transfer of a phosphoryl group from ATP to a deoxyribonucleoside (dN), a key step in DNA precursor synthesis. Recently structural information concerning dNKs has been obtained, but no structure of a bacterial dCK/dGK enzyme is known. Here we report the structure of such an enzyme, represented by deoxyadenosine kinase from Mycoplasma mycoides subsp. mycoides small colony type (Mm-dAK). Superposition of Mm-dAK with its human counterpart's deoxyguanosine kinase (dGK) and deoxycytidine kinase (dCK) reveals that the overall structures are very similar with a few amino acid alterations in the proximity of the active site. To investigate the substrate specificity, Mm-dAK has been crystallized in complex with dATP and dCTP, as well as the products dCMP and dCDP. Both dATP and dCTP bind to the enzyme in a feedback-inhibitory manner with the dN part in the deoxyribonucleoside binding site and the triphosphates in the P-loop. Substrate specificity studies with clinically important nucleoside analogs as well as several phosphate donors were performed. Thus, in this study we combine structural and kinetic data to gain a better understanding of the substrate specificity of the dCK/dGK family of enzymes. The structure of Mm-dAK provides a starting point for making new anti bacterial agents against pathogenic bacteria.

  11. Changes in the potential functional diversity of the bacterial community in biofilters

    Energy Technology Data Exchange (ETDEWEB)

    Grove, J.A.; Anderson, W.A.; Moo-Young, M. [Waterloo Univ., ON (Canada). Dept. of Chemical Engineering

    2007-12-15

    The bacterial community structure in a biofilter treating ethanol was investigated using community level physiological profiling. Laboratory scale biofilters of two sizes (5 or 11.5 cm internal diameter with 30 or 67 cm packed height, respectively) were packed with compost and a humidified airstream loaded with ethanol passed through them. Good removal efficiencies (82-100%) and elimination capacities (49-205 g ethanol m{sup -3} h{sup -1}) were observed in all units. Compost packing media samples were extracted and the community level physiological profiles assayed using Biolog Ecoplates. The community structure was found to be similar over a range of a few centimetres. No differences were observed between sample sizes of 0.5-1 and 6 g, and therefore, the smaller sample size (typical of that used in previous studies) is appropriate for use in the future. Two studies of parallel systems showed that the community structure diverged during the acclimation period (10 days) in one pair, but in another pair, no divergence was observed and a similar shift in community profile was observed in both units between 25 and 40 days of operation. Community level physiological profiling with Biolog Ecoplates is a useful method for detecting differences between and changes within the bacterial communities in biofilters. (orig.)

  12. Influence of dietary nucleotide restriction on bacterial sepsis and phagocytic cell function in mice.

    Science.gov (United States)

    Kulkarni, A D; Fanslow, W C; Drath, D B; Rudolph, F B; Van Buren, C T

    1986-02-01

    Although enzyme defects in purine metabolism have revealed the importance of these substrates to maintenance of a normal immune response, the role of exogenous nucleotides on the cells that mediate the host defense system has remained largely unexplored. Recent investigations have revealed that dietary nucleotides are vital to the maintenance of cell-mediated responses to antigen stimulation. To test the influence of dietary nucleotide deprivation on resistance to infection, Balb/c mice were maintained on chow, a nucleotide-free (NF) diet, or an NF diet repleted with adenine, uracil, or RNA. Mice on the NF diet suffered 100% mortality following intravenous challenge with Staphylococcus aureus, while chow-fed and RNA- or uracil-repleted mice demonstrated significantly greater resistance to this bacterial challenge. Macrophages from mice on the NF diet had decreased phagocytic activity as measured by uptake of radiolabeled bacteria compared with mice maintained on the NF diet supplemented with adenine, uracil, or RNA. No change in S aureus antibody response was noted on the various diets. Although the mechanism of this suppression of nonspecific immunity remains unclear, provision of nucleotides to defined diets appears vital to maintain host resistance to bacterial challenge. PMID:3947217

  13. Insight into the assembly properties and functional organisation of the magnetotactic bacterial actin-like homolog, MamK.

    Directory of Open Access Journals (Sweden)

    Sanjiv Sonkaria

    Full Text Available Magnetotactic bacteria (MTB synthesize magnetosomes, which are intracellular vesicles comprising a magnetic particle. A series of magnetosomes arrange themselves in chains to form a magnetic dipole that enables the cell to orient itself along the Earth's magnetic field. MamK, an actin-like homolog of MreB has been identified as a central component in this organisation. Gene deletion, fluorescence microscopy and in vitro studies have yielded mechanistic differences in the filament assembly of MamK with other bacterial cytoskeletal proteins within the cell. With little or no information on the structural and behavioural characteristics of MamK outside the cell, the mamK gene from Magnetospirillium gryphiswaldense was cloned and expressed to better understand the differences in the cytoskeletal properties with its bacterial homologues MreB and acitin. Despite the low sequence identity shared between MamK and MreB (22% and actin (18%, the behaviour of MamK monitored by light scattering broadly mirrored that of its bacterial cousin MreB primarily in terms of its pH, salt, divalent metal-ion and temperature dependency. The broad size variability of MamK filaments revealed by light scattering studies was supported by transmission electron microscopy (TEM imaging. Filament morphology however, indicated that MamK conformed to linearly orientated filaments that appeared to be distinctly dissimilar compared to MreB suggesting functional differences between these homologues. The presence of a nucleotide binding domain common to actin-like proteins was demonstrated by its ability to function both as an ATPase and GTPase. Circular dichroism and structural homology modelling showed that MamK adopts a protein fold that is consistent with the 'classical' actin family architecture but with notable structural differences within the smaller domains, the active site region and the overall surface electrostatic potential.

  14. Bacterial polysaccharide levan as stabilizing, non-toxic and functional coating material for microelement-nanoparticles.

    Science.gov (United States)

    Bondarenko, Olesja M; Ivask, Angela; Kahru, Anne; Vija, Heiki; Titma, Tiina; Visnapuu, Meeri; Joost, Urmas; Pudova, Ksenia; Adamberg, Signe; Visnapuu, Triinu; Alamäe, Tiina

    2016-01-20

    Levan, fructose-composed biopolymer of bacterial origin, has potential in biotechnology due to its prebiotic and immunostimulatory properties. In this study levan synthesized by levansucrase from Pseudomonas syringae was thoroughly characterized and used as multifunctional biocompatible coating material for microelement-nanoparticles (NPs) of selenium, iron and cobalt. Transmission electron microscopy (TEM), hydrodynamic size measurements (DLS) and X-ray photoelectron spectroscopy (XPS) showed the interaction of levan with NPs. Levan stabilized the dispersions of NPs, decreased their toxicity and had protective effect on human intestinal cells Caco-2. In addition, levan attached to cobalt NPs remained accessible as a substrate for the colon bacteria Bacteroides thetaiotaomicron. We suggest that the combination of levan and nutritionally important microelements in the form of NPs serves as a first step towards a novel "2 in 1" approach for food supplements to provide safe and efficient delivery of microelements for humans and support beneficial gut microbiota with nutritional oligosaccharides. PMID:26572404

  15. Advances in biomedical and pharmaceutical applications of functional bacterial cellulose-based nanocomposites.

    Science.gov (United States)

    Ullah, Hanif; Wahid, Fazli; Santos, Hélder A; Khan, Taous

    2016-10-01

    Bacterial cellulose (BC) synthesized by certain species of bacteria, is a fascinating biopolymer with unique physical and mechanical properties. BC's applications range from traditional dessert, gelling, stabilizing and thickening agent in the food industry to advanced high-tech applications, such as immobilization of enzymes, bacteria and fungi, tissue engineering, heart valve prosthesis, artificial blood vessels, bone, cartilage, cornea and skin, and dental root treatment. Various BC-composites have been designed and investigated in order to enhance its biological applicability. This review focuses on the application of BC-based composites for microbial control, wound dressing, cardiovascular, ophthalmic, skeletal, and endodontics systems. Moreover, applications in controlled drug delivery, biosensors/bioanalysis, immobilization of enzymes and cells, stem cell therapy and skin tissue repair are also highlighted. This review will provide new insights for academia and industry to further assess the BC-based composites in terms of practical applications and future commercialization for biomedical and pharmaceutical purposes. PMID:27312644

  16. Functional properties of peanut fractions on the growth of probiotics and foodborne bacterial pathogens.

    Science.gov (United States)

    Peng, Mengfei; Bitsko, Elizabeth; Biswas, Debabrata

    2015-03-01

    Various compounds found in peanut (Arachis hypogaea) have been shown to provide multiple benefits to human health and may influence the growth of a broad range of gut bacteria. In this study, we investigated the effects of peanut white kernel and peanut skin on 3 strains of Lactobacillus and 3 major foodborne enteric bacterial pathogens. Significant (P microbes. We also found that within 72 h, PF inhibited growth of enterohemorrhagic Escherichia coli O157:H7 (EHEC), while PSE significantly (P < 0.05) inhibited Listeria monocytogenes but promoted the growth of both EHEC and Salmonella Typhimurium. The cell adhesion and invasion abilities of 3 pathogens to the host cells were also significantly (P < 0.05) reduced by 0.5% PF and 0.5% PSE. These results suggest that peanut white kernel might assist in improving human gut flora as well as reducing EHEC, whereas the beneficial effects of peanut skins require further research and investigation.

  17. Phylogeny and functions of bacterial communities associated with field-grown rice shoots.

    Science.gov (United States)

    Okubo, Takashi; Ikeda, Seishi; Sasaki, Kazuhiro; Ohshima, Kenshiro; Hattori, Masahira; Sato, Tadashi; Minamisawa, Kiwamu

    2014-09-17

    Metagenomic analysis was applied to bacterial communities associated with the shoots of two field-grown rice cultivars, Nipponbare and Kasalath. In both cultivars, shoot microbiomes were dominated by Alphaproteobacteria (51-52%), Actinobacteria (11-15%), Gammaproteobacteria (9-10%), and Betaproteobacteria (4-10%). Compared with other rice microbiomes (root, rhizosphere, and phyllosphere) in public databases, the shoot microbiomes harbored abundant genes for C1 compound metabolism and 1-aminocyclopropane-1-carboxylate catabolism, but fewer genes for indole-3-acetic acid production and nitrogen fixation. Salicylate hydroxylase was detected in all microbiomes, except the rhizosphere. These genomic features facilitate understanding of plant-microbe interactions and biogeochemical metabolism in rice shoots. PMID:25130883

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

    Science.gov (United States)

    Hauryliuk, Vasili; Atkinson, Gemma C; Murakami, Katsuhiko S; Tenson, Tanel; Gerdes, Kenn

    2015-05-01

    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 (p)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 of transcriptional regulation by (p)ppGpp and the role of (p)ppGpp in GTP metabolism and in the emergence of bacterial persisters.

  19. Purification and functional analysis of the recombinant protein isolated from E. coli by employing three different methods of bacterial lysis

    Directory of Open Access Journals (Sweden)

    MARIJA MOJSIN

    2005-07-01

    Full Text Available In this paper, the purification of the human recombinant protein expressed in E. coli using the GSTGene Fusion System, by applying various methods of bacterial lysis: sonication, freeze/thaw and beadbeating, is presented. The study was an attempt to compare the properties of the proteins obtained by the sonication method, recommended by manufacturers but inaccessible for many researchers, with those obtained using two other readily available lysis methods. The data show that all purified proteins were soluble and intact with the highest protein yield being obtained via the freeze/thaw method. The results of functional analysis indicate that the proteins purified using the sonication and freeze/thaw methods of lysis exhibited similar DNA binding affinity, while the protein purified by beadbeating was also functional but with a lower binding affinity. The conclusion of this study is that all three lysis methods could be successfully employed for protein purification.

  20. Denitrification in agriculturally impacted streams: seasonal changes in structure and function of the bacterial community.

    Directory of Open Access Journals (Sweden)

    Erin Manis

    Full Text Available Denitrifiers remove fixed nitrogen from aquatic environments and hydrologic conditions are one potential driver of denitrification rate and denitrifier community composition. In this study, two agriculturally impacted streams in the Sugar Creek watershed in Indiana, USA with different hydrologic regimes were examined; one stream is seasonally ephemeral because of its source (tile drainage, whereas the other stream has permanent flow. Additionally, a simulated flooding experiment was performed on the riparian benches of the ephemeral stream during a dry period. Denitrification activity was assayed using the chloramphenicol amended acetylene block method and bacterial communities were examined based on quantitative PCR and terminal restriction length polymorphisms of the nitrous oxide reductase (nosZ and 16S rRNA genes. In the stream channel, hydrology had a substantial impact on denitrification rates, likely by significantly lowering water potential in sediments. Clear patterns in denitrification rates were observed among pre-drying, dry, and post-drying dates; however, a less clear scenario was apparent when analyzing bacterial community structure suggesting that denitrifier community structure and denitrification rate were not strongly coupled. This implies that the nature of the response to short-term hydrologic changes was physiological rather than increases in abundance of denitrifiers or changes in composition of the denitrifier community. Flooding of riparian bench soils had a short-term, transient effect on denitrification rate. Our results imply that brief flooding of riparian zones is unlikely to contribute substantially to removal of nitrate (NO3- and that seasonal drying of stream channels has a negative impact on NO3- removal, particularly because of the time lag required for denitrification to rebound. This time lag is presumably attributable to the time required for the denitrifiers to respond physiologically rather than a change

  1. In silico analysis of bacterial arsenic islands reveals remarkable synteny and functional relatedness between arsenate and phosphate

    Directory of Open Access Journals (Sweden)

    Christopher eRensing

    2013-11-01

    Full Text Available In order to construct a more universal model for understanding the genetic requirements for bacterial AsIII oxidation, an in silico examination of the available sequences in the GenBank was assessed and revealed 21 conserved 5-71 kb arsenic islands within phylogenetically diverse bacterial genomes. The arsenic islands included the AsIII oxidase structural genes aioBA, ars operons (e.g. arsRCB which code for arsenic resistance, and pho, pst, and phn genes known to be part of the classical phosphate stress response and that encode functions associated with regulating and acquiring organic and inorganic phosphorus. The regulatory genes aioXSR were also an island component, but only in Proteobacteria and orientated differently depending on whether they were in α-Proteobacteria or β-/γ-Proteobacteria. Curiously though, while these regulatory genes have been shown to be essential to AsIII oxidation in the Proteobacteria, they are absent in most other organisms examined, inferring different regulatory mechanism(s yet to be discovered. Phylogenetic analysis of the aio, ars, pst and phn genes revealed evidence of both vertical inheritance and horizontal gene transfer. It is therefore likely the arsenic islands did not evolve as a whole unit but formed independently by acquisition of functionally related genes and operons in respective strains. Considering gene synteny and structural analogies between arsenate and phosphate, we presumed that these genes function together in helping these microbes to be able to use even low concentrations of phosphorus needed for vital functions under high concentrations of arsenic, and defined these sequences as the arsenic islands.

  2. Applying meta-pathway analyses through metagenomics to identify the functional properties of the major bacterial communities of a single spontaneous cocoa bean fermentation process sample.

    Science.gov (United States)

    Illeghems, Koen; Weckx, Stefan; De Vuyst, Luc

    2015-09-01

    A high-resolution functional metagenomic analysis of a representative single sample of a Brazilian spontaneous cocoa bean fermentation process was carried out to gain insight into its bacterial community functioning. By reconstruction of microbial meta-pathways based on metagenomic data, the current knowledge about the metabolic capabilities of bacterial members involved in the cocoa bean fermentation ecosystem was extended. Functional meta-pathway analysis revealed the distribution of the metabolic pathways between the bacterial members involved. The metabolic capabilities of the lactic acid bacteria present were most associated with the heterolactic fermentation and citrate assimilation pathways. The role of Enterobacteriaceae in the conversion of substrates was shown through the use of the mixed-acid fermentation and methylglyoxal detoxification pathways. Furthermore, several other potential functional roles for Enterobacteriaceae were indicated, such as pectinolysis and citrate assimilation. Concerning acetic acid bacteria, metabolic pathways were partially reconstructed, in particular those related to responses toward stress, explaining their metabolic activities during cocoa bean fermentation processes. Further, the in-depth metagenomic analysis unveiled functionalities involved in bacterial competitiveness, such as the occurrence of CRISPRs and potential bacteriocin production. Finally, comparative analysis of the metagenomic data with bacterial genomes of cocoa bean fermentation isolates revealed the applicability of the selected strains as functional starter cultures. PMID:25998815

  3. Applying meta-pathway analyses through metagenomics to identify the functional properties of the major bacterial communities of a single spontaneous cocoa bean fermentation process sample.

    Science.gov (United States)

    Illeghems, Koen; Weckx, Stefan; De Vuyst, Luc

    2015-09-01

    A high-resolution functional metagenomic analysis of a representative single sample of a Brazilian spontaneous cocoa bean fermentation process was carried out to gain insight into its bacterial community functioning. By reconstruction of microbial meta-pathways based on metagenomic data, the current knowledge about the metabolic capabilities of bacterial members involved in the cocoa bean fermentation ecosystem was extended. Functional meta-pathway analysis revealed the distribution of the metabolic pathways between the bacterial members involved. The metabolic capabilities of the lactic acid bacteria present were most associated with the heterolactic fermentation and citrate assimilation pathways. The role of Enterobacteriaceae in the conversion of substrates was shown through the use of the mixed-acid fermentation and methylglyoxal detoxification pathways. Furthermore, several other potential functional roles for Enterobacteriaceae were indicated, such as pectinolysis and citrate assimilation. Concerning acetic acid bacteria, metabolic pathways were partially reconstructed, in particular those related to responses toward stress, explaining their metabolic activities during cocoa bean fermentation processes. Further, the in-depth metagenomic analysis unveiled functionalities involved in bacterial competitiveness, such as the occurrence of CRISPRs and potential bacteriocin production. Finally, comparative analysis of the metagenomic data with bacterial genomes of cocoa bean fermentation isolates revealed the applicability of the selected strains as functional starter cultures.

  4. Expression and function profiling of orphan nuclear receptors using bacterial artificial chromosome (BAC) transgenesis.

    OpenAIRE

    Nemoz-Gaillard, Eric; Tsai, Ming-Jer; Tsai, Sophia Y.

    2003-01-01

    The long term goal of the Nuclear Receptor Signaling Atlas (NURSA) resides in unraveling the physiological and pathological functions of nuclear receptors (NRs) at the molecular, biochemical and cellular levels. This multi-oriented task requires complementary approaches in order to determine the specific function(s) and precise expression and receptor activity patterns for each individual conventional or orphan receptor. To attain this objective, we have chose to turn to technologies recently...

  5. Effects of zinc oxide nanoparticles on Kupffer cell phagosomal motility, bacterial clearance, and liver function

    Directory of Open Access Journals (Sweden)

    Watson CY

    2015-06-01

    Full Text Available Christa Y Watson, Ramon M Molina, Andressa Louzada, Kimberly M Murdaugh, Thomas C Donaghey, Joseph D BrainCenter for Nanotechnology and Nanotoxicology, Molecular and Integrative Physiological Sciences Program, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USABackground: Zinc oxide engineered nanoparticles (ZnO ENPs have potential as nanomedicines due to their inherent properties. Studies have described their pulmonary impact, but less is known about the consequences of ZnO ENP interactions with the liver. This study was designed to describe the effects of ZnO ENPs on the liver and Kupffer cells after intravenous (IV administration.Materials and methods: First, pharmacokinetic studies were conducted to determine the tissue distribution of neutron-activated 65ZnO ENPs post-IV injection in Wistar Han rats. Then, a noninvasive in vivo method to assess Kupffer cell phagosomal motility was employed using ferromagnetic iron particles and magnetometry. We also examined whether prior IV injection of ZnO ENPs altered Kupffer cell bactericidal activity on circulating Pseudomonas aeruginosa. Serum and liver tissues were collected to assess liver-injury biomarkers and histological changes, respectively.Results: We found that the liver was the major site of initial uptake of 65ZnO ENPs. There was a time-dependent decrease in tissue levels of 65Zn in all organs examined, reflecting particle dissolution. In vivo magnetometry showed a time-dependent and transient reduction in Kupffer cell phagosomal motility. Animals challenged with P. aeruginosa 24 hours post-ZnO ENP injection showed an initial (30 minutes delay in vascular bacterial clearance. However, by 4 hours, IV-injected bacteria were cleared from the blood, liver, spleen, lungs, and kidneys. Seven days post-ZnO ENP injection, creatine phosphokinase and aspartate aminotransferase levels in serum were significantly increased. Histological evidence of

  6. Prevention of bacterial adhesion

    DEFF Research Database (Denmark)

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

    2010-01-01

    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. Effect of polybrominated diphenyl ether (PBDE) treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis.

    KAUST Repository

    Tian, Ren-Mao

    2014-01-01

    Marine sponges play important roles in benthic environments and are sensitive to environmental stresses. Polybrominated diphenyl ethers (PBDEs) have been widely used as flame retardants since the 1970s and are cytotoxic and genotoxic to organisms. In the present study, we studied the short-period effect of PBDE-47 (2,2\\',4,4\\'-tetrabromodiphenyl ether) treatment on the community structure and functional gene composition of the bacterial community inhabiting the marine sponge Haliclona cymaeformis. Our results showed that the bacterial community shifted from an autotrophic bacteria-dominated community to a heterotrophic bacteria-dominated community in response to PBDE-47 in a time- and concentration-dependent manner. A potentially symbiotic sulfur-oxidizing bacterium (SOB) was dominant (>80% in abundance) in the untreated sponge. However, exposure to a high concentration (1 μg/L) of PBDE-47 caused a substantial decrease in the potential symbiont and an enrichment of heterotrophic bacteria like Clostridium. A metagenomic analysis showed a selective effect of the high concentration treatment on the functional gene composition of the enriched heterotrophic bacteria, revealing an enrichment for the functions responsible for DNA repair, multidrug efflux pumping, and bacterial chemotaxis and motility. This study demonstrated that PBDE-47 induced a shift in the composition of the community and functional genes in the sponge-associated bacterial community, revealing the selective effect of PBDE-47 treatment on the functions of the bacterial community in the microenvironment of the sponge.

  8. Effect of polybrominated diphenyl ether (PBDE treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis

    Directory of Open Access Journals (Sweden)

    Renmao eTian

    2015-01-01

    Full Text Available Marine sponges play important roles in benthic environments and are sensitive to environmental stresses. Polybrominated diphenyl ethers (PBDEs have been widely used as flame retardants since the 1970s and are cytotoxic and genotoxic to organisms. In the present study, we studied the short-period effect of PBDE-47 (2,2',4,4'-tetrabromodiphenyl ether treatment on the community structure and functional gene composition of the bacterial community inhabiting the marine sponge Haliclona cymaeformis. Our results showed that the bacterial community shifted from an autotrophic bacteria-dominated community to a heterotrophic bacteria-dominated community in response to PBDE-47 in a time- and concentration-dependent manner. A potentially symbiotic sulfur-oxidizing bacterium (SOB was dominant (>80% in abundance in the untreated sponge. However, exposure to a high concentration (1 µg/L of PBDE-47 caused a substantial decrease in the potential symbiont and an enrichment of heterotrophic bacteria like Clostridium. A metagenomic analysis showed a selective effect of the high concentration treatment on the functional gene composition of the enriched heterotrophic bacteria, revealing an enrichment for the functions responsible for DNA repair, multidrug efflux pumping, and bacterial chemotaxis and motility. This study demonstrated that PBDE-47 induced a shift in the composition of the community and functional genes in the sponge-associated bacterial community, revealing the selective effect of PBDE-47 treatment on the functions of the bacterial community in the microenvironment of the sponge.

  9. Protecting enzymatic function through directed packaging into bacterial outer membrane vesicles.

    Science.gov (United States)

    Alves, Nathan J; Turner, Kendrick B; Medintz, Igor L; Walper, Scott A

    2016-01-01

    Bacteria possess innate machinery to transport extracellular cargo between cells as well as package virulence factors to infect host cells by secreting outer membrane vesicles (OMVs) that contain small molecules, proteins, and genetic material. These robust proteoliposomes have evolved naturally to be resistant to degradation and provide a supportive environment to extend the activity of encapsulated cargo. In this study, we sought to exploit bacterial OMV formation to package and maintain the activity of an enzyme, phosphotriesterase (PTE), under challenging storage conditions encountered for real world applications. Here we show that OMV packaged PTE maintains activity over free PTE when subjected to elevated temperatures (>100-fold more activity after 14 days at 37 °C), iterative freeze-thaw cycles (3.4-fold post four-cycles), and lyophilization (43-fold). We also demonstrate how lyophilized OMV packaged PTE can be utilized as a cell free reagent for long term environmental remediation of pesticide/chemical warfare contaminated areas. PMID:27117743

  10. The impact of hypoxia on intestinal epithelial cell functions: consequences for invasion by bacterial pathogens.

    Science.gov (United States)

    Zeitouni, Nathalie E; Chotikatum, Sucheera; von Köckritz-Blickwede, Maren; Naim, Hassan Y

    2016-12-01

    The maintenance of oxygen homeostasis in human tissues is mediated by several cellular adaptations in response to low-oxygen stress, called hypoxia. A decrease in tissue oxygen levels is initially counteracted by increasing local blood flow to overcome diminished oxygenation and avoid hypoxic stress. However, studies have shown that the physiological oxygen concentrations in several tissues are much lower than atmospheric (normoxic) conditions, and the oxygen supply is finely regulated in individual cell types. The gastrointestinal tract has been described to subsist in a state of physiologically low oxygen level and is thus depicted as a tissue in the state of constant low-grade inflammation. The intestinal epithelial cell layer plays a vital role in the immune response to inflammation and infections that occur within the intestinal tissue and is involved in many of the adaptation responses to hypoxic stress. This is especially relevant in the context of inflammatory disorders, such as inflammatory bowel disease (IBD). Therefore, this review aims to describe the intestinal epithelial cellular response to hypoxia and the consequences for host interactions with invading gastrointestinal bacterial pathogens. PMID:27002817

  11. Increasing Metagenomic Resolution of Microbiome Interactions Through Functional Phylogenomics and Bacterial Sub-Communities

    Science.gov (United States)

    Cibrián-Jaramillo, Angélica; Barona-Gómez, Francisco

    2016-01-01

    The genomic composition of the microbiome and its relationship with the environment is an exciting open question in biology. Metagenomics is a useful tool in the discovery of previously unknown taxa, but its use to understand the functional and ecological capacities of the microbiome is limited until taxonomy and function are understood in the context of the community. We suggest that this can be achieved using a combined functional phylogenomics and co-culture-based experimental strategy that can increase our capacity to measure sub-community interactions. Functional phylogenomics can identify and partition the genome such that hidden gene functions and gene clusters with unique evolutionary signals are revealed. We can test these phylogenomic predictions using an experimental model based on sub-community populations that represent a subset of the diversity directly obtained from environmental samples. These populations increase the detection of mechanisms that drive functional forces in the assembly of the microbiome, in particular the role of metabolites from key taxa in community interactions. Our combined approach leverages the potential of metagenomics to address biological questions from ecological systems. PMID:26904093

  12. Molecular and functional assessment of bacterial community convergence in metal-amended soils.

    Science.gov (United States)

    Anderson, J A H; Hooper, M J; Zak, J C; Cox, S B

    2009-07-01

    Species diversity and the structure of microbial communities in soils are thought to be a function of the cumulative selective pressures within the local environment. Shifts in microbial community structure, as a result of metal stress, may have lasting negative effects on soil ecosystem dynamics if critical microbial community functions are compromised. Three soils in the vicinity of a copper smelter, previously contaminated with background, low and high levels of aerially deposited metals, were amended with metal-salts to determine the potential for metal contamination to shape the structural and functional diversity of microbial communities in soils. We hypothesized that the microbial communities native to the three soils would initially be unique to each site, but would converge on a microbial community with similar structure and function, as a result of metal stress. Initially, the three different sites supported microbial communities with unique structural and functional diversity, and the nonimpacted site supported inherently higher levels of microbial activity and biomass, relative to the metal-contaminated sites. Amendment of the soils with metal-salts resulted in a decrease in microbial activity and biomass, as well as shifts in microbial community structure and function at each site. Soil microbial communities from each site were also observed to be sensitive to changes in soil pH as a result of metal-salt amendment; however, the magnitude of these pH-associated effects varied between soils. Microbial communities from each site did not converge on a structurally or functionally similar community following metal-salt amendment, indicating that other factors may be equally important in shaping microbial communities in soils. Among these factors, soil physiochemical parameters like organic matter and soil pH, which can both influence the bioavailability and toxicity of metals in soils, may be critical. PMID:19030917

  13. Comprehensive analysis reveals how single nucleotides contribute to noncoding RNA function in bacterial quorum sensing.

    Science.gov (United States)

    Rutherford, Steven T; Valastyan, Julie S; Taillefumier, Thibaud; Wingreen, Ned S; Bassler, Bonnie L

    2015-11-01

    Five homologous noncoding small RNAs (sRNAs), called the Qrr1-5 sRNAs, function in the Vibrio harveyi quorum-sensing cascade to drive its operation. Qrr1-5 use four different regulatory mechanisms to control the expression of ∼ 20 mRNA targets. Little is known about the roles individual nucleotides play in mRNA target selection, in determining regulatory mechanism, or in defining Qrr potency and dynamics of target regulation. To identify the nucleotides vital for Qrr function, we developed a method we call RSort-Seq that combines saturating mutagenesis, fluorescence-activated cell sorting, high-throughput sequencing, and mutual information theory to explore the role that every nucleotide in Qrr4 plays in regulation of two mRNA targets, luxR and luxO. Companion biochemical assays allowed us to assign specific regulatory functions/underlying molecular mechanisms to each important base. This strategy yielded a regional map of nucleotides in Qrr4 vital for stability, Hfq interaction, stem-loop formation, and base pairing to both luxR and luxO, to luxR only, and to luxO only. In terms of nucleotides critical for sRNA function, the RSort-Seq analysis provided strikingly different results from those predicted by commonly used regulatory RNA-folding algorithms. This approach is applicable to any RNA-RNA interaction, including sRNAs in other bacteria and regulatory RNAs in higher organisms.

  14. Functional substitution of a eukaryotic glycyl-tRNA synthetase with an evolutionarily unrelated bacterial cognate enzyme.

    Directory of Open Access Journals (Sweden)

    Chin-I Chien

    Full Text Available Two oligomeric types of glycyl-tRNA synthetase (GlyRS are found in nature: a α2 type and a α2β2 type. The former has been identified in all three kingdoms of life and often pairs with tRNAGly that carries an A73 discriminator base, while the latter is found only in bacteria and chloroplasts and is almost always coupled with tRNAGly that contains U73. In the yeast Saccharomyces cerevisiae, a single GlyRS gene, GRS1, provides both the cytoplasmic and mitochondrial functions, and tRNAGly isoacceptors in both compartments possess A73. We showed herein that Homo sapiens and Arabidopsis thaliana cytoplasmic GlyRSs (both α2-type enzymes can rescue both the cytoplasmic and mitochondrial defects of a yeast grs1- strain, while Escherichia coli GlyRS (a α2β2-type enzyme and A. thaliana organellar GlyRS (a (αβ2-type enzyme failed to rescue either defect of the yeast mull allele. However, a head-to-tail αβ fusion of E. coli GlyRS effectively supported the mitochondrial function. Our study suggests that a α2-type eukaryotic GlyRS may be functionally substituted with a α2β2-type bacterial cognate enzyme despite their remote evolutionary relationships.

  15. Slipping through the Cracks: Linking Low Immune Function and Intestinal Bacterial Imbalance to the Etiology of Rheumatoid Arthritis

    Directory of Open Access Journals (Sweden)

    Kuniaki Terato

    2015-01-01

    Full Text Available Autoimmune diseases (ADs are considered to be caused by the host immune system which attacks and destroys its own tissue by mistake. A widely accepted hypothesis to explain the pathogenic mechanism of ADs is “molecular mimicry,” which states that antibodies against an infectious agent cross-react with a self-antigen sharing an identical or similar antigenic epitope. However, this hypothesis was most likely established based on misleading antibody assay data largely influenced by intense false positive reactions involved in immunoassay systems. Thus reinvestigation of this hypothesis using an appropriate blocking agent capable of eliminating all types of nonspecific reactions and proper assay design is strongly encouraged. In this review, we discuss the possibility that low immune function may be the fundamental, common defect in ADs, which increases the susceptibility to potential disease causative pathogens located in the gastrointestinal tract (GI, such as bacteria and their components or dietary components. In addition to these exogenous agents, aberrations in the host’s physical condition may disrupt the host defense system, which is tightly orchestrated by “immune function,” “mucosal barrier function,” and “intestinal bacterial balance.” These disturbances may initiate a downward spiral, which can lead to chronic health problems that will evolve to an autoimmune disorder.

  16. Single-Step Production of a Recyclable Nanobiocatalyst for Organophosphate Pesticides Biodegradation Using Functionalized Bacterial Magnetosomes

    OpenAIRE

    Ginet, Nicolas; Pardoux, Romain; Adryanczyk, Géraldine; Garcia, Daniel; Brutesco, Catherine; Pignol, David

    2011-01-01

    Enzymes are versatile catalysts in laboratories and on an industrial scale; improving their immobilization would be beneficial to broadening their applicability and ensuring their (re)use. Lipid-coated nano-magnets produced by magnetotactic bacteria are suitable for a universally applicable single-step method of enzyme immobilization. By genetically functionalizing the membrane surrounding these magnetite particles with a phosphohydrolase, we engineered an easy-to-purify, robust and recyclabl...

  17. Contagious epididymitis due to Brucella ovis: relationship between sexual function, serology and bacterial shedding in semen.

    OpenAIRE

    Picard-Hagen, Nicole; Berthelot, Xavier; Champion, Jean Luc; Eon, Laure; Lyazrhi, Faouzi; Marois, Maxime; Peglion, Marceline; Schuster, Aude; Trouche, Christel

    2015-01-01

    Background Contagious Epididymitis (CE) due to Brucella ovis (B. ovis) is a contagious disease that impairs rams’ fertility due to epididymis, testicle and accessory sexual gland alterations. An increased incidence of CE has been observed in South Eastern France (“PACA” region) since the Rev.1 vaccination against B. melitensis has been stopped in 2008. The objective of this study was to evaluate the relationship between the infection by B. ovis and the sexual function of rams. Two-hundred eig...

  18. Effects of Dispersal and Initial Diversity on the Composition and Functional Performance of Bacterial Communities

    OpenAIRE

    Yinghua Zha; Mercè Berga; Jérôme Comte; Silke Langenheder

    2016-01-01

    Natural communities are open systems and consequently dispersal can play an important role for the diversity, composition and functioning of communities at the local scale. It is, however, still unclear how effects of dispersal differ depending on the initial diversity of local communities. Here we implemented an experiment where we manipulated the initial diversity of natural freshwater bacterioplankton communities using a dilution-to-extinction approach as well as dispersal from a regional ...

  19. Secretion activity of white lupin’s cluster roots influences bacterial abundance, function and community structure

    OpenAIRE

    Weisskopf, Laure; Fromin, Nathalie; Tomasi, Nicola; Aragno, Michel; Martinoia, Enrico

    2007-01-01

    White lupin (Lupinus albus L. cv. Amiga) reacts to phosphate deficiency by producing cluster roots which exude large amounts of organic acids. The detailed knowledge of the excretion physiology of the different root parts makes it a good model plant to study plant-bacteria interaction. Since the effect of the organic acid exudation by cluster roots on the rhizosphere microflora is still poorly understood, we investigated the abundance, diversity and functions of bacteria associated with the c...

  20. Phylogenetic and Functional Biomakers as Indicators of Bacterial Community Responses to Mixed-Waste Contamination

    Energy Technology Data Exchange (ETDEWEB)

    Fields, Matthew Wayne [ORNL; Carroll, Sue L [ORNL; Watson, David B [ORNL; Jardine, Philip M [ORNL; Criddle, Craig [ORNL; Zhou, Jizhong [ORNL

    2006-03-01

    Few studies have demonstrated changes in community structure along a contaminant plume in terms of phylogenetic, functional, and geochemical changes, and such studies are essential to understand how a microbial ecosystem responds to perturbations. Clonal libraries of multiple genes (SSU rDNA, nirK, nirS, amoA, pmoA, and dsrAB) were analyzed from groundwater samples (n = 6) that varied in contaminant levels, and 107 geochemical parameters were measured. Principal components analyses (PCA) were used to compare the relationships among the sites with respect to the biomarker (n = 785 for all sequences) distributions and the geochemical variables. A major portion of the geochemical variance measured among the samples could be accounted for by tetrachloroethene, {sup 99}Tc, NO{sub 3}, SO{sub 4}, Al, and Th. The PCA based on the distribution of unique biomarkers resulted in different groupings compared to the geochemical analysis, but when the SSU rRNA gene libraries were directly compared ({Delta}C{sub xy} values) the sites were clustered in a similar fashion compared to geochemical measures. The PCA based upon functional gene distributions each predicted different relationships among the sites, and comparisons of Euclidean distances based upon diversity indices for all functional genes (n = 432) grouped the sites by extreme or intermediate contaminant levels. The data suggested that the sites with low and high perturbations were functionally more similar than sites with intermediate conditions, and perhaps captured the overall community structure better than a single phylogenetic biomarker. Moreover, even though the background site was phylogenetically and geochemically distinct from the acidic sites, the extreme conditions of the acidic samples might be more analogous to the limiting nutrient conditions of the background site. An understanding of microbial community-level responses within an ecological framework would provide better insight for restoration strategies

  1. Single-step production of a recyclable nanobiocatalyst for organophosphate pesticides biodegradation using functionalized bacterial magnetosomes.

    Directory of Open Access Journals (Sweden)

    Nicolas Ginet

    Full Text Available Enzymes are versatile catalysts in laboratories and on an industrial scale; improving their immobilization would be beneficial to broadening their applicability and ensuring their (reuse. Lipid-coated nano-magnets produced by magnetotactic bacteria are suitable for a universally applicable single-step method of enzyme immobilization. By genetically functionalizing the membrane surrounding these magnetite particles with a phosphohydrolase, we engineered an easy-to-purify, robust and recyclable biocatalyst to degrade ethyl-paraoxon, a commonly used pesticide. For this, we genetically fused the opd gene from Flavobacterium sp. ATCC 27551 encoding a paraoxonase to mamC, an abundant protein of the magnetosome membrane in Magnetospirillum magneticum AMB-1. The MamC protein acts as an anchor for the paraoxonase to the magnetosome surface, thus producing magnetic nanoparticles displaying phosphohydrolase activity. Magnetosomes functionalized with Opd were easily recovered from genetically modified AMB-1 cells: after cellular disruption with a French press, the magnetic nanoparticles are purified using a commercially available magnetic separation system. The catalytic properties of the immobilized Opd were measured on ethyl-paraoxon hydrolysis: they are comparable with the purified enzyme, with K(m (and k(cat values of 58 µM (and 178 s(-1 and 43 µM (and 314 s(-1 for the immobilized and purified enzyme respectively. The Opd, a metalloenzyme requiring a zinc cofactor, is thus properly matured in AMB-1. The recycling of the functionalized magnetosomes was investigated and their catalytic activity proved to be stable over repeated use for pesticide degradation. In this study, we demonstrate the easy production of functionalized magnetic nanoparticles with suitably genetically modified magnetotactic bacteria that are efficient as a reusable nanobiocatalyst for pesticides bioremediation in contaminated effluents.

  2. Functional Analysis of the Role of Toxin-Antitoxin (TA) Loci in Bacterial Persistence.

    Science.gov (United States)

    Butt, Aaron T; Titball, Richard W

    2016-01-01

    We have developed a method to analyze the functionality of putative TA loci by expressing them in Escherichia coli. Here, we describe the procedure for cloning recombinant TA genes into inducible plasmids and expressing these in E. coli. Following expression, toxicity, resuscitation of growth, and changes in persister cell formation are assayed. This can confirm whether predicted TA loci are active in E. coli and whether expression can affect persister cell formation. PMID:26468105

  3. Bacterial Long-Chain Polyunsaturated Fatty Acids: Their Biosynthetic Genes, Functions, and Practical Use

    Directory of Open Access Journals (Sweden)

    Kiyohito Yoshida

    2016-05-01

    Full Text Available The nutritional and pharmaceutical values of long-chain polyunsaturated fatty acids (LC-PUFAs such as arachidonic, eicosapentaenoic and docosahexaenoic acids have been well recognized. These LC-PUFAs are physiologically important compounds in bacteria and eukaryotes. Although little is known about the biosynthetic mechanisms and functions of LC-PUFAs in bacteria compared to those in higher organisms, a combination of genetic, bioinformatic, and molecular biological approaches to LC-PUFA-producing bacteria and some eukaryotes have revealed the notably diverse organization of the pfa genes encoding a polyunsaturated fatty acid synthase complex (PUFA synthase, the LC-PUFA biosynthetic processes, and tertiary structures of the domains of this enzyme. In bacteria, LC-PUFAs appear to take part in specific functions facilitating individual membrane proteins rather than in the adjustment of the physical fluidity of the whole cell membrane. Very long chain polyunsaturated hydrocarbons (LC-HCs such as hentriacontanonaene are considered to be closely related to LC-PUFAs in their biosynthesis and function. The possible role of LC-HCs in strictly anaerobic bacteria under aerobic and anaerobic environments and the evolutionary relationships of anaerobic and aerobic bacteria carrying pfa-like genes are also discussed.

  4. Gifsy-1 Prophage IsrK with Dual Function as Small and Messenger RNA Modulates Vital Bacterial Machineries.

    Science.gov (United States)

    Hershko-Shalev, Tal; Odenheimer-Bergman, Ahuva; Elgrably-Weiss, Maya; Ben-Zvi, Tamar; Govindarajan, Sutharsan; Seri, Hemda; Papenfort, Kai; Vogel, Jörg; Altuvia, Shoshy

    2016-04-01

    While an increasing number of conserved small regulatory RNAs (sRNAs) are known to function in general bacterial physiology, the roles and modes of action of sRNAs from horizontally acquired genomic regions remain little understood. The IsrK sRNA of Gifsy-1 prophage of Salmonella belongs to the latter class. This regulatory RNA exists in two isoforms. The first forms, when a portion of transcripts originating from isrK promoter reads-through the IsrK transcription-terminator producing a translationally inactive mRNA target. Acting in trans, the second isoform, short IsrK RNA, binds the inactive transcript rendering it translationally active. By switching on translation of the first isoform, short IsrK indirectly activates the production of AntQ, an antiterminator protein located upstream of isrK. Expression of antQ globally interferes with transcription termination resulting in bacterial growth arrest and ultimately cell death. Escherichia coli and Salmonella cells expressing AntQ display condensed chromatin morphology and localization of UvrD to the nucleoid. The toxic phenotype of AntQ can be rescued by co-expression of the transcription termination factor, Rho, or RNase H, which protects genomic DNA from breaks by resolving R-loops. We propose that AntQ causes conflicts between transcription and replication machineries and thus promotes DNA damage. The isrK locus represents a unique example of an island-encoded sRNA that exerts a highly complex regulatory mechanism to tune the expression of a toxic protein. PMID:27057757

  5. Rapid functional definition of extended spectrum β-lactamase activity in bacterial cultures via competitive inhibition of fluorescent substrate cleavage.

    Science.gov (United States)

    Sallum, Ulysses W; Zheng, Xiang; Verma, Sarika; Hasan, Tayyaba

    2010-01-01

    The functional definition of extended-spectrum β-lactamase (ESBL) activity is a clinical challenge. Here we report a rapid and convenient assay of β-lactamase activity through the competitive inhibition of fluorescent substrate hydrolysis that provides a read-out nearly 40× more rapidly than conventional techniques for functional definition. A panel of β-lactam antibiotics was used for competition against β-lactamase enzyme-activated photosensitizer (β-LEAP) yielding a competitive index (C(i)) in 30 min. Significant differences in the relative C(i) values of the panel of β-lactams were determined in vitro for Bacillus cereus penicillinase. Additionally, the relative C(i) values for whole bacterial cell suspensions of B. cereus 5/β were compared with the relative minimal inhibitory concentration (MIC) values and a correlation coefficient of 0.899 was determined. We further demonstrated the ability of β-LEAP to probe the capacity of ceftazidime to inhibit the enzyme activity of a panel of ESBL-producing Escherichia coli. The bacteria were assayed for susceptibility to ceftazidime and the relative MIC values were compared with the relative C(i) values for ceftazidime yielding a correlation coefficient of 0.984. This work demonstrates for the first time the whole cell assay of the competitive inhibition of β-lactamase enzyme activity and derivation of associated constants.

  6. Identity and functional analysis of bacterial populations involved in reductive acetogenesis

    International Nuclear Information System (INIS)

    Our current understanding of the microbial processes underpinning hydrogen utilization and methane production within the rumen is incomplete and the key to manipulating these emissions in the future will flow from fundamental improvements in our knowledge of methanogenesis and alternative hydrogenotrophic pathways. Reductive acetogenesis is an alternative hydrogen-utilising pathway to methanogenesis in the rumen and has potential as a strategy for reducing ruminant greenhouse gas emissions. The obligatory anaerobic bacteria responsible for reductive acetogenesis are known as homoacetogens. Homoacetogens use the acetyl-CoA pathway to reduce carbon dioxide to acetate, and most are able to use this pathway for growth on hydrogen and carbon dioxide as the sole energy source. Homoacetogens are present in the rumen and molecular tools are necessary to further investigate their ecology. The aim of the present work was to identify DNA sequences of genes present in homoacetogens that may be suitable as targets for the development of functional-group molecular tools for these microorganisms. The genes investigated were those of three key enzymes in the acetyl-CoA pathway: formyltetrahydrofolate synthetase (FTHFS), carbon monoxide dehydrogenase (CODH) and acetyl-CoA synthase (ACS). Several batch fermentation systems inoculated with rumen microbes were established, with 13C-carbonate as the principal carbon source, and in the presence or absence of methanogen inhibitors. Denaturing gradient gel electrophoresis (DGGE) was performed on samples to reveal minimal gross differences in community structure within the different systems. Metagenomic DNA was extracted and Isotope ratio mass spectrometry (IRMS) was used to confirm the uptake of 13C, followed by the separation of 13C-labeled DNA via isopycnic gradient ultracentrifugation. The 13C-labeled DNA was used as a template for the production of 16S rDNA phylogenetic and formyltetrahydrofolate synthetase (FTHFS) libraries, as well

  7. Solvent-free functionalization of silicone rubber and efficacy of PAAm brushes grafted from an amino-PPX layer against bacterial adhesion

    NARCIS (Netherlands)

    Fundeanu, Irina; Klee, Doris; Schouten, Arend J.; Busscher, Henk J.; van der Mei, Henny C.

    2010-01-01

    Silicone rubber is a frequently employed biomaterial that is prone to bacterial adhesion and biofilm formation. In this study, the surface of silicone rubber was solvent-free functionalized by chemical vapor deposition (CVD) of poly(o-amino-p-xylylene-co-p-xylylene (amino-PPX). Subsequently, the ami

  8. PPARγ Expression and Function in Mycobacterial Infection: Roles in Lipid Metabolism, Immunity, and Bacterial Killing

    Directory of Open Access Journals (Sweden)

    Patricia E. Almeida

    2012-01-01

    Full Text Available Tuberculosis continues to be a global health threat, with drug resistance and HIV coinfection presenting challenges for its control. Mycobacterium tuberculosis, the etiological agent of tuberculosis, is a highly adapted pathogen that has evolved different strategies to subvert the immune and metabolic responses of host cells. Although the significance of peroxisome proliferator-activated receptor gamma (PPARγ activation by mycobacteria is not fully understood, recent findings are beginning to uncover a critical role for PPARγ during mycobacterial infection. Here, we will review the molecular mechanisms that regulate PPARγ expression and function during mycobacterial infection. Current evidence indicates that mycobacterial infection causes a time-dependent increase in PPARγ expression through mechanisms that involve pattern recognition receptor activation. Mycobacterial triggered increased PPARγ expression and activation lead to increased lipid droplet formation and downmodulation of macrophage response, suggesting that PPARγ expression might aid the mycobacteria in circumventing the host response acting as an escape mechanism. Indeed, inhibition of PPARγ enhances mycobacterial killing capacity of macrophages, suggesting a role of PPARγ in favoring the establishment of chronic infection. Collectively, PPARγ is emerging as a regulator of tuberculosis pathogenesis and an attractive target for the development of adjunctive tuberculosis therapies.

  9. Ongoing functional evolution of the bacterial atrazine chlorohydrolase AtzA.

    Science.gov (United States)

    Noor, Sajid; Changey, Frédérique; Oakeshott, John G; Scott, Colin; Martin-Laurent, Fabrice

    2014-02-01

    Triazine herbicides such as atrazine and simazine which were heavily used in the latter half of the twentieth century constituted a rich new source of nitrogen for soil microbes. An atzA dechlorinase active against both atrazine and simazine was isolated from various soil bacteria from diverse locations in the mid 1990s. We have surveyed the atzA genes from eight triazine-degrading Aminobacter aminovorans strains isolated from French agricultural soils recurrently exposed to triazines in 2000. Six amino acid differences from the original isolate were each found in more than one of the A. aminovorans strains. Three of these in particular (V92L, A170T and A296T) were recovered from a majority of the isolates and from locations separated by up to 900 km, so may reflect ongoing selection for the new function. Two of the latter (A170T and A296T) were indeed found to confer higher specificity for simazine, albeit not atrazine, and greater affinity for a metal ion required for activity, than did the original variant. In contrast, we found that ongoing maintenance of the original atzA-containing isolate in laboratory culture for 12 years in a medium containing high concentrations of atrazine has led to the fixation of another amino acid substitution that substantially reduces activity for the triazines. The high concentrations of atrazine in the medium may have relaxed the selection for a highly efficient triazine dechlorinase activity, and that there is some, as yet uncharacterised, counter selection against the activity of this enzyme under these conditions.

  10. Structural and functional response of the soil bacterial community to application of manure from difloxacin-treated pigs

    NARCIS (Netherlands)

    Jechalke, S.; Focks, A.; Rosendahl, I.; Groeneweg, J.; Siemens, J.; Heuer, H.; Smalla, K.

    2014-01-01

    Difloxacin (DIF) belongs to the class of fluoroquinolone antibiotics that have been intensively used for the treatment of bacterial infections in veterinary and human medicine. The aim of this field study was to compare the effect of manure from DIF-treated pigs and untreated pigs on the bacterial c

  11. Effects of the Membrane Action of Tetralin on the Functional and Structural Properties of Artificial and Bacterial Membranes

    NARCIS (Netherlands)

    SIKKEMA, J; POOLMAN, B; KONINGS, WN; DEBONT, JAM

    1992-01-01

    Tetralin is toxic to bacterial cells at concentrations below 100-mu-mol/liter. To assess the inhibitory action of tetralin on bacterial membranes, a membrane model system, consisting of proteoliposomes in which beef heart cytochrome c oxidase was reconstituted as the proton motive force-generating m

  12. Complex Role of the Mitochondrial Targeting Signal in the Function of Steroidogenic Acute Regulatory Protein Revealed by Bacterial Artificial Chromosome Transgenesis in Vivo

    OpenAIRE

    Sasaki, Goro; Ishii, Tomohiro; Jeyasuria, Pancharatnam; Jo, Youngah; Bahat, Assaf; Orly, Joseph; Hasegawa, Tomonobu; Parker, Keith L.

    2008-01-01

    The steroidogenic acute regulatory protein (StAR) stimulates the regulated production of steroid hormones in the adrenal cortex and gonads by facilitating the delivery of cholesterol to the inner mitochondrial membrane. To explore key aspects of StAR function within bona fide steroidogenic cells, we used a transgenic mouse model to explore the function of StAR proteins in vivo. We first validated this transgenic bacterial artificial chromosome reconstitution system by targeting enhanced green...

  13. Impact of long-term N, P, K, and NPK fertilization on the composition and potential functions of the bacterial community in grassland soil.

    Science.gov (United States)

    Pan, Yao; Cassman, Noriko; de Hollander, Mattias; Mendes, Lucas W; Korevaar, Hein; Geerts, Rob H E M; van Veen, Johannes A; Kuramae, Eiko E

    2014-10-01

    Soil abiotic and biotic interactions govern important ecosystem processes. However, the mechanisms behind these interactions are complex, and the links between specific environmental factors, microbial community structures, and functions are not well understood. Here, we applied DNA shotgun metagenomic techniques to investigate the effect of inorganic fertilizers N, P, K, and NPK on the bacterial community composition and potential functions in grassland soils in a 54-year experiment. Differences in total and available nutrients were found in the treatment soils; interestingly, Al, As, Mg, and Mn contents were variable in N, P, K, and NPK treatments. Bacterial community compositions shifted and Actinobacteria were overrepresented under the four fertilization treatments compared to the control. Redundancy analysis of the soil parameters and the bacterial community profiles showed that Mg, total N, Cd, and Al were linked to community variation. Using correlation analysis, Acidobacteria, Bacteroidetes, and Verrucomicrobia were linked similarly to soil parameters, and Actinobacteria and Proteobacteria were linked separately to different suites of parameters. Surprisingly, we found no fertilizers effect on microbial functional profiles which supports functional redundancy as a mechanism for stabilization of functions during changes in microbial composition. We suggest that functional profiles are more resistant to environmental changes than community compositions in the grassland ecosystem. PMID:25046442

  14. Biodiversity, Ecosystem Services, and Climate Change : The Economic Problem

    OpenAIRE

    World Bank

    2010-01-01

    Climate change is both a cause and an effect of biodiversity change. Along with anthropogenic dispersion, climate change is the main driver of change in the geographical distribution of both beneficial and harmful species, crops, livestock, harvested wild species, pests, predators and pathogens. And the capacity of ecosystems to adapt to climate change depends on the diversity of species t...

  15. Solid-phase differential display and bacterial expression systems in selection and functional analysis of cDNAs.

    Science.gov (United States)

    Ståhl, S; Odeberg, J; Larsson, M; Røsok, O; Ree, A H; Lundeberg, J

    1999-01-01

    Differential gene expression can be expected during activation and differentiation of cells as well as during pathological conditions, such as cancer. A number of strategies have been described to identify and understand isolated differentially expressed genes. The differential display methodology has rapidly become a widely used technique to identify differentially expressed mRNAs. In this chapter we described a variant of the differential display method based on solid-phase technology. The solid-phase procedure offers an attractive alternative to solution-based differential display because minute amounts of sample can be analyzed in considerably less time than previously. The employed solid support, monodisperse super paramagnetic beads, which circumvents precipitation and centrifugations steps, has also allowed for optimization of the critical enzymatic and preparative steps in the differential display methodology. We also described how bacterial expression can be used as a means to elucidate gene function. An efficient dual-expression system was presented, together with a basic concept describing how parallel expression of selected portions of cDNAs can be used for production of cDNA-encoded proteins as parts of affinity-tagged fusion proteins. The fusion proteins are suitable both for the generation of antibodies reactive to the target cDNA-encoded protein and for the subsequent affinity enrichment of such antibodies. Affinity-enriched antibodies have proved to be valuable tools in various assays, including immunoblotting and immunocytochemical staining, and can thus be used to localize the target cDNA-encoded protein to certain cells in a tissue section or even to a specific cell compartment or organelle within a cell. High-resolution localization of a cDNA-encoded protein would provide valuable information toward the understanding of protein function. PMID:10349662

  16. Human Bacterial Artificial Chromosome (BAC) Transgenesis Fully Rescues Noradrenergic Function in Dopamine β-Hydroxylase Knockout Mice.

    Science.gov (United States)

    Cubells, Joseph F; Schroeder, Jason P; Barrie, Elizabeth S; Manvich, Daniel F; Sadee, Wolfgang; Berg, Tiina; Mercer, Kristina; Stowe, Taylor A; Liles, L Cameron; Squires, Katherine E; Mezher, Andrew; Curtin, Patrick; Perdomo, Dannie L; Szot, Patricia; Weinshenker, David

    2016-01-01

    Dopamine β-hydroxylase (DBH) converts dopamine (DA) to norepinephrine (NE) in noradrenergic/adrenergic cells. DBH deficiency prevents NE production and causes sympathetic failure, hypotension and ptosis in humans and mice; DBH knockout (Dbh -/-) mice reveal other NE deficiency phenotypes including embryonic lethality, delayed growth, and behavioral defects. Furthermore, a single nucleotide polymorphism (SNP) in the human DBH gene promoter (-970C>T; rs1611115) is associated with variation in serum DBH activity and with several neurological- and neuropsychiatric-related disorders, although its impact on DBH expression is controversial. Phenotypes associated with DBH deficiency are typically treated with L-3,4-dihydroxyphenylserine (DOPS), which can be converted to NE by aromatic acid decarboxylase (AADC) in the absence of DBH. In this study, we generated transgenic mice carrying a human bacterial artificial chromosome (BAC) encompassing the DBH coding locus as well as ~45 kb of upstream and ~107 kb of downstream sequence to address two issues. First, we characterized the neuroanatomical, neurochemical, physiological, and behavioral transgenic rescue of DBH deficiency by crossing the BAC onto a Dbh -/- background. Second, we compared human DBH mRNA abundance between transgenic lines carrying either a "C" or a "T" at position -970. The BAC transgene drove human DBH mRNA expression in a pattern indistinguishable from the endogenous gene, restored normal catecholamine levels to the peripheral organs and brain of Dbh -/- mice, and fully rescued embryonic lethality, delayed growth, ptosis, reduced exploratory activity, and seizure susceptibility. In some cases, transgenic rescue was superior to DOPS. However, allelic variation at the rs1611115 SNP had no impact on mRNA levels in any tissue. These results indicate that the human BAC contains all of the genetic information required for tissue-specific, functional expression of DBH and can rescue all measured Dbh deficiency

  17. Functionally and phylogenetically diverse plant communities key to soil biota.

    Science.gov (United States)

    Milcu, Alexandru; Allan, Eric; Roscher, Christiane; Jenkins, Tania; Meyer, Sebastian T; Flynn, Dan; Bessler, Holger; Buscot, François; Engels, Christof; Gubsch, Marlén; König, Stephan; Lipowsky, Annett; Loranger, Jessy; Renker, Carsten; Scherber, Christoph; Schmid, Bernhard; Thébault, Elisa; Wubet, Tesfaye; Weisser, Wolfgang W; Scheu, Stefan; Eisenhauer, Nico

    2013-08-01

    Recent studies assessing the role of biological diversity for ecosystem functioning indicate that the diversity of functional traits and the evolutionary history of species in a community, not the number of taxonomic units, ultimately drives the biodiversity--ecosystem-function relationship. Here, we simultaneously assessed the importance of plant functional trait and phylogenetic diversity as predictors of major trophic groups of soil biota (abundance and diversity), six years from the onset of a grassland biodiversity experiment. Plant functional and phylogenetic diversity were generally better predictors of soil biota than the traditionally used species or functional group richness. Functional diversity was a reliable predictor for most biota, with the exception of soil microorganisms, which were better predicted by phylogenetic diversity. These results provide empirical support for the idea that the diversity of plant functional traits and the diversity of evolutionary lineages in a community are important for maintaining higher abundances and diversity of soil communities.

  18. Impact of hepatic function on serum procalcitonin for the diagnosis of bacterial infections in patients with chronic liver disease: A retrospective analysis of 324 cases.

    Science.gov (United States)

    Qu, Junyan; Feng, Ping; Luo, Yan; Lü, Xiaoju

    2016-07-01

    Although procalcitonin (PCT) is a valid marker for early diagnosis of bacterial infections, it is unclear whether its accuracy in predicting bacterial infections is affected by impaired liver function. This study aimed to assess the impact of compromised liver function on the diagnostic value of PCT.This retrospective study was conducted between January 2013 and May 2015. A total of 324 patients with chronic liver disease were enrolled. Routine laboratory measurements and PCT were performed. Patients were divided into 3 groups according to clinical diagnosis: chronic hepatitis (group 1), decompensated cirrhosis (group 2), and acute-on-chronic liver failure/chronic liver failure (group 3). The correlation between PCT and liver function was analyzed. The area under the receiver operating characteristic (AUCROC) curve of PCT was analyzed according to infection status and liver function.PCT was more accurate than white blood cell count (P PCT had a moderate positive correlation with serum total bilirubin (TBIL) (r = 0.592), and a weak correlation with model for end-stage liver disease score (r = 0.483) and international normalized ratio (r = 0.389). The AUCROC and optimum thresholds of PCT and for predicting bacterial infections at different levels of TBIL were 0.907 (95% CI 0.828-0.958) and 0.38 ng/mL, respectively, for TBIL PCT was a valuable marker of bacterial infection in patients with chronic liver diseases. TBIL affected PCT threshold, so different cut-offs should be used according to different TBIL values. PMID:27472699

  19. 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

    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...... species are specific to the mouse intestine and that a minimal consortium of 18 strains covered 50-75% of the known functional potential of metagenomes. The present work will sustain future research on microbiota-host interactions in health and disease, as it will facilitate targeted colonization...

  20. The influence of balanced and imbalanced resource supply on biodiversity-functioning relationship across ecosystems.

    Science.gov (United States)

    Lewandowska, Aleksandra M; Biermann, Antje; Borer, Elizabeth T; Cebrián-Piqueras, Miguel A; Declerck, Steven A J; De Meester, Luc; Van Donk, Ellen; Gamfeldt, Lars; Gruner, Daniel S; Hagenah, Nicole; Harpole, W Stanley; Kirkman, Kevin P; Klausmeier, Christopher A; Kleyer, Michael; Knops, Johannes M H; Lemmens, Pieter; Lind, Eric M; Litchman, Elena; Mantilla-Contreras, Jasmin; Martens, Koen; Meier, Sandra; Minden, Vanessa; Moore, Joslin L; Venterink, Harry Olde; Seabloom, Eric W; Sommer, Ulrich; Striebel, Maren; Trenkamp, Anastasia; Trinogga, Juliane; Urabe, Jotaro; Vyverman, Wim; Van de Waal, Dedmer B; Widdicombe, Claire E; Hillebrand, Helmut

    2016-05-19

    Numerous studies show that increasing species richness leads to higher ecosystem productivity. This effect is often attributed to more efficient portioning of multiple resources in communities with higher numbers of competing species, indicating the role of resource supply and stoichiometry for biodiversity-ecosystem functioning relationships. Here, we merged theory on ecological stoichiometry with a framework of biodiversity-ecosystem functioning to understand how resource use transfers into primary production. We applied a structural equation model to define patterns of diversity-productivity relationships with respect to available resources. Meta-analysis was used to summarize the findings across ecosystem types ranging from aquatic ecosystems to grasslands and forests. As hypothesized, resource supply increased realized productivity and richness, but we found significant differences between ecosystems and study types. Increased richness was associated with increased productivity, although this effect was not seen in experiments. More even communities had lower productivity, indicating that biomass production is often maintained by a few dominant species, and reduced dominance generally reduced ecosystem productivity. This synthesis, which integrates observational and experimental studies in a variety of ecosystems and geographical regions, exposes common patterns and differences in biodiversity-functioning relationships, and increases the mechanistic understanding of changes in ecosystems productivity. PMID:27114584

  1. Effect of Activated Carbon Amendment on Bacterial Community Structure and Functions in a PAH Impacted Urban Soil

    OpenAIRE

    Meynet, Paola; Hale, Sarah E.; Davenport, Russell J; Cornelissen, Gerard; Breedveld, Gijs D.; Werner, David

    2012-01-01

    We collected urban soil samples impacted by polycyclic aromatic hydrocarbons (PAHs) from a sorbent-based remediation field trial to address concerns about unwanted side-effects of 2% powdered (PAC) or granular (GAC) activated carbon amendment on soil microbiology and pollutant biodegradation. After three years, total microbial cell counts and respiration rates were highest in the GAC amended soil. The predominant bacterial community structure derived from denaturing gradient gel electrophores...

  2. Abundance and diversity of bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants revealed by high-throughput sequencing.

    Directory of Open Access Journals (Sweden)

    Zhu Wang

    Full Text Available Biological nitrification/denitrification is frequently used to remove nitrogen from tannery wastewater containing high concentrations of ammonia. However, information is limited about the bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants (WWTPs due to the low-throughput of the previously used methods. In this study, 454 pyrosequencing and Illumina high-throughput sequencing, combined with molecular methods, were used to comprehensively characterize structures and functions of nitrification and denitrification bacterial communities in aerobic and anaerobic sludge of two full-scale tannery WWTPs. Pyrosequencing of 16S rRNA genes showed that Proteobacteria and Synergistetes dominated in the aerobic and anaerobic sludge, respectively. Ammonia-oxidizing bacteria (AOB amoA gene cloning revealed that Nitrosomonas europaea dominated the ammonia-oxidizing community in the WWTPs. Metagenomic analysis showed that the denitrifiers mainly included the genera of Thauera, Paracoccus, Hyphomicrobium, Comamonas and Azoarcus, which may greatly contribute to the nitrogen removal in the two WWTPs. It is interesting that AOB and ammonia-oxidizing archaea had low abundance although both WWTPs demonstrated high ammonium removal efficiency. Good correlation between the qPCR and metagenomic analysis is observed for the quantification of functional genes amoA, nirK, nirS and nosZ, indicating that the metagenomic approach may be a promising method used to comprehensively investigate the abundance of functional genes of nitrifiers and denitrifiers in the environment.

  3. Vimentin in Bacterial Infections

    Directory of Open Access Journals (Sweden)

    Tim N. Mak

    2016-04-01

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

  4. An Inner Membrane Protein (Imp) of Xanthomonas oryzae pv. oryzicola Functions in Carbon Acquisition, EPS Production, Bacterial Motility and Virulence in Rice

    Institute of Scientific and Technical Information of China (English)

    CHEN Gong-you

    2014-01-01

    Xanthomonas oryzae pv. oryzicola (Xoc) causes bacterial leaf streak, a devastating disease in rice-growing regions worldwide. A Tn5-insertion mutant in Xoc_3248, encoding an inner membrane protein (Imp), showed reduced virulence in rice. To explore the potential function of this gene in virulence, a deletion mutant R∆imp was constructed in the wild-type RS105. The R∆imp mutant was signiifcantly impaired for bacterial virulence and growth in planta. The mutation in imp made the pathogen insufifciently utilize glucose, fructose, mannose or pyruvate as a sole carbon source, leading to less extracellular polysaccharide (EPS) production and reduced motility. The deifciencies noted for the mutant were restored to wild-type levels when imp was introduced in trans. Transcription of imp was signiifcantly declined when hrpG and hrpX was mutated and the expression of hrpG and hrpX was also signiifcantly declined when imp was deleted. Cell sublocalization in planta showed Imp membrane-binding feature. These results suggest that Imp is a virulence factor with roles in the catabolism of sugars, EPS production, and bacterial motility.

  5. Bacterial community composition and predicted functional ecology of sponges, sediment and seawater from the thousand islands reef complex, West Java, Indonesia.

    Science.gov (United States)

    de Voogd, Nicole J; Cleary, Daniel F R; Polónia, Ana R M; Gomes, Newton C M

    2015-04-01

    In the present study, we assessed the composition of Bacteria in four biotopes namely sediment, seawater and two sponge species (Stylissa massa and Xestospongia testudinaria) at four different reef sites in a coral reef ecosystem in West Java, Indonesia. In addition to this, we used a predictive metagenomic approach to estimate to what extent nitrogen metabolic pathways differed among bacterial communities from different biotopes. We observed marked differences in bacterial composition of the most abundant bacterial phyla, classes and orders among sponge species, water and sediment. Proteobacteria were by far the most abundant phylum in terms of both sequences and Operational Taxonomic Units (OTUs). Predicted counts for genes associated with the nitrogen metabolism suggested that several genes involved in the nitrogen cycle were enriched in sponge samples, including nosZ, nifD, nirK, norB and nrfA genes. Our data show that a combined barcoded pyrosequencing and predictive metagenomic approach can provide novel insights into the potential ecological functions of the microbial communities. Not only is this approach useful for our understanding of the vast microbial diversity found in sponges but also to understand the potential response of microbial communities to environmental change.

  6. Research Status of Nano- functional Material Bacterial Cellulose%纳米功能材料细菌纤维素研究进展

    Institute of Scientific and Technical Information of China (English)

    李小维; 朱艳彬; 范艺苑; 李方

    2012-01-01

    The bacterial cellulose was widely applied to food, medicine, paper- making, textile, and acoustics equipment industry as a novel nano -functional material. Using static fermentation systems and dynamic fermentation systems can obtain bacterial cellulose with different structural characteristics and material properties. The selection of fermentation reactor types and optimization of fermentation condition became the focus of bacterial cellulose development for the industrialized production.%细菌纤维素是生物质纳米功能材料,在食品、医疗、造纸、纺织、声学器材等方面有广泛的应用前景。采用静态和动态发酵方式得到的细菌纤维素具有不同的结构特征和材料性能。改进发酵工艺,开发和优化更为合理的发酵条件和发酵反应器,已成为细菌纤维素从实验室走向工业化生产的研究重点。

  7. Lipopolysaccharide Clearance, Bacterial Clearance, and Systemic Inflammatory Responses Are Regulated by Cell Type–Specific Functions of TLR4 during Sepsis

    OpenAIRE

    Deng, Meihong; Scott, Melanie J.; Loughran, Patricia; Gibson, Gregory; Sodhi, Chhinder; Watkins, Simon; Hackam, David; Billiar, Timothy R

    2013-01-01

    The morbidity associated with bacterial sepsis is the result of host immune responses to pathogens, which are dependent on pathogen recognition by pattern recognition receptors, such as TLR4. TLR4 is expressed on a range of cell types, yet the mechanisms by which cell-specific functions of TLR4 lead to an integrated sepsis response are poorly understood. To address this, we generated mice in which TLR4 was specifically deleted from myeloid cells (LysMTLR4KO) or hepatocytes (HCTLR4KO) and then...

  8. Anhydride-functional silane immobilized onto titanium surfaces induces osteoblast cell differentiation and reduces bacterial adhesion and biofilm formation.

    Science.gov (United States)

    Godoy-Gallardo, Maria; Guillem-Marti, Jordi; Sevilla, Pablo; Manero, José M; Gil, Francisco J; Rodriguez, Daniel

    2016-02-01

    Bacterial infection in dental implants along with osseointegration failure usually leads to loss of the device. Bioactive molecules with antibacterial properties can be attached to titanium surfaces with anchoring molecules such as silanes, preventing biofilm formation and improving osseointegration. Properties of silanes as molecular binders have been thoroughly studied, but research on the biological effects of these coatings is scarce. The aim of the present study was to determine the in vitro cell response and antibacterial effects of triethoxysilypropyl succinic anhydride (TESPSA) silane anchored on titanium surfaces. X-ray photoelectron spectroscopy confirmed a successful silanization. The silanized surfaces showed no cytotoxic effects. Gene expression analyses of Sarcoma Osteogenic (SaOS-2) osteoblast-like cells cultured on TESPSA silanized surfaces reported a remarkable increase of biochemical markers related to induction of osteoblastic cell differentiation. A manifest decrease of bacterial adhesion and biofilm formation at early stages was observed on treated substrates, while favoring cell adhesion and spreading in bacteria-cell co-cultures. Surfaces treated with TESPSA could enhance a biological sealing on implant surfaces against bacteria colonization of underlying tissues. Furthermore, it can be an effective anchoring platform of biomolecules on titanium surfaces with improved osteoblastic differentiation and antibacterial properties.

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

    Science.gov (United States)

    Lagkouvardos, Ilias; Pukall, Rüdiger; Abt, Birte; Foesel, Bärbel U; Meier-Kolthoff, Jan P; Kumar, Neeraj; Bresciani, Anne; Martínez, Inés; Just, Sarah; Ziegler, Caroline; Brugiroux, Sandrine; Garzetti, Debora; Wenning, Mareike; Bui, Thi P N; Wang, Jun; Hugenholtz, Floor; Plugge, Caroline M; Peterson, Daniel A; Hornef, Mathias W; Baines, John F; Smidt, Hauke; Walter, Jens; Kristiansen, Karsten; Nielsen, Henrik B; Haller, Dirk; Overmann, Jörg; Stecher, Bärbel; Clavel, Thomas

    2016-01-01

    Intestinal bacteria influence mammalian physiology, but many types of bacteria are still uncharacterized. Moreover, reference strains of mouse gut bacteria are not easily available, although mouse models are extensively used in medical research. These are major limitations for the investigation 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 (miBC), 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 species are specific to the mouse intestine and that a minimal consortium of 18 strains covered 50-75% of the known functional potential of metagenomes. The present work will sustain future research on microbiota-host interactions in health and disease, as it will facilitate targeted colonization and molecular studies. The resource is available at www.dsmz.de/miBC. PMID:27670113

  10. Bacterial Vaginosis

    Science.gov (United States)

    ... 586. Related Content STDs during Pregnancy Fact Sheet Pregnancy and HIV, Viral Hepatitis, and STD Prevention Pelvic Inflammatory Disease ( ... Bacterial Vaginosis (BV) Chlamydia Gonorrhea Genital Herpes Hepatitis HIV/AIDS & STDs Human Papillomavirus ... STDs See Also Pregnancy Reproductive ...

  11. Bacterial Meningitis

    Science.gov (United States)

    ... Schedules Preteen & Teen Vaccines Meningococcal Disease Sepsis Bacterial Meningitis Recommend on Facebook Tweet Share Compartir On this ... serious disease. Laboratory Methods for the Diagnosis of Meningitis This manual summarizes laboratory methods used to isolate, ...

  12. Predicting richness effects on ecosystem function in natural communities

    DEFF Research Database (Denmark)

    Dangles, Olivier; Crespo-Pérez, Verónica; Andino, Patricio;

    2011-01-01

    . Despite the increased complexity of experimental and theoretical studies on the biodiversity-ecosystem functioning (B-EF) relationship, a major challenge is to demonstrate whether the observed importance of biodiversity in controlled experimental systems also persists in nature. Due...... to their structural simplicity and their low levels of human impacts, extreme species-poor ecosystems may provide new insights into B-EF relationships in natural systems. We address this issue using shredder invertebrate communities and organic matter decomposition rates in 24 high-altitude (3200-3900 m) Neotropical...... among the three shredder species, indicating complementary resource use and/or facilitation. By integrating survey and experimental data in surface response analyses we found that observed B-EF patterns fit those predicted by a linear model that described litter decomposition rates as a function...

  13. Evidence of the presence of a functional Dot/Icm type IV-B secretion system in the fish bacterial pathogen Piscirickettsia salmonis.

    Directory of Open Access Journals (Sweden)

    Fernando A Gómez

    Full Text Available Piscirickettsia salmonis is a fish bacterial pathogen that has severely challenged the sustainability of the Chilean salmon industry since its appearance in 1989. As this Gram-negative bacterium has been poorly characterized, relevant aspects of its life cycle, virulence and pathogenesis must be identified in order to properly design prophylactic procedures. This report provides evidence of the functional presence in P. salmonis of four genes homologous to those described for Dot/Icm Type IV Secretion Systems. The Dot/Icm System, the major virulence mechanism of phylogenetically related pathogens Legionella pneumophila and Coxiella burnetii, is responsible for their intracellular survival and multiplication, conditions that may also apply to P. salmonis. Our results demonstrate that the four P. salmonis dot/icm homologues (dotB, dotA, icmK and icmE are expressed both during in vitro tissue culture cells infection and growing in cell-free media, suggestive of their putative constitutive expression. Additionally, as it happens in other referential bacterial systems, temporal acidification of cell-free media results in over expression of all four P. salmonis genes, a well-known strategy by which SSTIV-containing bacteria inhibit phagosome-lysosome fusion to survive. These findings are very important to understand the virulence mechanisms of P. salmonis in order to design new prophylactic alternatives to control the disease.

  14. Effect of activated carbon amendment on bacterial community structure and functions in a PAH impacted urban soil.

    Science.gov (United States)

    Meynet, Paola; Hale, Sarah E; Davenport, Russell J; Cornelissen, Gerard; Breedveld, Gijs D; Werner, David

    2012-05-01

    We collected urban soil samples impacted by polycyclic aromatic hydrocarbons (PAHs) from a sorbent-based remediation field trial to address concerns about unwanted side-effects of 2% powdered (PAC) or granular (GAC) activated carbon amendment on soil microbiology and pollutant biodegradation. After three years, total microbial cell counts and respiration rates were highest in the GAC amended soil. The predominant bacterial community structure derived from denaturing gradient gel electrophoresis (DGGE) shifted more strongly with time than in response to AC amendment. DGGE band sequencing revealed the presence of taxa with closest affiliations either to known PAH degraders, e.g. Rhodococcus jostii RHA-1, or taxa known to harbor PAH degraders, e.g. Rhodococcus erythropolis, in all soils. Quantification by real-time polymerase chain reaction yielded similar dioxygenases gene copy numbers in unamended, PAC-, or GAC-amended soil. PAH availability assessments in batch tests showed the greatest difference of 75% with and without biocide addition for unamended soil, while the lowest PAH availability overall was measured in PAC-amended, live soil. We conclude that AC had no detrimental effects on soil microbiology, AC-amended soils retained the potential to biodegrade PAHs, but the removal of available pollutants by biodegradation was most notable in unamended soil. PMID:22455603

  15. Aloe vera extract functionalized zinc oxide nanoparticles as nanoantibiotics against multi-drug resistant clinical bacterial isolates.

    Science.gov (United States)

    Ali, Khursheed; Dwivedi, Sourabh; Azam, Ameer; Saquib, Quaiser; Al-Said, Mansour S; Alkhedhairy, Abdulaziz A; Musarrat, Javed

    2016-06-15

    ZnO nanoparticles (ZnONPs) were synthesised through a simple and efficient biogenic synthesis approach, exploiting the reducing and capping potential of Aloe barbadensis Miller (A. vera) leaf extract (ALE). ALE-capped ZnO nanoparticles (ALE-ZnONPs) were characterized using UV-Vis spectroscopy, X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDX), and transmission electron microscopy (TEM) analyses. XRD analysis provided the average size of ZnONPs as 15 nm. FTIR spectral analysis suggested the role of phenolic compounds, terpenoids and proteins present in ALE, in nucleation and stability of ZnONPs. Flow cytometry and atomic absorption spectrophotometry (AAS) data analyses revealed the surface binding and internalization of ZnONPs in Gram +ve (Staphylococcus aureus) and Gram -ve (Escherichia coli) cells, respectively. Significant antibacterial activity of ALE-ZnONPs was observed against extended spectrum beta lactamases (ESBL) positive E. coli, Pseudomonas aeruginosa, and methicillin resistant S. aureus (MRSA) clinical isolates exhibiting the MIC and MBC values of 2200, 2400 μg/ml and 2300, 2700 μg/ml, respectively. Substantial inhibitory effects of ALE-ZnONPs on bacterial growth kinetics, exopolysaccharides and biofilm formation, unequivocally suggested the antibiotic and anti-biofilm potential. Overall, the results elucidated a rapid, environmentally benign, cost-effective, and convenient method for ALE-ZnONPs synthesis, for possible applications as nanoantibiotics or drug carriers. PMID:27031596

  16. Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography.

    Science.gov (United States)

    Marzinelli, Ezequiel M; Campbell, Alexandra H; Zozaya Valdes, Enrique; Vergés, Adriana; Nielsen, Shaun; Wernberg, Thomas; de Bettignies, Thibaut; Bennett, Scott; Caporaso, J Gregory; Thomas, Torsten; Steinberg, Peter D

    2015-10-01

    Interactions between hosts and associated microbial communities can fundamentally shape the development and ecology of 'holobionts', from humans to marine habitat-forming organisms such as seaweeds. In marine systems, planktonic microbial community structure is mainly driven by geography and related environmental factors, but the large-scale drivers of host-associated microbial communities are largely unknown. Using 16S-rRNA gene sequencing, we characterized 260 seaweed-associated bacterial and archaeal communities on the kelp Ecklonia radiata from three biogeographical provinces spanning 10° of latitude and 35° of longitude across the Australian continent. These phylogenetically and taxonomically diverse communities were more strongly and consistently associated with host condition than geographical location or environmental variables, and a 'core' microbial community characteristic of healthy kelps appears to be lost when hosts become stressed. Microbial communities on stressed individuals were more similar to each other among locations than those on healthy hosts. In contrast to biogeographical patterns of planktonic marine microbial communities, host traits emerge as critical determinants of associated microbial community structure of these holobionts, even at a continental scale.

  17. Coupled cryoconite ecosystem structure-function relationships are revealed by comparing bacterial communities in alpine and Arctic glaciers

    DEFF Research Database (Denmark)

    Edwards, Arwyn; Mur, Luis A. J.; Girdwood, Susan E.;

    2014-01-01

    Cryoconite holes are known as foci of microbial diversity and activity on polar glacier surfaces, but are virtually unexplored microbial habitats in alpine regions. In addition, whether cryoconite community structure reflects ecosystem functionality is poorly understood. Terminal restriction frag...

  18. Rapid Functional Definition of Extended Spectrum β-Lactamase Activity in Bacterial Cultures via Competitive Inhibition of Fluorescent Substrate Cleavage

    OpenAIRE

    Sallum, Ulysses W; Zheng, Xiang; Verma, Sarika; Hasan, Tayyaba

    2010-01-01

    The functional definition of extended-spectrum β-lactamase (ESBL) activity is a clinical challenge. Here we report a rapid and convenient assay of β-lactamase activity through the competitive inhibition of fluorescent substrate hydrolysis that provides a read-out nearly 40x more rapidly than conventional techniques for functional definition. A panel of β-lactam antibiotics was used for competition against β-lactamase enzyme activated photosensitizer (β-LEAP) yielding a competitive index (Ci) ...

  19. Bacterial clearance, heterophil function, and hematological parameters of transport-stressed turkey poults supplemented with dietary yeast extract.

    Science.gov (United States)

    Huff, G R; Huff, W E; Farnell, M B; Rath, N C; Solis de Los Santos, F; Donoghue, A M

    2010-03-01

    Yeast extracts (YE) contain biological response modifiers that may be useful as alternatives to antibiotics for controlling pathogens in poultry production and mitigating the deleterious effects of production stressors. The objective of the present study was to determine the ability of a commercial dietary YE (Alphamune) to modulate the immune response in male turkey poults challenged with Escherichia coli and subjected to transport stress. Alphamune was added to turkey poult diets at 0, 500, or 1,000 g/ton. Poults were challenged by air sac injection with 60 cfu of E. coli at 1 wk of age. At 3 wk of age, these challenged birds were subjected to transport stress and birds were bled and necropsied the following morning. Blood cell numbers and percentages, hematological parameters, and clinical chemistry values were determined. Oxidative burst activity of isolated heterophils was measured using stimulation with phorbol myristate acetate and a 2',7'-dichlorofluorescein diacetate assay. Data were analyzed using GLM and least squares means procedures of the SAS program. The numbers and percentages of heterophils in peripheral blood were increased and their oxidative burst activity was stimulated by YE. The stress challenge dramatically increased oxidative burst and this increase was significantly modulated by YE treatment. Serum levels of calcium, phosphorus, and triglycerides were decreased and uric acid levels, erythrocyte numbers, hemoglobin, and hematocrit were increased by YE supplementation. Bacteria were isolated from the air sac and liver of a lower percentage of birds provided with YE. These results suggest that dietary YE has potential as a nonantibiotic alternative for decreasing bacterial pathogens in turkey production. PMID:20181859

  20. Bacterial carbonatogenesis

    International Nuclear Information System (INIS)

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

  1. The topology of the bacterial co-conserved protein network and its implications for predicting protein function

    Directory of Open Access Journals (Sweden)

    Leach Sonia M

    2008-06-01

    Full Text Available Abstract Background Protein-protein interactions networks are most often generated from physical protein-protein interaction data. Co-conservation, also known as phylogenetic profiles, is an alternative source of information for generating protein interaction networks. Co-conservation methods generate interaction networks among proteins that are gained or lost together through evolution. Co-conservation is a particularly useful technique in the compact bacteria genomes. Prior studies in yeast suggest that the topology of protein-protein interaction networks generated from physical interaction assays can offer important insight into protein function. Here, we hypothesize that in bacteria, the topology of protein interaction networks derived via co-conservation information could similarly improve methods for predicting protein function. Since the topology of bacteria co-conservation protein-protein interaction networks has not previously been studied in depth, we first perform such an analysis for co-conservation networks in E. coli K12. Next, we demonstrate one way in which network connectivity measures and global and local function distribution can be exploited to predict protein function for previously uncharacterized proteins. Results Our results showed, like most biological networks, our bacteria co-conserved protein-protein interaction networks had scale-free topologies. Our results indicated that some properties of the physical yeast interaction network hold in our bacteria co-conservation networks, such as high connectivity for essential proteins. However, the high connectivity among protein complexes in the yeast physical network was not seen in the co-conservation network which uses all bacteria as the reference set. We found that the distribution of node connectivity varied by functional category and could be informative for function prediction. By integrating of functional information from different annotation sources and using the

  2. Synchronized dynamics of bacterial niche-specific functions during biofilm development in a cold seep brine pool

    KAUST Repository

    Zhang, Weipeng

    2015-07-14

    The biology of biofilm in deep-sea environments is barely being explored. Here, biofilms were developed at the brine pool (characterized by limited carbon sources) and the normal bottom water adjacent to Thuwal cold seeps. Comparative metagenomics based on 50 Gb datasets identified polysaccharide degradation, nitrate reduction, and proteolysis as enriched functional categories for brine biofilms. The genomes of two dominant species: a novel deltaproteobacterium and a novel epsilonproteobacterium in the brine biofilms were reconstructed. Despite rather small genome sizes, the deltaproteobacterium possessed enhanced polysaccharide fermentation pathways, whereas the epsilonproteobacterium was a versatile nitrogen reactor possessing nar, nap and nif gene clusters. These metabolic functions, together with specific regulatory and hypersaline-tolerant genes, made the two bacteria unique compared with their close relatives including those from hydrothermal vents. Moreover, these functions were regulated by biofilm development, as both the abundance and the expression level of key functional genes were higher in later-stage biofilms, and co-occurrences between the two dominant bacteria were demonstrated. Collectively, unique mechanisms were revealed: i) polysaccharides fermentation, proteolysis interacted with nitrogen cycling to form a complex chain for energy generation; ii) remarkably, exploiting and organizing niche-specific functions would be an important strategy for biofilm-dependent adaptation to the extreme conditions.

  3. Minimal short-term effect of dietary 2'-fucosyllactose on bacterial colonisation, intestinal function and necrotising enterocolitis in preterm pigs

    DEFF Research Database (Denmark)

    Cilieborg, Malene Skovsted; Bering, Stine B.; Østergaard, Mette V.;

    2016-01-01

    . Abundant α1,2-fucose was detected in the intestine with no difference between groups, and intestinal structure (villus height, permeability) and digestive function (hexose absorption, brush border enzyme activities) were not affected by 2'-FL. Formula enrichment with 2'-FL does not affect gut microbiology...

  4. Structural and functional similarity between the bacterial type III secretion system needle protein PrgI and the eukaryotic apoptosis Bcl-2 proteins.

    Directory of Open Access Journals (Sweden)

    Matthew D Shortridge

    Full Text Available BACKGROUND: Functional similarity is challenging to identify when global sequence and structure similarity is low. Active-sites or functionally relevant regions are evolutionarily more stable relative to the remainder of a protein structure and provide an alternative means to identify potential functional similarity between proteins. We recently developed the FAST-NMR methodology to discover biochemical functions or functional hypotheses of proteins of unknown function by experimentally identifying ligand binding sites. FAST-NMR utilizes our CPASS software and database to assign a function based on a similarity in the structure and sequence of ligand binding sites between proteins of known and unknown function. METHODOLOGY/PRINCIPAL FINDINGS: The PrgI protein from Salmonella typhimurium forms the needle complex in the type III secretion system (T3SS. A FAST-NMR screen identified a similarity between the ligand binding sites of PrgI and the Bcl-2 apoptosis protein Bcl-xL. These ligand binding sites correlate with known protein-protein binding interfaces required for oligomerization. Both proteins form membrane pores through this oligomerization to release effector proteins to stimulate cell death. Structural analysis indicates an overlap between the PrgI structure and the pore forming motif of Bcl-xL. A sequence alignment indicates conservation between the PrgI and Bcl-xL ligand binding sites and pore formation regions. This active-site similarity was then used to verify that chelerythrine, a known Bcl-xL inhibitor, also binds PrgI. CONCLUSIONS/SIGNIFICANCE: A structural and functional relationship between the bacterial T3SS and eukaryotic apoptosis was identified using our FAST-NMR ligand affinity screen in combination with a bioinformatic analysis based on our CPASS program. A similarity between PrgI and Bcl-xL is not readily apparent using traditional global sequence and structure analysis, but was only identified because of conservation in

  5. Bacterial glycosyltransferase toxins.

    Science.gov (United States)

    Jank, Thomas; Belyi, Yury; Aktories, Klaus

    2015-12-01

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

  6. The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function

    International Nuclear Information System (INIS)

    The crystal structure of the BVU2987 gene product from B. vulgatus (UniProt A6L4L1) reveals that members of the new Pfam family PF11396 (domain of unknown function; DUF2874) are similar to β-lactamase inhibitor protein and YpmB. Proteins that contain the DUF2874 domain constitute a new Pfam family PF11396. Members of this family have predominantly been identified in microbes found in the human gut and oral cavity. The crystal structure of one member of this family, BVU2987 from Bacteroides vulgatus, has been determined, revealing a β-lactamase inhibitor protein-like structure with a tandem repeat of domains. Sequence analysis and structural comparisons reveal that BVU2987 and other DUF2874 proteins are related to β-lactamase inhibitor protein, PepSY and SmpA-OmlA proteins and hence are likely to function as inhibitory proteins

  7. MyD88-deficient Hydra reveal an ancient function of TLR signaling in sensing bacterial colonizers

    OpenAIRE

    Franzenburg, Sören; Fraune, Sebastian; Künzel, Sven; Baines, John F; Domazet-Lošo, Tomislav; Bosch, Thomas C. G.

    2012-01-01

    Toll-like receptor (TLR) signaling is one of the most important signaling cascades of the innate immune system of vertebrates. Studies in invertebrates have focused on the fruit fly Drosophila melanogaster and the nematode Caenorhabditis elegans, and there is little information regarding the evolutionary origin and ancestral function of TLR signaling. In Drosophila, members of the Toll-like receptor family are involved in both embryonic development and innate immunity. In C. elegans, a clear ...

  8. Functional correlation of bacterial LuxS with their quaternary associations: interface analysis of the structure networks

    OpenAIRE

    Vishveshwara Saraswathi; Bhattacharyya Moitrayee

    2009-01-01

    Abstract Background The genome of a wide variety of prokaryotes contains the luxS gene homologue, which encodes for the protein S-ribosylhomocysteinelyase (LuxS). This protein is responsible for the production of the quorum sensing molecule, AI-2 and has been implicated in a variety of functions such as flagellar motility, metabolic regulation, toxin production and even in pathogenicity. A high structural similarity is present in the LuxS structures determined from a few species. In this stud...

  9. Effect of the pollution level on the functional bacterial groups aiming at degrading bisphenol A and nonylphenol in natural biofilms of an urban river.

    Science.gov (United States)

    Cai, Wei; Li, Yi; Wang, Peifang; Niu, Lihua; Zhang, Wenlong; Wang, Chao

    2016-08-01

    Bisphenol A (BPA) and 4-nonylphenol (NP) are ubiquitous pollutants with estrogenic activity in aquatic environment and have attracted global concern due to their disruption of endocrine systems. This study investigated the spatial distribution characteristics of the bacterial groups involved in the degradation of BPA and NP within biofilms in an urban river using terminal restriction fragment length polymorphism based on 16S rRNA gene sequences. The effects of the pollution level and water parameters on these groups were also assessed. Hierarchical cluster analysis grouped the sampling sites into three clusters reflecting their varying nutrient pollution levels of relatively slight pollution (SP), moderate pollution (MP), and high pollution (HP) based on water quality data and Environmental Quality Standard for Surface Water of China (GB3838-2002). The BPA and NP concentration in river water ranged from 0.8 to 77.5 and 10.2 to 162.9 ng L(-1), respectively. Comamonadaceae, Pseudomonadaceae, Alcaligenaceae, Bacillaceae, Sphingomonadacea, Burkholderiaceae, and Rhizobiaceae were the dominant bacterial taxa involved in BPA and NP degradation, comprising an average of 9.8, 8.1, 7.6, 6.7, 6.2, 4.1, and 2.8 % of total sequences, respectively. The total abundance of these groups showed a slight upward trend and subsequently rapidly decreased with increasing pollution levels. The average proportion of Comamonadaceae in MP river sections was almost 1.5-2 times than that in SP or HP one. The distribution of functional groups was found related to environmental variables, especially pH, conductivity, ammonium nitrogen (NH3-N), and BPA. The abundance of Comamonadaceae and Rhizobiaceae was both closely related to higher values of pH and conductivity as well as lower concentrations of NP and BPA. Alcaligenaceae and Pseudomonadaceae were associated with higher concentrations of TP and CODMn and inversely correlated with DO concentration. This study might provide effective data on

  10. Effect of the pollution level on the functional bacterial groups aiming at degrading bisphenol A and nonylphenol in natural biofilms of an urban river.

    Science.gov (United States)

    Cai, Wei; Li, Yi; Wang, Peifang; Niu, Lihua; Zhang, Wenlong; Wang, Chao

    2016-08-01

    Bisphenol A (BPA) and 4-nonylphenol (NP) are ubiquitous pollutants with estrogenic activity in aquatic environment and have attracted global concern due to their disruption of endocrine systems. This study investigated the spatial distribution characteristics of the bacterial groups involved in the degradation of BPA and NP within biofilms in an urban river using terminal restriction fragment length polymorphism based on 16S rRNA gene sequences. The effects of the pollution level and water parameters on these groups were also assessed. Hierarchical cluster analysis grouped the sampling sites into three clusters reflecting their varying nutrient pollution levels of relatively slight pollution (SP), moderate pollution (MP), and high pollution (HP) based on water quality data and Environmental Quality Standard for Surface Water of China (GB3838-2002). The BPA and NP concentration in river water ranged from 0.8 to 77.5 and 10.2 to 162.9 ng L(-1), respectively. Comamonadaceae, Pseudomonadaceae, Alcaligenaceae, Bacillaceae, Sphingomonadacea, Burkholderiaceae, and Rhizobiaceae were the dominant bacterial taxa involved in BPA and NP degradation, comprising an average of 9.8, 8.1, 7.6, 6.7, 6.2, 4.1, and 2.8 % of total sequences, respectively. The total abundance of these groups showed a slight upward trend and subsequently rapidly decreased with increasing pollution levels. The average proportion of Comamonadaceae in MP river sections was almost 1.5-2 times than that in SP or HP one. The distribution of functional groups was found related to environmental variables, especially pH, conductivity, ammonium nitrogen (NH3-N), and BPA. The abundance of Comamonadaceae and Rhizobiaceae was both closely related to higher values of pH and conductivity as well as lower concentrations of NP and BPA. Alcaligenaceae and Pseudomonadaceae were associated with higher concentrations of TP and CODMn and inversely correlated with DO concentration. This study might provide effective data on

  11. Bacterial Adhesion & Blocking Bacterial Adhesion

    DEFF Research Database (Denmark)

    Vejborg, Rebecca Munk

    2008-01-01

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

  12. Bacterial lipases

    NARCIS (Netherlands)

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

    1994-01-01

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

  13. The abundance of functional genes, cbbL, nifH, amoA and apsA, and bacterial community structure of intertidal soil from Arabian Sea.

    Science.gov (United States)

    Keshri, Jitendra; Yousuf, Basit; Mishra, Avinash; Jha, Bhavanath

    2015-06-01

    The Gulf of Cambay is a trumpet-shaped inlet of the Arabian Sea, located along the west coast of India and confronts a high tidal range with strong water currents. The region belongs to a semi-arid zone and saline alkaline intertidal soils are considered biologically extreme. The selected four soil types (S1-S4) were affected by salinity, alkalinity and sodicity. Soil salinity ranged from 20 to 126 dS/m, soil pH 8.6-10.0 with high sodium adsorption ratio (SAR) and exchangeable sodium percentage (ESP). Abundance of the key functional genes like cbbL, nifH, amoA and apsA involved in biogeochemical cycling were targeted using qPCR, which varied from (2.36 ± 0.03) × 10(4) to (2.87 ± 0.26) × 10(8), (1.18 ± 0.28) × 10(6) to (1.01 ± 0.26) × 10(9), (1.41 ± 0.21) × 10(6) to (1.29 ± 0.05) × 10(8) and (8.47 ± 0.23) × 10(4) to (1.73 ± 0.01) × 10(6) per gram dry weight, respectively. The microbial community structure revealed that soils S1 and S3 were dominated by phylum Firmicutes whereas S4 and S2 showed an abundance of Proteobacterial clones. These soils also represented Bacteroidetes, Chloroflexi, Actinobacteria, Planctomycetes and Acidobacteria clones. Molecular phylogeny showed a significant variation in the bacterial community distribution among the intertidal soil types. A high number of novel taxonomic units were observed which makes the intertidal zone a unique reservoir of unidentified bacterial taxa that may be explored further. PMID:25862282

  14. 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.

  15. The bacterial lipocalins.

    Science.gov (United States)

    Bishop, R E

    2000-10-18

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

  16. Function of FlhB, a membrane protein implicated in the bacterial flagellar type III secretion system.

    Science.gov (United States)

    Meshcheryakov, Vladimir A; Barker, Clive S; Kostyukova, Alla S; Samatey, Fadel A

    2013-01-01

    The membrane protein FlhB is a highly conserved component of the flagellar secretion system, and it plays an active role in the regulation of protein export. In this study conserved properties of FlhB that are important for its function were investigated. Replacing the flhB gene (or part of the gene) in Salmonella typhimurium with the flhB gene of the distantly related bacterium Aquifex aeolicus greatly reduces motility. However, motility can be restored to some extent by spontaneous mutations in the part of flhB gene coding for the cytoplasmic domain of Aquifex FlhB. Structural analysis suggests that these mutations destabilize the structure. The secondary structure and stability of the mutated cytoplasmic fragments of FlhB have been studied by circular dichroism spectroscopy. The results suggest that conformational flexibility could be important for FlhB function. An extragenic suppressor mutation in the fliS gene, which decreases the affinity of FliS to FliC, partially restores motility of the FlhB substitution mutants. PMID:23874605

  17. Function of FlhB, a membrane protein implicated in the bacterial flagellar type III secretion system.

    Directory of Open Access Journals (Sweden)

    Vladimir A Meshcheryakov

    Full Text Available The membrane protein FlhB is a highly conserved component of the flagellar secretion system, and it plays an active role in the regulation of protein export. In this study conserved properties of FlhB that are important for its function were investigated. Replacing the flhB gene (or part of the gene in Salmonella typhimurium with the flhB gene of the distantly related bacterium Aquifex aeolicus greatly reduces motility. However, motility can be restored to some extent by spontaneous mutations in the part of flhB gene coding for the cytoplasmic domain of Aquifex FlhB. Structural analysis suggests that these mutations destabilize the structure. The secondary structure and stability of the mutated cytoplasmic fragments of FlhB have been studied by circular dichroism spectroscopy. The results suggest that conformational flexibility could be important for FlhB function. An extragenic suppressor mutation in the fliS gene, which decreases the affinity of FliS to FliC, partially restores motility of the FlhB substitution mutants.

  18. Minimal short-term effect of dietary 2'-fucosyllactose on bacterial colonisation, intestinal function and necrotising enterocolitis in preterm pigs.

    Science.gov (United States)

    Cilieborg, Malene S; Bering, Stine B; Østergaard, Mette V; Jensen, Michael L; Krych, Łukasz; Newburg, David S; Sangild, Per T

    2016-09-01

    Human milk decreases the risk of necrotising enterocolitis (NEC), a severe gastrointestinal disease that occurs in 5-10 % of preterm infants. The prebiotic and immune-modulatory effects of milk oligosaccharides may contribute to this protection. Preterm pigs were used to test whether infant formula enriched with α1,2-fucosyllactose (2'-FL, the most abundant oligosaccharide in human milk) would benefit gut microbial colonisation and NEC resistance after preterm birth. Caesarean-delivered preterm pigs were fed formula (Controls, n 17) or formula with 5 g/l 2'-FL (2'-FL, n 16) for 5 d; eight 2'-FL pigs (50 %) and twelve Controls (71 %) developed NEC, with no difference in lesion scores (P=0·35); 2'-FL pigs tended to have less anaerobic bacteria in caecal contents (P=0·22), but no difference in gut microbiota between groups were observed by fluorescence in situ hybridisation and 454 pyrosequencing. Abundant α1,2-fucose was detected in the intestine with no difference between groups, and intestinal structure (villus height, permeability) and digestive function (hexose absorption, brush border enzyme activities) were not affected by 2'-FL. Formula enrichment with 2'-FL does not affect gut microbiology, digestive function or NEC sensitivity in pigs within the first few days after preterm birth. Milk 2'-FL may not be critical in the immediate postnatal period of preterm neonates when gut colonisation and intestinal immunity are still immature. PMID:27452119

  19. Graphene Oxide/Silver Nanohybrid as Multi-functional Material for Highly Efficient Bacterial Disinfection and Detection of Organic Dye

    Science.gov (United States)

    Tam, Le Thi; Dinh, Ngo Xuan; Van Cuong, Nguyen; Van Quy, Nguyen; Huy, Tran Quang; Ngo, Duc-The; Mølhave, Kristian; Le, Anh-Tuan

    2016-10-01

    In this work, a multi-functional hybrid system consisting of graphene oxide and silver nanoparticles (GO-Ag NPs) was successfully synthesized by using a two-step chemical process. We firstly demonstrated noticeable bactericidal ability of the GO-Ag hybrid system. We provide more chemo-physical evidence explaining the antibacterial behavior of GO-Ag nanohybrid against Gram-negative Escherichia Coli and Gram-positive Staphylococcus aureus in light of ultrastructural damage analyses and Ag1+ ions release rate onto the cells/medium. A further understanding of the mode of antimicrobial action is very important for designing and developing advanced antimicrobial systems. Secondly, we have also demonstrated that the GO-Ag nanohybrid material could be used as a potential surface enhanced Raman scattering (SERS) substrate to detect and quantify organic dyes, e.g., methylene blue (MB), in aqueous media. Our findings revealed that the GO-Ag hybrid system showed better SERS performance of MB detection than that of pure Ag-NPs. MB could be detected at a concentration as low as 1 ppm. The GO-Ag-based SERS platform can be effectively used to detect trace concentrations of various types of organic dyes in aqueous media. With the aforementioned properties, the GO-Ag hybrid system is found to be very promising as a multi-functional material for advanced biomedicine and environmental monitoring applications.

  20. Graphene Oxide/Silver Nanohybrid as Multi-functional Material for Highly Efficient Bacterial Disinfection and Detection of Organic Dye

    Science.gov (United States)

    Tam, Le Thi; Dinh, Ngo Xuan; Van Cuong, Nguyen; Van Quy, Nguyen; Huy, Tran Quang; Ngo, Duc-The; Mølhave, Kristian; Le, Anh-Tuan

    2016-06-01

    In this work, a multi-functional hybrid system consisting of graphene oxide and silver nanoparticles (GO-Ag NPs) was successfully synthesized by using a two-step chemical process. We firstly demonstrated noticeable bactericidal ability of the GO-Ag hybrid system. We provide more chemo-physical evidence explaining the antibacterial behavior of GO-Ag nanohybrid against Gram-negative Escherichia Coli and Gram-positive Staphylococcus aureus in light of ultrastructural damage analyses and Ag1+ ions release rate onto the cells/medium. A further understanding of the mode of antimicrobial action is very important for designing and developing advanced antimicrobial systems. Secondly, we have also demonstrated that the GO-Ag nanohybrid material could be used as a potential surface enhanced Raman scattering (SERS) substrate to detect and quantify organic dyes, e.g., methylene blue (MB), in aqueous media. Our findings revealed that the GO-Ag hybrid system showed better SERS performance of MB detection than that of pure Ag-NPs. MB could be detected at a concentration as low as 1 ppm. The GO-Ag-based SERS platform can be effectively used to detect trace concentrations of various types of organic dyes in aqueous media. With the aforementioned properties, the GO-Ag hybrid system is found to be very promising as a multi-functional material for advanced biomedicine and environmental monitoring applications.

  1. Electrostatic Potential as a Descriptor of Anti-Bacterial Activities of Some Anacardic Acid Derivatives: A Study Using Density Functional Theory

    CERN Document Server

    Tiwari, Manish K

    2015-01-01

    Structures and minimum molecular electrostatic potential (MEP) distributions in anacardic acid and some of its derivatives have been studied by full geometry optimization at the M06-2X/6-31G(d,p), WB97XD/6-31G(d,p) and B3LYP/6-31G(d,p) levels of density functional theory (DFT) in gas phase as well as in DMSO and aqueous solutions. Solvent effect was treated employing the integral equation formalism of the polarizable continuum model. Effects of modifications of the C1-side chain on the minimum MEP values in various regions were studied. Minimum MEP values near the oxygen atoms of the C2-OH group, oxygen or sulfur atoms of the C1-attached urea or thiourea groups and above or below the ring plane considered to be involved in interaction with the receptor were used to perform multiple linear regression. Experimentally observed anti-bacterial activities of these molecules against S. aureus are thus shown to be related to minimum MEP values in the above mentioned regions. Among the three DFT functionals used in th...

  2. Functional correlation of bacterial LuxS with their quaternary associations: interface analysis of the structure networks

    Directory of Open Access Journals (Sweden)

    Vishveshwara Saraswathi

    2009-02-01

    Full Text Available Abstract Background The genome of a wide variety of prokaryotes contains the luxS gene homologue, which encodes for the protein S-ribosylhomocysteinelyase (LuxS. This protein is responsible for the production of the quorum sensing molecule, AI-2 and has been implicated in a variety of functions such as flagellar motility, metabolic regulation, toxin production and even in pathogenicity. A high structural similarity is present in the LuxS structures determined from a few species. In this study, we have modelled the structures from several other species and have investigated their dimer interfaces. We have attempted to correlate the interface features of LuxS with the phenotypic nature of the organisms. Results The protein structure networks (PSN are constructed and graph theoretical analysis is performed on the structures obtained from X-ray crystallography and on the modelled ones. The interfaces, which are known to contain the active site, are characterized from the PSNs of these homodimeric proteins. The key features presented by the protein interfaces are investigated for the classification of the proteins in relation to their function. From our analysis, structural interface motifs are identified for each class in our dataset, which showed distinctly different pattern at the interface of LuxS for the probiotics and some extremophiles. Our analysis also reveals potential sites of mutation and geometric patterns at the interface that was not evident from conventional sequence alignment studies. Conclusion The structure network approach employed in this study for the analysis of dimeric interfaces in LuxS has brought out certain structural details at the side-chain interaction level, which were elusive from the conventional structure comparison methods. The results from this study provide a better understanding of the relation between the luxS gene and its functional role in the prokaryotes. This study also makes it possible to explore the

  3. Symbiotic Bacterial Metabolites Regulate Gastrointestinal Barrier Function via the Xenobiotic Sensor PXR and Toll-like Receptor 4

    Science.gov (United States)

    Venkatesh, Madhukumar; Mukherjee, Subhajit; Wang, Hongwei; Li, Hao; Sun, Katherine; Benechet, Alaxandre P.; Qiu, Zhijuan; Maher, Leigh; Redinbo, Matthew R.; Phillips, Robert S.; Fleet, James C.; Kortagere, Sandhya; Mukherjee, Paromita; Fasano, Alessio; Le Ven, Jessica; Nicholson, Jeremy K.; Dumas, Marc E.; Khanna, Kamal M.; Mani, Sridhar

    2014-01-01

    SUMMARY Intestinal microbial metabolites are conjectured to affect mucosal integrity through an incompletely characterized mechanism. Here we showed microbial-specific indoles regulated intestinal barrier function through the xenobiotic sensor, pregnane X receptor (PXR). Indole 3-propionic acid (IPA), in the context of indole, is as a ligand for PXR in vivo, and IPA down-regulated enterocyte TNF–α while up-regulated junctional protein-coding mRNAs. PXR-deficient (Nr1i2−/−) mice showed a distinctly “leaky” gut physiology coupled with up-regulation of the Toll-like receptor (TLR) signaling pathway. These defects in the epithelial barrier were corrected in Nr1i2−/−Tlr4−/− mice. Our results demonstrate that a direct chemical communication between the intestinal symbionts and PXR regulates mucosal integrity through a pathway which involves luminal sensing and signaling by TLR4. PMID:25065623

  4. Protein and DNA technologies for functional expression of membrane-associated cytochromes P450 in bacterial cell factories

    DEFF Research Database (Denmark)

    Vazquez Albacete, Dario

    , metabolic engineering and protein engineering to provide new solutions to the P450 expression bottleneck in bacteria. The work primarily focuses on developing a fluorescence high-throughput platform to easily assess proper folding and expression levels of plant cytochromes P450. The platform has been...... designed to fit in metabolic engineering and structural biology applications. Furthermore in this thesis a systematic engineering rationale is proposed to improve P450 expression. For this, anew set of N-terminal tags has been developed in order to provide a streamlined optimization scheme for P450......450 engineering guidelines and serves as platform to improve performance of microbial cells, thereby boosting recombinant production of complex plant P450-derived biochemicals. The knowledge generated, could guide future reconstruction of functional plant metabolic pathways leading to high valuable...

  5. SEVA 2.0: an update of the Standard European Vector Architecture for de-/re-construction of bacterial functionalities.

    Science.gov (United States)

    Martínez-García, Esteban; Aparicio, Tomás; Goñi-Moreno, Angel; Fraile, Sofía; de Lorenzo, Víctor

    2015-01-01

    The Standard European Vector Architecture 2.0 database (SEVA-DB 2.0, http://seva.cnb.csic.es) is an improved and expanded version of the platform released in 2013 (doi: 10.1093/nar/gks1119) aimed at assisting the choice of optimal genetic tools for de-constructing and re-constructing complex prokaryotic phenotypes. By adopting simple compositional rules, the SEVA standard facilitates combinations of functional DNA segments that ease both the analysis and the engineering of diverse Gram-negative bacteria for fundamental or biotechnological purposes. The large number of users of the SEVA-DB during its first two years of existence has resulted in a valuable feedback that we have exploited for fixing DNA sequence errors, improving the nomenclature of the SEVA plasmids, expanding the vector collection, adding new features to the web interface and encouraging contributions of materials from the community of users. The SEVA platform is also adopting the Synthetic Biology Open Language (SBOL) for electronic-like description of the constructs available in the collection and their interfacing with genetic devices developed by other Synthetic Biology communities. We advocate the SEVA format as one interim asset for the ongoing transition of genetic design of microorganisms from being a trial-and-error endeavor to become an authentic engineering discipline.

  6. Complete metagenome sequencing based bacterial diversity and functional insights from basaltic hot spring of Unkeshwar, Maharashtra, India

    Directory of Open Access Journals (Sweden)

    Gajanan T. Mehetre

    2016-03-01

    Full Text Available Unkeshwar hot springs are located at geographical South East Deccan Continental basalt of India. Here, we report the microbial community analysis of this hot spring using whole metagenome shotgun sequencing approach. The analysis revealed a total of 848,096 reads with 212.87 Mbps with 50.87% G + C content. Metagenomic sequences were deposited in SRA database with accession number (SUB1242219. Community analysis revealed 99.98% sequences belonging to bacteria and 0.01% to archaea and 0.01% to Viruses. The data obtained revealed 41 phyla including bacteria and Archaea and including 719 different species. In taxonomic analysis, the dominant phyla were found as, Actinobacteria (56%, Verrucomicrobia (24%, Bacteriodes (13%, Deinococcus-Thermus (3% and firmicutes (2% and Viruses (2%. Furthermore, functional annotation using pathway information revealed dynamic potential of hot spring community in terms of metabolism, environmental information processing, cellular processes and other important aspects. Kyoto Encyclopedia of Genes and Genomes (KEGG pathway analysis of each contig sequence by assigning KEGG Orthology (KO numbers revealed contig sequences that were assigned to metabolism, organismal system, Environmental Information Processing, cellular processes and human diseases with some unclassified sequences. The Unkeshwar hot springs offer rich phylogenetic diversity and metabolic potential for biotechnological applications.

  7. Deuterium Labeling Strategies for Creating Contrast in Structure-Function Studies of Model Bacterial Outer Membranes Using Neutron Reflectometry.

    Science.gov (United States)

    Le Brun, Anton P; Clifton, Luke A; Holt, Stephen A; Holden, Peter J; Lakey, Jeremy H

    2016-01-01

    Studying the outer membrane of Gram-negative bacteria is challenging due to the complex nature of its structure. Therefore, simplified models are required to undertake structure-function studies of processes that occur at the outer membrane/fluid interface. Model membranes can be created by immobilizing bilayers to solid supports such as gold or silicon surfaces, or as monolayers on a liquid support where the surface pressure and fluidity of the lipids can be controlled. Both model systems are amenable to having their structure probed by neutron reflectometry, a technique that provides a one-dimensional depth profile through a membrane detailing its thickness and composition. One of the strengths of neutron scattering is the ability to use contrast matching, allowing molecules containing hydrogen and those enriched with deuterium to be highlighted or matched out against the bulk isotopic composition of the solvent. Lipopolysaccharides, a major component of the outer membrane, can be isolated for incorporation into model membranes. Here, we describe the deuteration of lipopolysaccharides from rough strains of Escherichia coli for incorporation into model outer membranes, and how the use of deuterated materials enhances structural analysis of model membranes by neutron reflectometry. PMID:26791981

  8. Deuterium Labeling Strategies for Creating Contrast in Structure-Function Studies of Model Bacterial Outer Membranes Using Neutron Reflectometry.

    Science.gov (United States)

    Le Brun, Anton P; Clifton, Luke A; Holt, Stephen A; Holden, Peter J; Lakey, Jeremy H

    2016-01-01

    Studying the outer membrane of Gram-negative bacteria is challenging due to the complex nature of its structure. Therefore, simplified models are required to undertake structure-function studies of processes that occur at the outer membrane/fluid interface. Model membranes can be created by immobilizing bilayers to solid supports such as gold or silicon surfaces, or as monolayers on a liquid support where the surface pressure and fluidity of the lipids can be controlled. Both model systems are amenable to having their structure probed by neutron reflectometry, a technique that provides a one-dimensional depth profile through a membrane detailing its thickness and composition. One of the strengths of neutron scattering is the ability to use contrast matching, allowing molecules containing hydrogen and those enriched with deuterium to be highlighted or matched out against the bulk isotopic composition of the solvent. Lipopolysaccharides, a major component of the outer membrane, can be isolated for incorporation into model membranes. Here, we describe the deuteration of lipopolysaccharides from rough strains of Escherichia coli for incorporation into model outer membranes, and how the use of deuterated materials enhances structural analysis of model membranes by neutron reflectometry.

  9. 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...... biogeochemical processes are carried exclusively by bacteria. * Bacteria play an important role in all types of habitats including some that cannot support eukaryotic life....

  10. [Bacterial vaginosis].

    Science.gov (United States)

    Romero Herrero, Daniel; Andreu Domingo, Antonia

    2016-07-01

    Bacterial vaginosis (BV) is the main cause of vaginal dysbacteriosis in the women during the reproductive age. It is an entity in which many studies have focused for years and which is still open for discussion topics. This is due to the diversity of microorganisms that cause it and therefore, its difficult treatment. Bacterial vaginosis is probably the result of vaginal colonization by complex bacterial communities, many of them non-cultivable and with interdependent metabolism where anaerobic populations most likely play an important role in its pathogenesis. The main symptoms are an increase of vaginal discharge and the unpleasant smell of it. It can lead to serious consequences for women, such as an increased risk of contracting sexually transmitted infections including human immunodeficiency virus and upper genital tract and pregnancy complications. Gram stain is the gold standard for microbiological diagnosis of BV, but can also be diagnosed using the Amsel clinical criteria. It should not be considered a sexually transmitted disease but it is highly related to sex. Recurrence is the main problem of medical treatment. Apart from BV, there are other dysbacteriosis less characterized like aerobic vaginitis of which further studies are coming slowly but are achieving more attention and consensus among specialists. PMID:27474242

  11. Studies of the structure and function of Mms6, a bacterial protein that promotes the formation of magnetic nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Lijun [Iowa State Univ., Ames, IA (United States)

    2011-01-01

    Here we report structural and functional studies of Mms6, a biomineralization protein that can promote the formation in vitro of magnetic nanoparticles with sizes and morphologies similar to the magnetites synthesized by magnetotactic bacteria. We found the binding pattern of Mms6 to ferric ion to be two-phase and multivalent. We quantatively determined that Mms6 binds one Fe3+ with a very high affinity (Kd = 1016 M). The second phase of iron binding is multivalent and cooperative with respect to iron with a Kd in the μM range and a stoichiometry of about 20 ferric ion per protein molecule. We found that Mms6 exists in large particles of two sizes, one consisting of 20-40 monomeric units and the other of 200 units. From proteolytic digestion, ultracentrifugation and liposome fusion studies, we found that Mms6 forms a large micellar quaternary structure with the N-terminal domain self-assembling into a uniformly sized micelle and the C-terminal domain on the surface. The two-phase iron-binding pattern may be relevant to iron crystal formation. We propose that the first high affinity phase may stabilize a new conformation of the C-terminal domain that allows interaction with other C-terminal domains leading to a structural change in the multimeric protein complex that enables the second low affinity iron binding phase to organize iron and initiate crystal formation. We also observed a dimeric apparent molecular mass of the Mms6 C-terminal peptide (C21Mms6). We speculate that the C-terminal domain may form higher order quaternary arrangements on the surface of the micelle or when anchored to a membrane by the N-terminal domain. The change in fluorescence quenching in the N-terminal domain with iron binding suggests a structural integrity between the C- and N-terminal domains. The slow change in trp fluorescence as a function of time after adding iron suggests a very slow conformational change in the protein that involves

  12. Studies of the structure and function of Mms6, a bacterial protein that promotes the formation of magnetic nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Lijun [Iowa State Univ., Ames, IA (United States)

    2011-01-01

    Here we report structural and functional studies of Mms6, a biomineralization protein that can promote the formation in vitro of magnetic nanoparticles with sizes and morphologies similar to the magnetites synthesized by magnetotactic bacteria. We found the binding pattern of Mms6 to ferric ion to be two-phase and multivalent. We quantatively determined that Mms6 binds one Fe3+ with a very high affinity (Kd = 1016 M). The second phase of iron binding is multivalent and cooperative with respect to iron with a Kd in the μM range and a stoichiometry of about 20 ferric ion per protein molecule. We found that Mms6 exists in large particles of two sizes, one consisting of 20-40 monomeric units and the other of 200 units. From proteolytic digestion, ultracentrifugation and liposome fusion studies, we found that Mms6 forms a large micellar quaternary structure with the N-terminal domain self-assembling into a uniformly sized micelle and the C-terminal domain on the surface. The two-phase iron-binding pattern may be relevant to iron crystal formation. We propose that the first high affinity phase may stabilize a new conformation of the C-terminal domain that allows interaction with other C-terminal domains leading to a structural change in the multimeric protein complex that enables the second low affinity iron binding phase to organize iron and initiate crystal formation. We also observed a dimeric apparent molecular mass of the Mms6 C-terminal peptide (C21Mms6). We speculate that the C-terminal domain may form higher order quaternary arrangements on the surface of the micelle or when anchored to a membrane by the N-terminal domain. The change in fluorescence quenching in the N-terminal domain with iron binding suggests a structural integrity between the C- and N-terminal domains. The slow change in trp fluorescence as a function of time after adding iron suggests a very slow conformational change in the protein that involves

  13. Bacterial Protein-Tyrosine Kinases

    DEFF Research Database (Denmark)

    Shi, Lei; Kobir, Ahasanul; Jers, Carsten;

    2010-01-01

    in exopolysaccharide production, virulence, DNA metabolism, stress response and other key functions of the bacterial cell. BY-kinases act through autophosphorylation (mainly in exopolysaccharide production) and phosphorylation of other proteins, which have in most cases been shown to be activated by tyrosine......Bacteria and Eukarya share essentially the same family of protein-serine/threonine kinases, also known as the Hanks-type kinases. However, when it comes to protein-tyrosine phosphorylation, bacteria seem to have gone their own way. Bacterial protein-tyrosine kinases (BY-kinases) are bacterial...... and highlighted their importance in bacterial physiology. Having no orthologues in Eukarya, BY-kinases are receiving a growing attention from the biomedical field, since they represent a particularly promising target for anti-bacterial drug design....

  14. Expression and extracellular release of a functional anti-trypanosome Nanobody® in Sodalis glossinidius, a bacterial symbiont of the tsetse fly

    Directory of Open Access Journals (Sweden)

    De Vooght Linda

    2012-02-01

    Full Text Available Abstract Background Sodalis glossinidius, a gram-negative bacterial endosymbiont of the tsetse fly, has been proposed as a potential in vivo drug delivery vehicle to control trypanosome parasite development in the fly, an approach known as paratransgenesis. Despite this interest of S. glossinidius as a paratransgenic platform organism in tsetse flies, few potential effector molecules have been identified so far and to date none of these molecules have been successfully expressed in this bacterium. Results In this study, S. glossinidius was transformed to express a single domain antibody, (Nanobody® Nb_An33, that efficiently targets conserved cryptic epitopes of the variant surface glycoprotein (VSG of the parasite Trypanosoma brucei. Next, we analyzed the capability of two predicted secretion signals to direct the extracellular delivery of significant levels of active Nb_An33. We show that the pelB leader peptide was successful in directing the export of fully functional Nb_An33 to the periplasm of S. glossinidius resulting in significant levels of extracellular release. Finally, S. glossinidius expressing pelBNb_An33 exhibited no significant reduction in terms of fitness, determined by in vitro growth kinetics, compared to the wild-type strain. Conclusions These data are the first demonstration of the expression and extracellular release of functional trypanosome-interfering Nanobodies® in S. glossinidius. Furthermore, Sodalis strains that efficiently released the effector protein were not affected in their growth, suggesting that they may be competitive with endogenous microbiota in the midgut environment of the tsetse fly. Collectively, these data reinforce the notion for the potential of S. glossinidius to be developed into a paratransgenic platform organism.

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

    Science.gov (United States)

    Abromaitis, Stephanie

    2013-01-01

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

  16. Per capita interactions and stress tolerance drive stress-induced changes in biodiversity effects on ecosystem functions.

    Science.gov (United States)

    Baert, Jan M; Janssen, Colin R; Sabbe, Koen; De Laender, Frederik

    2016-01-01

    Environmental stress changes the relationship between biodiversity and ecosystem functions, but the underlying mechanisms are poorly understood. Because species interactions shape biodiversity-ecosystem functioning relationships, changes in per capita interactions under stress (as predicted by the stress gradient hypothesis) can be an important driver of stress-induced changes in these relationships. To test this hypothesis, we measure productivity in microalgae communities along a diversity and herbicide gradient. On the basis of additive partitioning and a mechanistic community model, we demonstrate that changes in per capita interactions do not explain effects of herbicide stress on the biodiversity-productivity relationship. Instead, assuming that the per capita interactions remain unaffected by stress, causing species densities to only change through differences in stress tolerance, suffices to predict the stress-induced changes in the biodiversity-productivity relationship and community composition. We discuss how our findings set the stage for developing theory on how environmental stress changes biodiversity effects on ecosystem functions. PMID:27534986

  17. GPR109A is a G-protein-coupled receptor for the bacterial fermentation product butyrate and functions as a tumor suppressor in colon

    OpenAIRE

    Thangaraju, Muthusamy; Cresci, Gail A.; Liu, Kebin; Ananth, Sudha; Gnanaprakasam, Jaya P.; Browning, Darren D.; Mellinger, John D.; Smith, Sylvia B.; Digby, Gregory J.; Lambert, Nevin A.; Prasad, Puttur D.; Ganapathy, Vadivel

    2009-01-01

    Short-chain fatty acids, generated in colon by bacterial fermentation of dietary fiber, protect against colorectal cancer and inflammatory bowel disease. Among these bacterial metabolites, butyrate is biologically most relevant. GPR109A is a G-protein-coupled receptor for nicotinate, but recognizes butyrate with low affinity. Millimolar concentrations of butyrate are needed to activate the receptor. Although concentrations of butyrate in colonic lumen are sufficient to activate the receptor m...

  18. Bacterial Hydrodynamics

    Science.gov (United States)

    Lauga, Eric

    2016-01-01

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

  19. Bacterial hydrodynamics

    CERN Document Server

    Lauga, Eric

    2015-01-01

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

  20. Phylogenetic organization of bacterial activity.

    Science.gov (United States)

    Morrissey, Ember M; Mau, Rebecca L; Schwartz, Egbert; Caporaso, J Gregory; Dijkstra, Paul; van Gestel, Natasja; Koch, Benjamin J; Liu, Cindy M; Hayer, Michaela; McHugh, Theresa A; Marks, Jane C; Price, Lance B; Hungate, Bruce A

    2016-09-01

    Phylogeny is an ecologically meaningful way to classify plants and animals, as closely related taxa frequently have similar ecological characteristics, functional traits and effects on ecosystem processes. For bacteria, however, phylogeny has been argued to be an unreliable indicator of an organism's ecology owing to evolutionary processes more common to microbes such as gene loss and lateral gene transfer, as well as convergent evolution. Here we use advanced stable isotope probing with (13)C and (18)O to show that evolutionary history has ecological significance for in situ bacterial activity. Phylogenetic organization in the activity of bacteria sets the stage for characterizing the functional attributes of bacterial taxonomic groups. Connecting identity with function in this way will allow scientists to begin building a mechanistic understanding of how bacterial community composition regulates critical ecosystem functions. PMID:26943624

  1. Bacterial Colony Optimization

    Directory of Open Access Journals (Sweden)

    Ben Niu

    2012-01-01

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

  2. Functional assignment of gene AAC16202.1 from Rhodobacter capsulatus SB1003: new insights into the bacterial SDR sorbitol dehydrogenases family.

    Science.gov (United States)

    Sola-Carvajal, Agustín; García-García, María Inmaculada; Sánchez-Carrón, Guiomar; García-Carmona, Francisco; Sánchez-Ferrer, Alvaro

    2012-11-01

    Short-chain dehydrogenases/reductases (SDR) constitute one of the largest enzyme superfamilies with over 60,000 non-redundant sequences in the database, many of which need a correct functional assignment. Among them, the gene AAC16202.1 (NCBI) from Rhodobacter capsulatus SB1003 has been assigned in Uniprot both as a sorbitol dehydrogenase (#D5AUY1) and, as an N-acetyl-d-mannosamine dehydrogenase (#O66112), both enzymes being of biotechnological interest. When the gene was overexpressed in Escherichia coli Rosetta (DE3)pLys, the purified enzyme was not active toward N-acetyl-d-mannosamine, whereas it was active toward d-sorbitol and d-fructose. However, the relative activities toward xylitol and l-iditol (0.45 and 6.9%, respectively) were low compared with that toward d-sorbitol. Thus, the enzyme could be considered sorbitol dehydrogenase (SDH) with very low activity toward xylitol, which could increase its biotechnological interest for determining sorbitol without the unspecific cross-determination of added xylitol in food and pharma compositions. The tetrameric enzyme (120 kDa) showed similar catalytic efficiency (2.2 × 10(3) M(-1) s(-1)) to other sorbitol dehydrogenases for d-sorbitol, with an optimum pH of 9.0 and an optimum temperature of 37 °C. The enzyme was also more thermostable than other reported SDH, ammonium sulfate being the best stabilizer in this respect, increasing the melting temperature (T(m)) up to 52.9 °C. The enzyme can also be considered as a new member of the Zn(2+) independent SDH family since no effect on activity was detected in the presence of divalent cations or chelating agents. Finally, its in silico analysis enabled the specific conserved sequence blocks that are the fingerprints of bacterial sorbitol dehydrogenases and mainly located at C-terminal of the protein, to be determined for the first time. This knowledge will facilitate future data curation of present databases and a better functional assignment of newly described

  3. Phytoplankton and Bacterial Assemblages in Ballast Water of U.S. Military Ships as a Function of Port of Origin, Voyage Time, and Ocean Exchange Practices

    Science.gov (United States)

    We characterized the physical/chemical conditions and the algal and bacterial assemblages in ballast water from 62 ballast tanks aboard 28 ships operated by the U.S. Military Sealift Command and the Maritime Administration, sampled at 9 ports on the U.S. West Coast and 4 ports on the U.S. East Coast...

  4. Remodeling bacterial polysaccharides by metabolic pathway engineering

    OpenAIRE

    Yi, Wen; Liu, Xianwei; Li, Yanhong; Li, Jianjun; Xia, Chengfeng; Zhou, Guangyan; Zhang, Wenpeng; Zhao, Wei; Chen, Xi; Wang, Peng George

    2009-01-01

    Introducing structural modifications into biomolecules represents a powerful approach to dissect their functions and roles in biological processes. Bacterial polysaccharides, despite their rich structural information and essential roles in bacterium-host interactions and bacterial virulence, have largely been unexplored for in vivo structural modifications. In this study, we demonstrate the incorporation of a panel of monosaccharide analogs into bacterial polysaccharides in a highly homogenou...

  5. Do calcium-mediated cellular signalling pathways, prostaglandin E2 (PGE2), estrogen or progesterone receptor antagonists, or bacterial endotoxins affect bovine placental function in vitro?

    Science.gov (United States)

    Weems, Y S; Randel, R D; Carstens, G E; Welsh, T H; Weems, C W

    2004-04-01

    .05). Concentrations of PGE2 in media at 4 and 8 h were lower (P or = 0.05). PGF2alpha was increased (P < or = 0.05) by RU-486 at 8h and no other treatment affected PGF2alpha at 4 or 8 h (P < or = 0.05). In conclusion, modulators of cellular calcium signalling pathways given alone do not affect bovine placental progesterone secretion at the days studied and progesterone receptor-mediated events appear to suppress placental progesterone, PGF2alpha, and PGE2 secretion in cattle. In addition, PGE2 does not appear to regulate bovine placental progesterone secretion when the corpus luteum is functional and bacterial endotoxin does not appear to affect bovine placental secretion of PGF2alpha or PGE2. PMID:15287156

  6. Bacterial disease

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    2009141 Clinical analysis and study of immunological function in syphilis patients with seroresistance.LI Jun(李军),et al.Dept Dermatol & Venereol,CAMS & PUMC,Beijing 100730,Natl Med J China,2009;89(12):813-816.

  7. A novel functional T cell hybridoma recognizes macrophage cell death induced by bacteria: a possible role for innate lymphocytes in bacterial infection.

    Science.gov (United States)

    Kubota, Koichi

    2006-06-15

    We have established a novel TCRalphabeta (TCRVbeta6)(+)CD4(-)CD8(-) T cell hybridoma designated B6HO3. When the B6HO3 cells were cocultured with bacterial-infected J774 macrophage-like cells, IFN-gamma production by B6HO3 cells was triggered through direct cell-cell contact with dying J774 cells infected with Listeria monocytogenes (LM), Shigella flexneri, or Salmonella typhimurium that expressed the type III secretion system, but not with intact J774 cells infected with heat-killed LM, nonhemolytic lysteriolysin O-deficient (Hly(-)) LM, plasmid-cured Shigella, or stationary-phase Salmonella. However, the triggering of B6HO3 cells for IFN-gamma production involved neither dying hepatoma cells infected with LM nor dying J774 cells caused by gliotoxin treatment or freeze thawing. Cycloheximide and Abs to H-2K(d), H-2D(d), Ia(d), CD1d, TCRVbeta6, and IL-12 did not inhibit the contact-dependent IFN-gamma response, indicating that this IFN-gamma response did not require de novo protein synthesis in bacterial-infected J774 cells and was TCR and IL-12 independent. Thus, in an as yet undefined way, B6HO3 hybridoma recognizes a specialized form of macrophage cell death resulting from bacterial infection and consequently produces IFN-gamma. Moreover, contact-dependent interaction of minor subsets of splenic alphabeta T cells, including NKT cells with dying LM-infected J774 and bone marrow-derived macrophage (BMM) cells, proved to provide an IFN-gamma-productive stimulus for these minor T cell populations, to which the parental T cell of the B6HO3 hybridoma appeared to belong. Unexpectedly, subsets of gammadelta T and NK cells similarly responded to dying LM-infected macrophage cells. These results propose that innate lymphocytes may possess a recognition system sensing macrophage cell "danger" resulting from bacterial infection. PMID:16751404

  8. 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.

  9. A Single-Tube, Functional Marker-Based Multiplex PCR Assay for Simultaneous Detection of Major Bacterial Blight Resistance GenesXa21, xa13 andxa5 in Rice

    Institute of Scientific and Technical Information of China (English)

    S. K. HAJIRA; M. ANILA; S. BHASKAR; V. ABHILASH; H. K. MAHADEVASWAMY; M. KOUSIK; T. DILIPKUMAR; G. HARIKA; G. REKHA; R. M. SUNDARAM; G. S. LAHA; A. YUGANDER; S. M. BALACHANDRAN; B. C. VIRAKTAMATH; K. SUJATHA; C. H. BALACHIRANJEEVI; K. PRANATHI

    2016-01-01

    In marker-assisted breeding for bacterial blight (BB) resistance in rice, three major resistance genes, viz.,Xa21, xa13andxa5,are routinely deployed either singly or in combinations. As efficient and functional markers are yet to be developed forxa13 andxa5,we have developed simple PCR-based functional markers for both the genes.Forxa13,we designed a functional PCR-based marker, xa13-prom targeting the InDel polymorphism in the promoter of candidate geneOs8N3 located on chromosome 8 of rice. With respect toxa5, a multiplex-PCR based functional marker system, named xa5FM, consisting of two sets of primer pairs targeting the 2-bp functional nucleotide polymorphism in the exon II of the geneTFIIAɤ5 (candidate forxa5), has been developed. Both xa13-prom and xa5FM can differentiate the resistant and susceptible alleles forxa13 andxa5, respectively, in a co-dominant fashion. Using these two functional markers along with the already reported functional PCR-based marker forXa21 (pTA248),we designed a single-tube multiplex PCR based assay for simultaneous detection of all the three major resistance genes and demonstrated the utility of the multiplex marker system in a segregating population.

  10. [Small intestine bacterial overgrowth].

    Science.gov (United States)

    Leung Ki, E L; Roduit, J; Delarive, J; Guyot, J; Michetti, P; Dorta, G

    2010-01-27

    Small intestine bacterial overgrowth (SIBO) is a condition characterised by nutrient malabsorption and excessive bacteria in the small intestine. It typically presents with diarrhea, flatulence and a syndrome of malabsorption (steatorrhea, macrocytic anemia). However, it may be asymptomatic in the eldery. A high index of suspicion is necessary in order to differentiate SIBO from other similar presenting disorders such as coeliac disease, lactose intolerance or the irritable bowel syndrome. A search for predisposing factor is thus necessary. These factors may be anatomical (stenosis, blind loop), or functional (intestinal hypomotility, achlorydria). The hydrogen breath test is the most frequently used diagnostic test although it lacks standardisation. The treatment of SIBO consists of eliminating predisposing factors and broad-spectrum antibiotic therapy. PMID:20214190

  11. Bacterial proteases and virulence

    DEFF Research Database (Denmark)

    Frees, Dorte; Brøndsted, Lone; Ingmer, Hanne

    2013-01-01

    Bacterial pathogens rely on proteolysis for variety of purposes during the infection process. In the cytosol, the main proteolytic players are the conserved Clp and Lon proteases that directly contribute to virulence through the timely degradation of virulence regulators and indirectly by providing...... tolerance to adverse conditions such as those experienced in the host. In the membrane, HtrA performs similar functions whereas the extracellular proteases, in close contact with host components, pave the way for spreading infections by degrading host matrix components or interfering with host cell...... 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...

  12. Bacterial melanin promotes recovery after sciatic nerve injury in rats

    OpenAIRE

    Gevorkyan, Olga. V.; Meliksetyan, Irina B.; Petrosyan, Tigran R.; Hovsepyan, Anichka S.

    2015-01-01

    Bacterial melanin, obtained from the mutant strain of Bacillus Thuringiensis, has been shown to promote recovery after central nervous system injury. It is hypothesized, in this study, that bacterial melanin can promote structural and functional recovery after peripheral nerve injury. Rats subjected to sciatic nerve transection were intramuscularly administered bacterial melanin. The sciatic nerve transected rats that did not receive intramuscular administration of bacterial melanin served as...

  13. Can the Results of Biodiversity-Ecosystem Productivity Studies Be Translated to Bioenergy Production?

    Directory of Open Access Journals (Sweden)

    Timothy L Dickson

    Full Text Available Biodiversity experiments show that increases in plant diversity can lead to greater biomass production, and some researchers suggest that high diversity plantings should be used for bioenergy production. However, many methods used in past biodiversity experiments are impractical for bioenergy plantings. For example, biodiversity experiments often use intensive management such as hand weeding to maintain low diversity plantings and exclude unplanted species, but this would not be done for bioenergy plantings. Also, biodiversity experiments generally use high seeding densities that would be too expensive for bioenergy plantings. Here we report the effects of biodiversity on biomass production from two studies of more realistic bioenergy crop plantings in southern Michigan, USA. One study involved comparing production between switchgrass (Panicum virgatum monocultures and species-rich prairie plantings on private farm fields that were managed similarly to bioenergy plantings. The other study was an experiment where switchgrass was planted in monoculture and in combination with increasingly species-rich native prairie mixtures. Overall, we found that bioenergy plantings with higher species richness did not produce more biomass than switchgrass monocultures. The lack of a positive relationship between planted species richness and production in our studies may be due to several factors. Non-planted species (weeds were not removed from our studies and these non-planted species may have competed with planted species and also prevented realized species richness from equaling planted species richness. Also, we found that low seeding density of individual species limited the biomass production of these individual species. Production in future bioenergy plantings with high species richness may be increased by using a high density of inexpensive seed from switchgrass and other highly productive species, and future efforts to translate the results of biodiversity experiments to bioenergy plantings should consider the role of seeding density.

  14. Opportunities and challenges for private sector entrepreneurship and investment in biodiversity, ecosystem services and nature conservation

    NARCIS (Netherlands)

    Lambooy, T.E.; Levashova, Y.

    2011-01-01

    Private companies and investors can profit from the enhancement of nature in general and from specific investments allocated to improve biodiversity and ecosystem services (BES). The question is: What is the incentive, from a private sector point of view, to invest in nature, and what are the barrie

  15. Can the Results of Biodiversity-Ecosystem Productivity Studies Be Translated to Bioenergy Production?

    Science.gov (United States)

    Dickson, Timothy L; Gross, Katherine L

    2015-01-01

    Biodiversity experiments show that increases in plant diversity can lead to greater biomass production, and some researchers suggest that high diversity plantings should be used for bioenergy production. However, many methods used in past biodiversity experiments are impractical for bioenergy plantings. For example, biodiversity experiments often use intensive management such as hand weeding to maintain low diversity plantings and exclude unplanted species, but this would not be done for bioenergy plantings. Also, biodiversity experiments generally use high seeding densities that would be too expensive for bioenergy plantings. Here we report the effects of biodiversity on biomass production from two studies of more realistic bioenergy crop plantings in southern Michigan, USA. One study involved comparing production between switchgrass (Panicum virgatum) monocultures and species-rich prairie plantings on private farm fields that were managed similarly to bioenergy plantings. The other study was an experiment where switchgrass was planted in monoculture and in combination with increasingly species-rich native prairie mixtures. Overall, we found that bioenergy plantings with higher species richness did not produce more biomass than switchgrass monocultures. The lack of a positive relationship between planted species richness and production in our studies may be due to several factors. Non-planted species (weeds) were not removed from our studies and these non-planted species may have competed with planted species and also prevented realized species richness from equaling planted species richness. Also, we found that low seeding density of individual species limited the biomass production of these individual species. Production in future bioenergy plantings with high species richness may be increased by using a high density of inexpensive seed from switchgrass and other highly productive species, and future efforts to translate the results of biodiversity experiments to bioenergy plantings should consider the role of seeding density.

  16. Structural biology of bacterial RNA polymerase.

    Science.gov (United States)

    Murakami, Katsuhiko S

    2015-05-11

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

  17. Structural Biology of Bacterial RNA Polymerase

    Directory of Open Access Journals (Sweden)

    Katsuhiko S. Murakami

    2015-05-01

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

  18. Functional role of pyruvate kinase from Lactobacillus bulgaricus in acid tolerance and identification of its transcription factor by bacterial one-hybrid.

    Science.gov (United States)

    Zhai, Zhengyuan; An, Haoran; Wang, Guohong; Luo, Yunbo; Hao, Yanling

    2015-11-19

    Lactobacillus delbrueckii subsp. bulgaricus develops acid tolerance response when subjected to acid stress conditions, such as the induction of enzymes associated with carbohydrate metabolism. In this study, pyk gene encoding pyruvate kinase was over-expressed in heterologous host Lactococcus lactis NZ9000, and SDS-PAGE analysis revealed the successful expression of this gene in NZ9000. The survival rate of Pyk-overproducing strain was 45-fold higher than the control under acid stress condition (pH 4.0). In order to determine the transcription factor (TF) which regulates the expression of pyk by bacterial one-hybrid, we constructed a TF library including 65 TFs of L. bulgaricus. Western blotting indicated that TFs in this library could be successfully expressed in host strains. Subsequently, the promoter of pfk-pyk operon in L. bulgaricus was identified by 5'-RACE PCR. The bait plasmid pH3U3-p01 carrying the deletion fragment of pfk-pyk promoter captured catabolite control protein A (CcpA) which could regulate the expression of pyk by binding to a putative catabolite-responsive element (5'-TGTAAGCCCTAACA-3') upstream the -35 region. Real-time qPCR analysis revealed the transcription of pyk was positively regulated by CcpA. This is the first report about identifying the TF of pyk in L. bulgaricus, which will provide new insight into the regulatory network.

  19. 群体感应抑制剂对海洋生态功能菌生物膜形成的影响%The influence of quorum sensing inhibitors against marine functional bacterial biofilm formation

    Institute of Scientific and Technical Information of China (English)

    翟有朋; 董昆明; 周惠茹; 姜芸; 丁碧婷; 缪莉

    2013-01-01

    [目的]研究天然群体感应抑制剂(Quorum sensing inhibitors,QSI)分子对海洋生态功能菌生物膜形成的影响.[方法]以对污损生物幼虫附着具有诱导作用的海洋细菌为目标菌,通过在其生物膜的形成过程中添加天然群体感应抑制剂,研究其对目标菌成膜细菌数和浮游细菌数、生物膜形态以及生物膜表面胞外多糖含量的影响.[结果]呋喃酮和吡啶在50 mg/L时,对8株目标菌的成膜有显著的抑制作用,抑制率在80%左右,吲哚、青霉烷酸和香豆素在较高浓度800 mg/L才有比较好的抑制活性.生长抑制实验结果显示,同等浓度下,QSI分子对目标菌成膜的抑制活性明显高于其对浮游细菌生长的抑制活性.结果表明,QSI分子主要通过干扰目标菌群体感应系统以抑制生物膜的形成.[结论]研究证实QSI分子在海洋菌生物膜形成过程中具有一定的调控作用.通过添加QSI可能能够间接抑制由生物膜诱导的污损生物附着,从而以新的角度研制新型抗污损物质.%[Objective] To study the influence of natural quorum sensing inhibitors (QSI)against marine functional bacterial biofilm formation.[Methods] Some marine bacterial strains,which could induce the larval settlement of fouling organism,were regarded as target bacteria.Through adding natural quorum sensing inhibitors into the target bacterial cultures during their biofilm formation process,the influence of QSI on the biofilm and planktonic bacteria quantity,biofilm morphology as well as the surface extracellular polysaccharide were studied.[Results] Furanone and pyridine significantly inhibited the biofilm formation of all target bacterial strains at the concentration of 50 mg/L,with the inhibition rate of about 80%.However,indole,penicillanic acid and coumarin exhibited good inhibitory activity only at higher concentrations of 800 mg/L.The results of growth inhibition experiment showed that the inhibitory activity of QSI

  20. Impact of long-term N, P, K, and NPK fertilization on the composition and potential functions of the bacterial community in grassland soil

    NARCIS (Netherlands)

    Pan, Y.; Cassman, N.; Hollander, de M.; Mendes, L.W.; Korevaar, H.; Geerts, R.H.E.M.; Veen, van J.A.; Kuramae, E.E.

    2014-01-01

    Soil abiotic and biotic interactions govern important ecosystem processes. However, the mechanisms behind these interactions are complex, and the links between specific environmental factors, microbial community structures, and functions are not well understood. Here, we applied DNA shotgun metageno

  1. Function of an anti-lipopolysaccharide factor (ALF) isoform isolated from the hemocytes of the giant freshwater prawn Macrobrachium rosenbergii in protecting against bacterial infection.

    Science.gov (United States)

    Liu, Chia-Chen; Chung, Chien-Pang; Lin, Chang-Yi; Sung, Hung-Hung

    2014-02-01

    In this study, a 780-bp full-length cDNA encoding Macrobrachium rosenbergii anti-lipopolysaccharide factor (MrALF) from hemocytes was cloned and identified. The ALF isoform exhibited immune activities, and its concentration in hemolymph was determined. An in vivo expression study showed that the ALF mRNA level of hemocytes could be induced by lipopolysaccharides (LPSs) in an exposure time-dependent manner. Purified recombinant MrALF (rMrALF) expressed in the yeast Pichia pastoris SMD1168 eukaryotic protein expression system demonstrated antibacterial activity against the Gram-negative prawn pathogen Aeromonas hydrophila (minimum inhibitory concentration (MIC)=0.806μM, minimum bactericidal concentration (MBC)=1.606μM) but not the Gram-positive pathogen Lactococcus garvieae exposed to 25.696μM of rALF. However, rMrALF can bind to Gram-negative and -positive bacteria. An in vivo expression study demonstrated that the ALF concentrations in prawn hemocytes and plasma were 0.176μM and 0.168μM, respectively; following LPS treatment for 6h, the corresponding concentrations were 0.133μM in hemocytes and 0.272μM in plasma. Furthermore, the percentage of hemocytes phagocytosing bacteria cells was higher in hemoyctes previously treated with MrALF than those treated with sterile medium. These results suggest that in the innate immune response of M. rosenbergii, the MrALF from hemocytes may play an opsonin during a bacterial invasion.

  2. Tobacco use increases susceptibility to bacterial infection

    Directory of Open Access Journals (Sweden)

    Demuth Donald R

    2008-12-01

    Full Text Available Abstract Active smokers and those exposed to secondhand smoke are at increased risk of bacterial infection. Tobacco smoke exposure increases susceptibility to respiratory tract infections, including tuberculosis, pneumonia and Legionnaires disease; bacterial vaginosis and sexually transmitted diseases, such as chlamydia and gonorrhoea; Helicobacter pylori infection; periodontitis; meningitis; otitis media; and post-surgical and nosocomial infections. Tobacco smoke compromises the anti-bacterial function of leukocytes, including neutrophils, monocytes, T cells and B cells, providing a mechanistic explanation for increased infection risk. Further epidemiological, clinical and mechanistic research into this important area is warranted.

  3. Bacterial melanin promotes recovery after sciatic nerve injury in rats

    Institute of Scientific and Technical Information of China (English)

    Olga V Gevorkyan; Irina B Meliksetyan; Tigran R Petrosyan; Anichka S Hovsepyan

    2015-01-01

    Bacterial melanin, obtained from the mutant strain ofBacillus Thuringiensis, has been shown to promote recovery after central nervous system injury. It is hypothesized, in this study, that bacterial melanin can promote structural and functional recovery after peripheral nerve injury. Rats subjected to sciatic nerve transection were intramuscularly administered bacterial melanin. The sciatic nerve transected rats that did not receive intramuscular administration of bacterial melanin served as controls. Behavior tests showed that compared to control rats, the time taken for instrumental conditioned relfex recovery was signiifcantly shorter and the ability to keep the balance on the rotating bar was signiifcantly better in bacterial melanin-treated rats. Histomor-phological tests showed that bacterial melanin promoted axon regeneration after sciatic nerve injury. These ifndings suggest that bacterial melanin exhibits neuroprotective effects on injured sciatic nerve, contributes to limb motor function recovery, and therefore can be used for rehabil-itation treatment of peripheral nerve injury.

  4. Rho-modifying bacterial protein toxins.

    Science.gov (United States)

    Aktories, Klaus

    2015-12-01

    Rho proteins are targets of numerous bacterial protein toxins, which manipulate the GTP-binding proteins by covalent modifications, including ADP ribosylation, glycosylation, adenylylation, proteolytic cleavage and deamidation. Bacterial toxins are important virulence factors but are also potent and efficient pharmacological tools to study the physiological functions of their eukaryotic targets. Recent studies indicate that amazing variations exist in the molecular mechanisms by which toxins attack Rho proteins, which are discussed here.

  5. In silico analysis of bacterial arsenic islands reveals remarkable synteny and functional relatedness between arsenate and phosphate

    DEFF Research Database (Denmark)

    Li, Hang; Li, Mingshun; Huang, Yinyan;

    2013-01-01

    in the Proteobacteria, they are absent in most other organisms examined, inferring different regulatory mechanism(s) yet to be discovered. Phylogenetic analysis of the aio, ars, pst, and phn genes revealed evidence of both vertical inheritance and horizontal gene transfer (HGT). It is therefore likely the arsenic...... islands did not evolve as a whole unit but formed independently by acquisition of functionally related genes and operons in respective strains. Considering gene synteny and structural analogies between arsenate and phosphate, we presumed that these genes function together in helping these microbes...

  6. Bacterial chromosome organization and segregation.

    Science.gov (United States)

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

    2015-01-01

    If fully stretched out, a typical bacterial chromosome would be nearly 1 mm long, approximately 1,000 times the length of a cell. Not only must cells massively compact their genetic material, but they must also organize their DNA in a manner that is compatible with a range of cellular processes, including DNA replication, DNA repair, homologous recombination, and horizontal gene transfer. Recent work, driven in part by technological advances, has begun to reveal the general principles of chromosome organization in bacteria. Here, drawing on studies of many different organisms, we review the emerging picture of how bacterial chromosomes are structured at multiple length scales, highlighting the functions of various DNA-binding proteins and the impact of physical forces. Additionally, we discuss the spatial dynamics of chromosomes, particularly during their segregation to daughter cells. Although there has been tremendous progress, we also highlight gaps that remain in understanding chromosome organization and segregation. PMID:26566111

  7. Species richness and biomass explain spatial turnover in ecosystem functioning across tropical and temperate ecosystems.

    Science.gov (United States)

    Barnes, Andrew D; Weigelt, Patrick; Jochum, Malte; Ott, David; Hodapp, Dorothee; Haneda, Noor Farikhah; Brose, Ulrich

    2016-05-19

    Predicting ecosystem functioning at large spatial scales rests on our ability to scale up from local plots to landscapes, but this is highly contingent on our understanding of how functioning varies through space. Such an understanding has been hampered by a strong experimental focus of biodiversity-ecosystem functioning research restricted to small spatial scales. To address this limitation, we investigate the drivers of spatial variation in multitrophic energy flux-a measure of ecosystem functioning in complex communities-at the landscape scale. We use a structural equation modelling framework based on distance matrices to test how spatial and environmental distances drive variation in community energy flux via four mechanisms: species composition, species richness, niche complementarity and biomass. We found that in both a tropical and a temperate study region, geographical and environmental distance indirectly influence species richness and biomass, with clear evidence that these are the dominant mechanisms explaining variability in community energy flux over spatial and environmental gradients. Our results reveal that species composition and trait variability may become redundant in predicting ecosystem functioning at the landscape scale. Instead, we demonstrate that species richness and total biomass may best predict rates of ecosystem functioning at larger spatial scales. PMID:27114580

  8. Comprehensive phylogenetic analysis of bacterial reverse transcriptases.

    Directory of Open Access Journals (Sweden)

    Nicolás Toro

    Full Text Available Much less is known about reverse transcriptases (RTs in prokaryotes than in eukaryotes, with most prokaryotic enzymes still uncharacterized. Two surveys involving BLAST searches for RT genes in prokaryotic genomes revealed the presence of large numbers of diverse, uncharacterized RTs and RT-like sequences. Here, using consistent annotation across all sequenced bacterial species from GenBank and other sources via RAST, available from the PATRIC (Pathogenic Resource Integration Center platform, we have compiled the data for currently annotated reverse transcriptases from completely sequenced bacterial genomes. RT sequences are broadly distributed across bacterial phyla, but green sulfur bacteria and cyanobacteria have the highest levels of RT sequence diversity (≤85% identity per genome. By contrast, phylum Actinobacteria, for which a large number of genomes have been sequenced, was found to have a low RT sequence diversity. Phylogenetic analyses revealed that bacterial RTs could be classified into 17 main groups: group II introns, retrons/retron-like RTs, diversity-generating retroelements (DGRs, Abi-like RTs, CRISPR-Cas-associated RTs, group II-like RTs (G2L, and 11 other groups of RTs of unknown function. Proteobacteria had the highest potential functional diversity, as they possessed most of the RT groups. Group II introns and DGRs were the most widely distributed RTs in bacterial phyla. Our results provide insights into bacterial RT phylogeny and the basis for an update of annotation systems based on sequence/domain homology.

  9. 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...

  10. Structural and functional characterization of cleavage and inactivation of human serine protease inhibitors by the bacterial SPATE protease EspPα from enterohemorrhagic E. coli.

    Directory of Open Access Journals (Sweden)

    André Weiss

    Full Text Available EspPα and EspI are serine protease autotransporters found in enterohemorrhagic Escherichia coli. They both belong to the SPATE autotransporter family and are believed to contribute to pathogenicity via proteolytic cleavage and inactivation of different key host proteins during infection. Here, we describe the specific cleavage and functional inactivation of serine protease inhibitors (serpins by EspPα and compare this activity with the related SPATE EspI. Serpins are structurally related proteins that regulate vital protease cascades, such as blood coagulation and inflammatory host response. For the rapid determination of serpin cleavage sites, we applied direct MALDI-TOF-MS or ESI-FTMS analysis of coincubations of serpins and SPATE proteases and confirmed observed cleavage positions using in-gel-digest of SDS-PAGE-separated degradation products. Activities of both serpin and SPATE protease were assessed in a newly developed photometrical assay using chromogenic peptide substrates. EspPα cleaved the serpins α1-protease inhibitor (α1-PI, α1-antichymotrypsin, angiotensinogen, and α2-antiplasmin. Serpin cleavage led to loss of inhibitory function as demonstrated for α1-PI while EspPα activity was not affected. Notably, EspPα showed pronounced specificity and cleaved procoagulatory serpins such as α2-antiplasmin while the anticoagulatory antithrombin III was not affected. Together with recently published research, this underlines the interference of EspPα with hemostasis or inflammatory responses during infection, while the observed interaction of EspI with serpins is likely to be not physiologically relevant. EspPα-mediated serpin cleavage occurred always in flexible loops, indicating that this structural motif might be required for substrate recognition.

  11. Plant species and functional group combinations affect green roof ecosystem functions.

    Directory of Open Access Journals (Sweden)

    Jeremy Lundholm

    facilitation as mechanisms governing biodiversity-ecosystem functioning relationships in green roof ecosystems.

  12. Plant Species and Functional Group Combinations Affect Green Roof Ecosystem Functions

    Science.gov (United States)

    Lundholm, Jeremy; MacIvor, J. Scott; MacDougall, Zachary; Ranalli, Melissa

    2010-01-01

    governing biodiversity-ecosystem functioning relationships in green roof ecosystems. PMID:20300196

  13. Analysis of the rhizosphere bacterial community and function diversity in cherry orchard of Dalian region%大连地区樱桃园根际土壤细菌群落功能多样性分析

    Institute of Scientific and Technical Information of China (English)

    吕德国; 侯爽; 秦嗣军; 刘灵芝; 马怀宇; 刘国成

    2011-01-01

    The microbial metabolic activity and functional diversities of sweet cherry orchards with clay soil,Sandy loam,Coarse soil in Dalian region were analyzed under Biolog Ecoplate method.The results showed that the amounts of soil microbe,microbial metabolic activity,Substrate richness(S),Shannon's diversity index(H)and Evenness index(J)were clay soil〉Sandy loam〉Coarse soil,and the carbon sources with highest utilization efficiency by soil microbes was carbohydrate in three soil texture.Microbes in the clay soil utilized phenolic compounds with higher efficiency and microbes in sandy loam and coarse soil utilized amines with higher efficiency.The results indicate that soil texture influences soil microbial functional diversity in cherry orchard,and the highest in clay soil,followed by in sandy loam and in coarse soil.But no significant difference was found in microbial metabolic activity,bacterial efficiency of carbon sources,bacterial variety of metabolic activity of three kinds ofsoil texture.Thus,the major factor responsible for bacterial community function diversity in cherry orchards is soil texture.%利用Biolog生态微平板法,分析了大连地区黏土、沙壤土、粗骨土3种不同质地土壤樱桃园微生物代谢活性及其功能多样性。结果表明,土壤微生物的数量、群落代谢活性、底物碳源利用数(S)、多样性指数(H)及均匀度指数(J)均为黏土〉沙壤土〉粗骨土,3种质地的土壤细菌碳源均以利用碳水化合物为主,而对芳香化合物和胺类化合物的利用喜好不同,其中黏土对芳香化合物的利用率相对较高,沙壤土和粗骨土对胺类化合物的利用率相对较高。说明,土壤质地可影响樱桃园的土壤微生物功能多样性,其中以黏土最丰富,沙壤土次之,粗骨土最差。3种土壤质地樱桃园的表土与根际土之间的土壤微生物群落代谢活性、土壤细菌碳源利用情况以及土壤细菌代谢功

  14. Bacterial Wound Culture

    Science.gov (United States)

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

  15. 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.

  16. 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...

  17. 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.

  18. Dimer-dimer interaction of the bacterial selenocysteine synthase SelA promotes functional active-site formation and catalytic specificity.

    Science.gov (United States)

    Itoh, Yuzuru; Bröcker, Markus J; Sekine, Shun-ichi; Söll, Dieter; Yokoyama, Shigeyuki

    2014-04-17

    The 21st amino acid, selenocysteine (Sec), is incorporated translationally into proteins and is synthesized on its specific tRNA (tRNA(Sec)). In Bacteria, the selenocysteine synthase SelA converts Ser-tRNA(Sec), formed by seryl-tRNA synthetase, to Sec-tRNA(Sec). SelA, a member of the fold-type-I pyridoxal 5'-phosphate-dependent enzyme superfamily, has an exceptional homodecameric quaternary structure with a molecular mass of about 500kDa. Our previously determined crystal structures of Aquifex aeolicus SelA complexed with tRNA(Sec) revealed that the ring-shaped decamer is composed of pentamerized SelA dimers, with two SelA dimers arranged to collaboratively interact with one Ser-tRNA(Sec). The SelA catalytic site is close to the dimer-dimer interface, but the significance of the dimer pentamerization in the catalytic site formation remained elusive. In the present study, we examined the quaternary interactions and demonstrated their importance for SelA activity by systematic mutagenesis. Furthermore, we determined the crystal structures of "depentamerized" SelA variants with mutations at the dimer-dimer interface that prevent pentamerization. These dimeric SelA variants formed a distorted and inactivated catalytic site and confirmed that the pentamer interactions are essential for productive catalytic site formation. Intriguingly, the conformation of the non-functional active site of dimeric SelA shares structural features with other fold-type-I pyridoxal 5'-phosphate-dependent enzymes with native dimer or tetramer (dimer-of-dimers) quaternary structures. PMID:24456689

  19. Application of Sub-Micrometer Vibrations to Mitigate Bacterial Adhesion

    OpenAIRE

    Will R. Paces; Holmes, Hal R.; Eli Vlaisavljevich; Snyder, Katherine L.; Ee Lim Tan; Rajachar, Rupak M.; Keat Ghee Ong

    2014-01-01

    As a prominent concern regarding implantable devices, eliminating the threat of opportunistic bacterial infection represents a significant benefit to both patient health and device function. Current treatment options focus on chemical approaches to negate bacterial adhesion, however, these methods are in some ways limited. The scope of this study was to assess the efficacy of a novel means of modulating bacterial adhesion through the application of vibrations using magnetoelastic materials. M...

  20. A genomic island present along the bacterial chromosome of the Parachlamydiaceae UWE25, an obligate amoebal endosymbiont, encodes a potentially functional F-like conjugative DNA transfer system

    Directory of Open Access Journals (Sweden)

    Guy Lionel

    2004-12-01

    Full Text Available Abstract Background The genome of Protochlamydia amoebophila UWE25, a Parachlamydia-related endosymbiont of free-living amoebae, was recently published, providing the opportunity to search for genomic islands (GIs. Results On the residual cumulative G+C content curve, a G+C-rich 19-kb region was observed. This sequence is part of a 100-kb chromosome region, containing 100 highly co-oriented ORFs, flanked by two 17-bp direct repeats. Two identical gly-tRNA genes in tandem are present at the proximal end of this genetic element. Several mobility genes encoding transposases and bacteriophage-related proteins are located within this chromosome region. Thus, this region largely fulfills the criteria of GIs. The G+C content analysis shows that several modules compose this GI. Surprisingly, one of them encodes all genes essential for F-like conjugative DNA transfer (traF, traG, traH, traN, traU, traW, and trbC, involved in sex pilus retraction and mating pair stabilization, strongly suggesting that, similarly to the other F-like operons, the parachlamydial tra unit is devoted to DNA transfer. A close relatedness of this tra unit to F-like tra operons involved in conjugative transfer is confirmed by phylogenetic analyses performed on concatenated genes and gene order conservation. These analyses and that of gly-tRNA distribution in 140 GIs suggest a proteobacterial origin of the parachlamydial tra unit. Conclusions A GI of the UWE25 chromosome encodes a potentially functional F-like DNA conjugative system. This is the first hint of a putative conjugative system in chlamydiae. Conjugation most probably occurs within free-living amoebae, that may contain hundreds of Parachlamydia bacteria tightly packed in vacuoles. Such a conjugative system might be involved in DNA transfer between internalized bacteria. Since this system is absent from the sequenced genomes of Chlamydiaceae, we hypothesize that it was acquired after the divergence between

  1. Nest Material Shapes Eggs Bacterial Environment

    Science.gov (United States)

    Ruiz-Castellano, Cristina; Tomás, Gustavo; Ruiz-Rodríguez, Magdalena; Martín-Gálvez, David; Soler, Juan José

    2016-01-01

    Selective pressures imposed by pathogenic microorganisms to embryos have selected in hosts for a battery of antimicrobial lines of defenses that includes physical and chemical barriers. Due to the antimicrobial properties of volatile compounds of green plants and of chemicals of feather degrading bacteria, the use of aromatic plants and feathers for nest building has been suggested as one of these barriers. However, experimental evidence suggesting such effects is scarce in the literature. During two consecutive years, we explored experimentally the effects of these nest materials on loads of different groups of bacteria (mesophilic bacteria, Enterobacteriaceae, Staphylococcus and Enterococcus) of eggshells in nests of spotless starlings (Sturnus unicolor) at the beginning and at the end of the incubation period. This was also explored in artificial nests without incubation activity. We also experimentally increased bacterial density of eggs in natural and artificial nests and explored the effects of nest lining treatments on eggshell bacterial load. Support for the hypothetical antimicrobial function of nest materials was mainly detected for the year and location with larger average values of eggshell bacterial density. The beneficial effects of feathers and plants were more easily detected in artificial nests with no incubation activity, suggesting an active role of incubation against bacterial colonization of eggshells. Pigmented and unpigmented feathers reduced eggshell bacterial load in starling nests and artificial nest boxes. Results from artificial nests allowed us to discuss and discard alternative scenarios explaining the detected association, particularly those related to the possible sexual role of feathers and aromatic plants in starling nests. All these results considered together confirm the antimicrobial functionality mainly of feathers but also of plants used as nest materials, and highlight the importance of temporally and geographically

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

    Science.gov (United States)

    Kerfeld, Cheryl A; Erbilgin, Onur

    2015-01-01

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

  3. 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.

  4. Autoproteolytic Activation of Bacterial Toxins

    Directory of Open Access Journals (Sweden)

    Aimee Shen

    2010-05-01

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

  5. Bacterial ice crystal controlling proteins.

    Science.gov (United States)

    Lorv, Janet S H; Rose, David R; Glick, Bernard R

    2014-01-01

    Across the world, many ice active bacteria utilize ice crystal controlling proteins for aid in freezing tolerance at subzero temperatures. Ice crystal controlling proteins include both antifreeze and ice nucleation proteins. Antifreeze proteins minimize freezing damage by inhibiting growth of large ice crystals, while ice nucleation proteins induce formation of embryonic ice crystals. Although both protein classes have differing functions, these proteins use the same ice binding mechanisms. Rather than direct binding, it is probable that these protein classes create an ice surface prior to ice crystal surface adsorption. Function is differentiated by molecular size of the protein. This paper reviews the similar and different aspects of bacterial antifreeze and ice nucleation proteins, the role of these proteins in freezing tolerance, prevalence of these proteins in psychrophiles, and current mechanisms of protein-ice interactions. PMID:24579057

  6. Developmental Changes in Bacterial Colonization and Digestive Function in Ileum of Lambs%山羊羔羊回肠细菌群落定植与消化功能的发育性变化

    Institute of Scientific and Technical Information of China (English)

    李小鹏; 焦金真; 颜琼娴; 谭支良

    2016-01-01

    本试验旨在研究山羊羔羊回肠细菌群落定植与消化功能的发育性变化。选用44只湘东黑山羊羔羊,随机选择4只在1、7、14日龄(非反刍阶段),28、42(过渡阶段)和56、70日龄(反刍阶段)屠宰取样。采集回肠食糜测定乙酸含量,淀粉酶、纤维素酶和木聚糖酶活性,总细菌数量和部分功能性细菌(普雷氏菌属、甲烷菌、纤维降解菌和淀粉降解菌)占总细菌百分比。结果表明:14日龄开始在回肠食糜中检出乙酸,日龄增长显著提高了其含量( P<0.05),56~70日龄增长最快;日龄增长显著或极显著提高了纤维素酶和木聚糖酶活性( P<0.05或P<0.01);日龄增长极显著提高了总细菌数量和甲烷菌(最早检出在7日龄)、普雷氏杆菌和栖瘤胃普雷氏菌占总细菌百分比( P<0.01);纤维降解菌(琥珀酸丝状杆菌和黄色瘤胃球菌)和淀粉降解菌(嗜淀粉瘤胃杆菌)均在28日龄开始检出。综合得出,山羊羔羊回肠纤维降解消化能力是在28日龄建立之后逐渐完善的,7日龄即可检出大量甲烷菌定植,之后逐渐趋于稳定。%The objective of this study was to investigate the developmental changes in bacterial colonization and digestive function in ileum of lambs.Forty four Xiangdong black lambs were used in this trial, and 4 of them were randomly slaughtered at 1, 7 and 14 days of age ( nonrumination period) , 28 and 42 days of age ( transi-tion period) , and 56 and 70 days of age ( rumination period) , respectively.The ileal chymus was sampled to determine acetate content, activities of amylase, cellulase and xylanase, as well as general bacteria number and selected functional bacterial species ( Prevotella, methanogen, and cellulolytic and amylolytic bacteria) .The results showed as follows:acetate could be detected in ileal chymus of lambs since at 25 days of age, and the content was significantly

  7. [Chemotherapy of severe bacterial infections in pediatrics].

    Science.gov (United States)

    Guggenbichler, J P

    1983-01-01

    Bacterial infections are frequent events in premature and newborn infants. The reason is a defective specific and nonspecific defence of bacterial organisms. Some immunoglobulins like IgM and IgA including secretory IgA are absent. Premature infants also show a decreased level of IgG. Cellular immunity is anatomically intact but functionally defective. A number of complement factors are lacking, the activation of the alternative pathway is impaired. Newborn infants with perinatal problems like asphyxia or difficult delivery, show defects of leucocyte function like decreased deformability, defective chemotaxis and defective killing of ingested bacteria. Certain diseases, like hypoxia and malformations of immature organ functions in this age group (decreased acid production in the stomach), facilitate bacterial colonization of surface epithelia and the invasion of tissues. Consequences of these pathogenetic mechanisms are an unimpaired propagation of bacterial organisms into the blood and meninges without localization of the infecting organisms at the entry site. Bacterial meningitis is not considered a separate disease entity but a complication of bacteremia and sepsis. Clinical symptoms are nonspecific at the onset of the infection. Fever is frequently absent; decreased appetite, vomiting, a bloated abdomen, diarrhea, tachycardia, tachypnea are early signs of a bacterial infection, a grey mottled appearance, cyanosis, jaundice, petechiae, apneic spells, seizure activity and a metabolic acidosis are symptoms of advanced infection. Successful treatment at this stage is often not possible. Every sign of a decreased well being of a newborn of premature infant warrants laboratory and bacteriologic work up for septicemia.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:6316669

  8. Seizures Complicating Bacterial Meningitis

    Directory of Open Access Journals (Sweden)

    J Gordon Millichap

    2004-09-01

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

  9. Bacterial extracellular lignin peroxidase

    Science.gov (United States)

    Crawford, Donald L.; Ramachandra, Muralidhara

    1993-01-01

    A newly discovered lignin peroxidase enzyme is provided. The enzyme is obtained from a bacterial source and is capable of degrading the lignin portion of lignocellulose in the presence of hydrogen peroxide. The enzyme is extracellular, oxidative, inducible by lignin, larch wood xylan, or related substrates and capable of attacking certain lignin substructure chemical bonds that are not degradable by fungal lignin peroxidases.

  10. Bacterial Skin Infections

    Science.gov (United States)

    ... or scraped, the injury should be washed with soap and water and covered with a sterile bandage. Petrolatum may be applied to open areas to keep the tissue moist and to try to prevent bacterial invasion. Doctors recommend that people do not use ...

  11. 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...

  12. Bacterial microflora of nectarines

    Science.gov (United States)

    Microflora of fruit surfaces has been the best source of antagonists against fungi causing postharvest decays of fruit. However, there is little information on microflora colonizing surfaces of fruits other than grapes, apples, and citrus fruit. We characterized bacterial microflora on nectarine f...

  13. Modeling intraocular bacterial infections.

    Science.gov (United States)

    Astley, Roger A; Coburn, Phillip S; Parkunan, Salai Madhumathi; Callegan, Michelle C

    2016-09-01

    Bacterial endophthalmitis is an infection and inflammation of the posterior segment of the eye which can result in significant loss of visual acuity. Even with prompt antibiotic, anti-inflammatory and surgical intervention, vision and even the eye itself may be lost. For the past century, experimental animal models have been used to examine various aspects of the pathogenesis and pathophysiology of bacterial endophthalmitis, to further the development of anti-inflammatory treatment strategies, and to evaluate the pharmacokinetics and efficacies of antibiotics. Experimental models allow independent control of many parameters of infection and facilitate systematic examination of infection outcomes. While no single animal model perfectly reproduces the human pathology of bacterial endophthalmitis, investigators have successfully used these models to understand the infectious process and the host response, and have provided new information regarding therapeutic options for the treatment of bacterial endophthalmitis. This review highlights experimental animal models of endophthalmitis and correlates this information with the clinical setting. The goal is to identify knowledge gaps that may be addressed in future experimental and clinical studies focused on improvements in the therapeutic preservation of vision during and after this disease. PMID:27154427

  14. Spatial patterns of fishing effort off San Diego: implications for zonal management and ecosystem function.

    Science.gov (United States)

    Parnell, P Ed; Dayton, Paul K; Fisher, Rachelle A; Loarie, Cina C; Darrow, Ryan D

    2010-12-01

    The essence of ecosystem-based management is managing human practices to conserve the ecosystem. Ecologists focus on understanding the ecosystem, but there are fundamental information gaps including patterns of human exploitation. In particular, the spatial distribution of fishing effort must be known at the scales needed for ecologically relevant management. Fishing is a primary impact on coastal ecosystems, yet catch distribution at scales relevant to habitats and processes are not well known for many fisheries. Here we utilized photographic time series, logbook records, and angler surveys to estimate the intensity and spatial pattern of commercial and recreational fishing. Effort was clearly aggregated for most types of fishing, the motivating factors for effort distribution varied among areas, and effort was coupled or uncoupled to habitat depending on the area and type of fishing. We estimated that approximately 60% and approximately 74% of private recreational and recreational charter vessel fishing effort, respectively, were concentrated into two small areas that also included approximately 78% of commercial sea urchin effort. Exploitation and effort were considerably greater in one kelp forest, which has important implications for patterns of kelp persistence, productivity, and ecosystem function. Areas subject to the greatest recreational fishing pressure appeared to have lower diversity. Our results indicate that fine-scale patterns of fishing effort and exploitation have profound consequences for ecosystem functioning and biodiversity. 'Ecosystem-based management of nearshore ecosystems depends on an understanding of the fine-scale patterns of exploitation. PMID:21265452

  15. Gut flora and bacterial translocation in chronic liver disease

    Institute of Scientific and Technical Information of China (English)

    John Almeida; Sumedha Galhenage; Jennifer Yu; Jelica Kurtovic; Stephen M Riordan

    2006-01-01

    Increasing evidence suggests that derangement of gut flora is of substantial clinical relevance to patients with cirrhosis. Intestinal bacterial overgrowth and increased bacterial translocation of gut flora from the intestinal lumen, in particular, predispose to an increased potential for bacterial infection in this group. Recent studies suggest that, in addition to their role in the pathogenesis of overt infective episodes and the clinical consequences of sepsis, gut flora contributes to the pro-inflammatory state of cirrhosis even in the absence of overt infection.Furthermore, manipulation of gut flora to augment the intestinal content of lactic acid-type bacteria at the expense of other gut flora species with more pathogenic potential may favourably influence liver function in cirrhotic patients. Here we review current concepts of the various inter-relationships between gut flora, bacterial translocation, bacterial infection, pro-inflammatory cytokine production and liver function in this group.

  16. Liver Cirrhosis and Intestinal Bacterial Translocation

    Institute of Scientific and Technical Information of China (English)

    2014-01-01

    Intestinal barrier dysfunction, facilitating translocation of bacteria and bacterial products, plays an important role in the pathophysiology of liver cirrhosis and its complications. Intestinal defense system including microbial barrier, immunologic barrier, mechanical barrier, chemical barrier, plays an important role in the maintenance of intestinal function. Under normal circumstances, the intestinal barrier can prevent intestinal bacteria through the intestinal wall from spreading to the body. Severe infection, trauma, shock, cirrhosis, malnutrition, immune suppression conditions, intestinal bacteria and endotoxin translocation, can lead to multiple organ dysfunction. The intestinal microlfora is not only involved in the digestion of nutrients, but also in local immunity, forming a barrier against pathogenic microorganisms. The derangement of the gut microlfora may lead to microbial translocation, deifned as the passage of viable microorganisms or bacterial products from the intestinal lumen to the mesenteric lymph nodes and other extraintestinal sites. In patients with cirrhosis, primary and intestinal lfora imbalance, intestinal bacterial overgrowth, intestinal mucosal barrier dysfunction, endotoxemia is associated with weakened immunity.

  17. Biofilms: an emergent form of bacterial life.

    Science.gov (United States)

    Flemming, Hans-Curt; Wingender, Jost; Szewzyk, Ulrich; Steinberg, Peter; Rice, Scott A; Kjelleberg, Staffan

    2016-08-11

    Bacterial biofilms are formed by communities that are embedded in a self-produced matrix of extracellular polymeric substances (EPS). Importantly, bacteria in biofilms exhibit a set of 'emergent properties' that differ substantially from free-living bacterial cells. In this Review, we consider the fundamental role of the biofilm matrix in establishing the emergent properties of biofilms, describing how the characteristic features of biofilms - such as social cooperation, resource capture and enhanced survival of exposure to antimicrobials - all rely on the structural and functional properties of the matrix. Finally, we highlight the value of an ecological perspective in the study of the emergent properties of biofilms, which enables an appreciation of the ecological success of biofilms as habitat formers and, more generally, as a bacterial lifestyle. PMID:27510863

  18. Forest restoration, biodiversity and ecosystem functioning

    Directory of Open Access Journals (Sweden)

    Aerts Raf

    2011-11-01

    Full Text Available Abstract Globally, forests cover nearly one third of the land area and they contain over 80% of terrestrial biodiversity. Both the extent and quality of forest habitat continue to decrease and the associated loss of biodiversity jeopardizes forest ecosystem functioning and the ability of forests to provide ecosystem services. In the light of the increasing population pressure, it is of major importance not only to conserve, but also to restore forest ecosystems. Ecological restoration has recently started to adopt insights from the biodiversity-ecosystem functioning (BEF perspective. Central is the focus on restoring the relation between biodiversity and ecosystem functioning. Here we provide an overview of important considerations related to forest restoration that can be inferred from this BEF-perspective. Restoring multiple forest functions requires multiple species. It is highly unlikely that species-poor plantations, which may be optimal for above-ground biomass production, will outperform species diverse assemblages for a combination of functions, including overall carbon storage and control over water and nutrient flows. Restoring stable forest functions also requires multiple species. In particular in the light of global climatic change scenarios, which predict more frequent extreme disturbances and climatic events, it is important to incorporate insights from the relation between biodiversity and stability of ecosystem functioning into forest restoration projects. Rather than focussing on species per se, focussing on functional diversity of tree species assemblages seems appropriate when selecting tree species for restoration. Finally, also plant genetic diversity and above - below-ground linkages should be considered during the restoration process, as these likely have prominent but until now poorly understood effects at the level of the ecosystem. The BEF-approach provides a useful framework to evaluate forest restoration in an

  19. Cerebral function assessment in the acute phase of neonatal bacterial meningitis caused by different pathogens%不同病原所致新生儿细菌性脑膜炎急性期脑功能评估

    Institute of Scientific and Technical Information of China (English)

    陈敏霞; 周伟; 唐娟; 王萍; 陈晓文

    2016-01-01

    Department of Neonatology,Guangzhou Women and Children's Medical Center in March 2011 to March 2015 as the objects of study.According to the results of etiological culture,the children were divided into streptococcus lactis group (14 cases),escherichia coli group (10 cases),other positive bacteria group (11cases) and culture-negative group (25 cases).The results of aEEG,BAEP and brain MRI of brain injury in the acute phase of these 4 groups were compared.Results Twenty-nine cases of the 60 patients (48.3%) showed positive blood culture,and 14 cases (23.3%) showed positive cerebrospinal fluid (CSF) culture.Streptococcus lactics and escherichia coli were found to be the most common pathogens that caused neonatal bacterial meningitis.By evaluating the cerebral function in the acute phase of 57 cases,it was found that aEEG total abnormal rate was 61.4%,escherichia coli group abnormal rate was 80.0%,while moderate to severe damage seemed to be the most remarkable feature.The abnormal rate was of statistical significance between escherichia coli group and culture-negative group (x2 =3.941,P =0.047).Forty-eight cases manifested potential anomaly evoked by brainstem auditory,with the total abnormal rate as 84.2%.A significant increase in the ratio of severe hearing loss was found in children with bacterial meningitis which was caused by escherichia coli and streptococcus agalactiae.The abnormal rate was of statistical significance between escherichia coli group and culture-negative group (x2 =4.399,P =0.036),and hearing damage caused by escherichia coli was more serious than that in other bacteria group.Of these 57 cases,MRI total abnormal rate was 77.2%,with hydrocephalus as the most common complication.Of the 44 abnormal cases,16 cases showed hydrocephalus,6 cases of which were from the escherichia coli group.The second most common complication was subdural effusion.And another 5 cases showed cerebral softening,3 cases of which were from the escherichia coli group

  20. Productivity and biochemical properties of green tea in response to full-length and functional fragments of HpaGXooc, a harpin protein from the bacterial rice leaf streak pathogen Xanthomonas oryzae pv. oryzicola

    Indian Academy of Sciences (India)

    Xiaojing Wu; Tingquan Wu; Juying Long; Qian Yin; Yong Zhang; Lei Chen; Ruoxue Liu; Tongchun Gao; Hansong Dong

    2007-09-01

    Harpin proteins from plant pathogenic bacteria can stimulate hypersensitive cell death (HCD), drought tolerance, defence responses against pathogens and insects in plants, as well as enhance plant growth. Recently, we identified nine functional fragments of HpaGXooc, a harpin protein from Xanthomonas oryzae pv. oryzicola, the pathogen that causes bacterial leaf streak in rice. Fragments HpaG1–94, HpaG10–42, and HpaG62–138, which contain the HpaGXooc regions of the amino acid sequence as indicated by the number spans, exceed the parent protein in promoting growth, pathogen defence and HCD in plants. Here we report improved productivity and biochemical properties of green tea (Camellia sinensis) in response to the fragments tested in comparison with HpaGXooc and an inactive protein control. Field tests suggested that the four proteins markedly increased the growth and yield of green tea, and increased the leaf content of tea catechols, a group of compounds that have relevance in the prevention and treatment of human diseases. In particular, HpaG1–94 was more active than HpaGXooc in expediting the growth of juvenile buds and leaves used as green tea material and increased the catechol content of processed teas. When tea shrubs were treated with HpaHXooc and HpaG1–94 compared with a control, green tea yields were over 55% and 39% greater, and leaf catechols were increased by more than 64% and 72%, respectively. The expression of three homologues of the expansin genes, which regulate plant cell growth, and the CsCHS gene encoding a tea chalcone synthase, which critically regulates the biosynthesis of catechols, were induced in germinal leaves of tea plants following treatment with HpaG1–94 or HpaGXooc. Higher levels of gene expression were induced by the application of HpaG1–94 than HpaGXooc. Our results suggest that the harpin protein, especially the functional fragment HpaG1–94, can be used to effectively increase the yield and improve the biochemical

  1. Heme uptake in bacterial pathogens

    OpenAIRE

    Contreras, Heidi; Chim, Nicholas; Credali, Alfredo; Goulding, Celia W.

    2014-01-01

    Iron is an essential nutrient for the survival of organisms. Bacterial pathogens possess specialized pathways to acquire heme from their human hosts. In this review, we present recent structural and biochemical data that provide mechanistic insights into several bacterial heme uptake pathways, encompassing the sequestration of heme from human hemoproteins to secreted or membrane-associated bacterial proteins, the transport of heme across bacterial membranes, and the degradation of heme within...

  2. Bacterial regulatory networks—from self-organizing molecules to cell shape and patterns in bacterial communities

    OpenAIRE

    Hengge, Regine; Sourjik, Victor

    2013-01-01

    The ESF–EMBO Conference on ‘Bacterial Networks' was held in March, 2013. It brought together molecular microbiologists, bacteral systems biologists and synthetic biologists to discuss the architecture, function and dynamics of regulatory networks in bacteria.

  3. The constancy of gene conservation across divergent bacterial orders

    Directory of Open Access Journals (Sweden)

    Ackermann Martin

    2009-01-01

    Full Text Available Abstract Background Orthologous genes are frequently presumed to perform similar functions. However, outside of model organisms, this is rarely tested. One means of inferring changes in function is if there are changes in the level of gene conservation and selective constraint. Here we compare levels of gene conservation across three bacterial groups to test for changes in gene functionality. Findings The level of gene conservation for different orthologous genes is highly correlated across clades, even for highly divergent groups of bacteria. These correlations do not arise from broad differences in gene functionality (e.g. informational genes vs. metabolic genes, but instead seem to result from very specific differences in gene function. Furthermore, these functional differences appear to be maintained over very long periods of time. Conclusion These results suggest that even over broad time scales, most bacterial genes are under a nearly constant level of purifying selection, and that bacterial evolution is thus dominated by selective and functional stasis.

  4. Bacterial chemoreceptors and chemoeffectors.

    Science.gov (United States)

    Bi, Shuangyu; Lai, Luhua

    2015-02-01

    Bacteria use chemotaxis signaling pathways to sense environmental changes. Escherichia coli chemotaxis system represents an ideal model that illustrates fundamental principles of biological signaling processes. Chemoreceptors are crucial signaling proteins that mediate taxis toward a wide range of chemoeffectors. Recently, in deep study of the biochemical and structural features of chemoreceptors, the organization of higher-order clusters in native cells, and the signal transduction mechanisms related to the on-off signal output provides us with general insights to understand how chemotaxis performs high sensitivity, precise adaptation, signal amplification, and wide dynamic range. Along with the increasing knowledge, bacterial chemoreceptors can be engineered to sense novel chemoeffectors, which has extensive applications in therapeutics and industry. Here we mainly review recent advances in the E. coli chemotaxis system involving structure and organization of chemoreceptors, discovery, design, and characterization of chemoeffectors, and signal recognition and transduction mechanisms. Possible strategies for changing the specificity of bacterial chemoreceptors to sense novel chemoeffectors are also discussed.

  5. [Bacterial diseases of rape].

    Science.gov (United States)

    Zakharova, O M; Mel'nychuk, M D; Dankevych, L A; Patyka, V P

    2012-01-01

    Bacterial destruction of the culture was described and its agents identified in the spring and winter rape crops. Typical symptoms are the following: browning of stem tissue and its mucilagization, chlorosis of leaves, yellowing and beginning of soft rot in the place of leaf stalks affixion to stems, loss of pigmentation (violet). Pathogenic properties of the collection strains and morphological, cultural, physiological, and biochemical properties of the agents of rape's bacterial diseases isolated by the authors have been investigated. It was found that all the isolates selected by the authors are highly or moderately aggressive towards different varieties of rape. According to the complex of phenotypic properties 44% of the total number of isolates selected by the authors are related to representatives of the genus Pseudomonas, 37% - to Xanthomonas and 19% - to Pectobacterium. PMID:23293826

  6. Bacterial transformation of terpenoids

    International Nuclear Information System (INIS)

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

  7. Supramolecular bacterial systems

    OpenAIRE

    Sankaran, Shrikrishnan

    2015-01-01

    For nearly over a decade, a wide variety of dynamic and responsive supramolecular architectures have been investigated and developed to address biological systems. Since the non-covalent interactions between individual molecular components in such architectures are similar to the interactions found in living systems, it was possible to integrate chemically-synthesized and naturally-occurring components to create platforms with interesting bioactive properties. Bacterial cells and recombinant ...

  8. Bacterial Colony Optimization

    OpenAIRE

    Ben Niu; Hong Wang

    2012-01-01

    This paper investigates the behaviors at different developmental stages in Escherichia coli (E. coli) lifecycle and developing a new biologically inspired optimization algorithm named bacterial colony optimization (BCO). BCO is based on a lifecycle model that simulates some typical behaviors of E. coli bacteria during their whole lifecycle, including chemotaxis, communication, elimination, reproduction, and migration. A newly created chemotaxis strategy combined with communication mechanism i...

  9. Preparation and properties of electromagnetic functional composite membrane based on bacterial cellulose%细菌纤维素基电磁功能复合膜的制备与性能研究∗

    Institute of Scientific and Technical Information of China (English)

    韩谨潞; 李琪琪; 汤廉; 陈仕艳; 王华平

    2015-01-01

    以细菌纤维素(BC)基体材料,通过共沉淀原位复合法制备纳米钴铁氧体(CoFe2 O4)/细菌纤维素磁性复合膜;并在此基础上,通过原位化学氧化聚合法,制备了聚吡咯/钴铁氧体/细菌纤维素(PPy/CoFe2 O4/BC)复合膜,对其结构性能及应用进行研究。结果表明,PPy/CoFe2 O4/BC复合膜仍然保持了 BC的三维网状结构。当吡咯单体浓度为0.07 mol/L时,复合膜由连续的核壳结构构成,电导率稳定在0.4 S/cm 左右,其电磁屏蔽效能在25 dB左右,是一种良好的民用或商用电磁屏蔽材料。%CoFe2 O4/BC magnetic composite membranes based on bacterial cellulose (BC)were prepared through coprecipitation and in situ composition.Then,the flexible PPy/CoFe2 O4/BC functional membranes with elec-tromagnetivity were synthesized successfully through in situ chemical synthesis and the structure,properties and applications were investigated.The results revealed that the PPy/CoFe2 O4/BC membranes remained the ul-trafine network architecture of BC template.The membranes demonstrated a continue core-shell structure when the concentration of pyrrole was 0.07 mol/L.Moreover,the conductivity of composite membranes were about 0.4 S/cm and the PPy/CoFe2 O4/BC composite membranes revealed a good electromagnetic shielding efficiency with the value of SE 25 dB,which indicate a good electromagnetic interference shielding material in daily life.

  10. Cascading effects of long-term land-use changes on plant traits and ecosystem functioning.

    Science.gov (United States)

    Laliberté, Etienne; Tylianakis, Jason M

    2012-01-01

    There is much concern that the functioning of ecosystems will be affected by human-induced changes in biodiversity, of which land-use change is the most important driver. However, changes in biodiversity may be only one of many pathways through which land use alters ecosystem functioning, and its importance relative to other pathways remains unclear. In particular, although biodiversity-ecosystem function research has focused primarily on grasslands, the increases in agricultural inputs (e.g., fertilization, irrigation) and grazing pressure that drive change in grasslands worldwide have been largely ignored. Here we show that long-term (27-year) manipulations of soil resource availability and sheep grazing intensity caused marked, consistent shifts in grassland plant functional composition and diversity, with cascading (i.e., causal chains of) direct, indirect, and interactive effects on multiple ecosystem functions. Resource availability exerted dominant control over above-ground net primary production (ANPP), both directly and indirectly via shifts in plant functional composition. Importantly, the effects of plant functional diversity and grazing intensity on ANPP shifted from negative to positive as agricultural inputs increased, providing strong evidence that soil resource availability modulates the impacts of plant diversity and herbivory on primary production. These changes in turn altered litter decomposition and, ultimately, soil carbon sequestration, highlighting the relevance of ANPP as a key integrator of ecosystem functioning. Our study reveals how human alterations of bottom-up (resources) and top-down (herbivory) forces together interact to control the functioning of grazing systems, the most extensive land use on Earth.

  11. Bacterial Toxins as Pathogen Weapons Against Phagocytes.

    Science.gov (United States)

    do Vale, Ana; Cabanes, Didier; Sousa, Sandra

    2016-01-01

    Bacterial toxins are virulence factors that manipulate host cell functions and take over the control of vital processes of living organisms to favor microbial infection. Some toxins directly target innate immune cells, thereby annihilating a major branch of the host immune response. In this review we will focus on bacterial toxins that act from the extracellular milieu and hinder the function of macrophages and neutrophils. In particular, we will concentrate on toxins from Gram-positive and Gram-negative bacteria that manipulate cell signaling or induce cell death by either imposing direct damage to the host cells cytoplasmic membrane or enzymatically modifying key eukaryotic targets. Outcomes regarding pathogen dissemination, host damage and disease progression will be discussed.

  12. Bacterial toxins as pathogen weapons against phagocytes

    Directory of Open Access Journals (Sweden)

    Ana edo Vale

    2016-02-01

    Full Text Available Bacterial toxins are virulence factors that manipulate host cell functions and take over the control of vital processes of living organisms to favour microbial infection. Some toxins directly target innate immune cells, thereby annihilating a major branch of the host immune response. In this review we will focus on bacterial toxins that act from the extracellular milieu and hinder the function of macrophages and neutrophils. In particular, we will concentrate on toxins from Gram-positive and Gram-negative bacteria that manipulate cell signalling or induce cell death by either imposing direct damage to the host cells cytoplasmic membrane or enzymatically modifying key eukaryotic targets. Outcomes regarding pathogen dissemination, host damage and disease progression will be discussed.

  13. Bacterial Artificial Chromosome Mutagenesis Using Recombineering

    OpenAIRE

    Kumaran Narayanan; Qingwen Chen

    2011-01-01

    Gene expression from bacterial artificial chromosome (BAC) clones has been demonstrated to facilitate physiologically relevant levels compared to viral and nonviral cDNA vectors. BACs are large enough to transfer intact genes in their native chromosomal setting together with flanking regulatory elements to provide all the signals for correct spatiotemporal gene expression. Until recently, the use of BACs for functional studies has been limited because their large size has inherently presented...

  14. Bacterial ice nucleation: significance and molecular basis.

    Science.gov (United States)

    Gurian-Sherman, D; Lindow, S E

    1993-11-01

    Several bacterial species are able to catalyze ice formation at temperatures as warm as -2 degrees C. These microorganisms efficiently catalyze ice formation at temperatures much higher than most organic or inorganic substances. Because of their ubiquity on the surfaces of frost-sensitive plants, they are responsible for initiating ice formation, which results in frost injury. The high temperature of ice catalysis conferred by bacterial ice nuclei makes them useful in ice nucleation-limited processes such as artificial snow production, the freezing of some food products, and possibly in future whether modification schemes. The rarity of other ice nuclei active at high subfreezing temperature, and the ease and sensitivity with which ice nuclei can be quantified, have made the use of a promoterless bacterial ice nucleation gene valuable as a reporter of transcription. Target genes to which this promoter is fused can be used in cells in natural habitats. Warm-temperature ice nucleation sites have also been extensively studied at a molecular level. Nucleation sites active at high temperatures (above -5 degrees C) are probably composed of bacterial ice nucleation protein molecules that form functionally aligned aggregates. Models of ice nucleation proteins predict that they form a planar array of hydrogen binding groups that closely complement that of an ice crystal face. Moreover, interdigitation of these molecules may produce a large contiguous template for ice formation.

  15. Bacterial ice nucleation: significance and molecular basis.

    Science.gov (United States)

    Gurian-Sherman, D; Lindow, S E

    1993-11-01

    Several bacterial species are able to catalyze ice formation at temperatures as warm as -2 degrees C. These microorganisms efficiently catalyze ice formation at temperatures much higher than most organic or inorganic substances. Because of their ubiquity on the surfaces of frost-sensitive plants, they are responsible for initiating ice formation, which results in frost injury. The high temperature of ice catalysis conferred by bacterial ice nuclei makes them useful in ice nucleation-limited processes such as artificial snow production, the freezing of some food products, and possibly in future whether modification schemes. The rarity of other ice nuclei active at high subfreezing temperature, and the ease and sensitivity with which ice nuclei can be quantified, have made the use of a promoterless bacterial ice nucleation gene valuable as a reporter of transcription. Target genes to which this promoter is fused can be used in cells in natural habitats. Warm-temperature ice nucleation sites have also been extensively studied at a molecular level. Nucleation sites active at high temperatures (above -5 degrees C) are probably composed of bacterial ice nucleation protein molecules that form functionally aligned aggregates. Models of ice nucleation proteins predict that they form a planar array of hydrogen binding groups that closely complement that of an ice crystal face. Moreover, interdigitation of these molecules may produce a large contiguous template for ice formation. PMID:8224607

  16. Bacterial Multidrug Efflux Pumps: Much More Than Antibiotic Resistance Determinants

    Directory of Open Access Journals (Sweden)

    Paula Blanco

    2016-02-01

    Full Text Available Bacterial multidrug efflux pumps are antibiotic resistance determinants present in all microorganisms. With few exceptions, they are chromosomally encoded and present a conserved organization both at the genetic and at the protein levels. In addition, most, if not all, strains of a given bacterial species present the same chromosomally-encoded efflux pumps. Altogether this indicates that multidrug efflux pumps are ancient elements encoded in bacterial genomes long before the recent use of antibiotics for human and animal therapy. In this regard, it is worth mentioning that efflux pumps can extrude a wide range of substrates that include, besides antibiotics, heavy metals, organic pollutants, plant-produced compounds, quorum sensing signals or bacterial metabolites, among others. In the current review, we present information on the different functions that multidrug efflux pumps may have for the bacterial behaviour in different habitats as well as on their regulation by specific signals. Since, in addition to their function in non-clinical ecosystems, multidrug efflux pumps contribute to intrinsic, acquired, and phenotypic resistance of bacterial pathogens, the review also presents information on the search for inhibitors of multidrug efflux pumps, which are currently under development, in the aim of increasing the susceptibility of bacterial pathogens to antibiotics.

  17. Spontaneous bacterial peritonitis

    Institute of Scientific and Technical Information of China (English)

    Anastasios Koulaouzidis; Shivaram Bhat; Athar A Saeed

    2009-01-01

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

  18. Antimicrobials for bacterial bioterrorism agents.

    Science.gov (United States)

    Sarkar-Tyson, Mitali; Atkins, Helen S

    2011-06-01

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

  19. Investigation of septins using infection by bacterial pathogens.

    Science.gov (United States)

    Krokowski, S; Mostowy, S

    2016-01-01

    Investigation of the host cytoskeleton during infection by bacterial pathogens has significantly contributed to our understanding of cell biology and host defense. Work has shown that septins are recruited to the phagocytic cup as collarlike structures and enable bacterial entry into host cells. In the cytosol, septins can entrap actin-polymerizing bacteria in cage-like structures for targeting to autophagy, a highly conserved intracellular degradation process. In this chapter, we describe methods to investigate septin assembly and function during infection by bacterial pathogens. Use of these methods can lead to in-depth understanding of septin biology and suggest therapeutic approaches to combat infectious disease.

  20. Proton dynamics in bacterial spores, a neutron scattering investigation

    Directory of Open Access Journals (Sweden)

    Noue Alexandre Colas de la

    2015-01-01

    Full Text Available Results from first neutron scattering experiments on bacterial spores are reported. The elastic intensities and mean square displacements have a non-linear behaviour as function of temperature, which is in agreement with a model presenting more pronounced variations at around 330 K (57 ∘C and 400 K (127 ∘C. Based on the available literature on thermal properties of bacterial spores, mainly referring to differential scanning calorimetry, they are suggested to be associated to main endothermic transitions induced by coat and/or core bacterial response to heat treatment.

  1. Viral-bacterial interactions in acute otitis media.

    Science.gov (United States)

    Marom, Tal; Nokso-Koivisto, Johanna; Chonmaitree, Tasnee

    2012-12-01

    Acute otitis media (AOM) is a polymicrobial disease, which usually occurs as a complication of viral upper respiratory tract infection (URI). While respiratory viruses alone may cause viral AOM, they increase the risk of bacterial middle ear infection and worsen clinical outcomes of bacterial AOM. URI viruses alter Eustachian tube (ET) function via decreased mucociliary action, altered mucus secretion and increased expression of inflammatory mediators among other mechanisms. Transient reduction in protective functions of the ET allows colonizing bacteria of the nasopharynx to ascend into the middle ear and cause AOM. Advances in research help us to better understand the host responses to viral URI, the mechanisms of viral-bacterial interactions in the nasopharynx and the development of AOM. In this review, we present current knowledge regarding viral-bacterial interactions in the pathogenesis and clinical course of AOM. We focus on the common respiratory viruses and their established role in AOM.

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

    Science.gov (United States)

    2016-01-01

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

  3. Studying bacterial multispecies biofilms

    DEFF Research Database (Denmark)

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

    2016-01-01

    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...... the approaches used to study these complex communities. This review focuses on the establishment of multispecies biofilms in vitro, interspecies interactions in microhabitats, and how to select communities for evaluation. Studies have used different experimental approaches; here we evaluate the benefits...... and drawbacks of varying the degree of complexity. This review aims to facilitate multispecies biofilm research in order to expand the current limited knowledge on interspecies interactions. Recent technological advances have enabled total diversity analysis of highly complex and diverse microbial communities...

  4. EnviroAtlas - Bird National Biodiversity Ecosystem Services Metrics by 12-digit HUC for the Conterminous United States

    Data.gov (United States)

    U.S. Environmental Protection Agency — This dataset was produced by a joint effort of New Mexico State University (NMSU), the U.S. Environmental Protection Agency (EPA), and the U.S. Geological Survey...

  5. Carbon nanotubes as in vivo bacterial probes

    Science.gov (United States)

    Bardhan, Neelkanth M.; Ghosh, Debadyuti; Belcher, Angela M.

    2014-09-01

    With the rise in antibiotic-resistant infections, non-invasive sensing of infectious diseases is increasingly important. Optical imaging, although safer and simpler, is less developed than other modalities such as radioimaging, due to low availability of target-specific molecular probes. Here we report carbon nanotubes (SWNTs) as bacterial probes for fluorescence imaging of pathogenic infections. We demonstrate that SWNTs functionalized using M13 bacteriophage (M13-SWNT) can distinguish between F‧-positive and F‧-negative bacterial strains. Moreover, through one-step modification, we attach an anti-bacterial antibody on M13-SWNT, making it easily tunable for sensing specific F‧-negative bacteria. We illustrate detection of Staphylococcus aureus intramuscular infections, with ~3.4 × enhancement in fluorescence intensity over background. SWNT imaging presents lower signal spread ~0.08 × and higher signal amplification ~1.4 × , compared with conventional dyes. We show the probe offers greater ~5.7 × enhancement in imaging of S. aureus infective endocarditis. These biologically functionalized, aqueous-dispersed, actively targeted, modularly tunable SWNT probes offer new avenues for exploration of deeply buried infections.

  6. Is long-term ecological functioning stable: The case of the marine benthos?

    Science.gov (United States)

    Frid, C. L. J.; Caswell, B. A.

    2015-04-01

    It is widely acknowledged that human activities are contributing to substantial biodiversity loss and that this threatens ecological processes underpinning human exploitation of 'ecosystem services' (defined by the Millennium Ecosystem Assessment as 'the benefits people obtain from ecosystems'). In the present study we consider three 'intermediate ecosystem services' in both contemporary and ancient marine systems and although 'ecosystem services' per se did not exist in the Jurassic our study seeks to consider the future provision of these services and so the term is retained. We consider the temporal patterns in benthic marine ecosystems: (1) spanning four decades at two offshore stations in the North Sea, UK and (2) over millennial scales in Late Jurassic UK palaeocommunities. Biological traits analysis is used to link changes in taxonomic composition to variations in ecological functioning and the potential supply of three 'intermediate' ecosystem services: the ability to provide food to fish and other predators, benthic nutrient regeneration and carbon cycling. We examine whether changes in taxonomic composition drive temporal variation in functioning, whether this variation increases over time and the extent to which species turnover is comparable in contemporary and ancient systems. Taxonomic variability was of a similar magnitude in all three systems and there was evidence for changes in functioning linked to changes in several (key or rivet) taxa. During other periods resilience maintained functioning in the face of taxonomic change. These results suggest that in these benthic systems the Biodiversity-Ecosystem Functioning relationship is idiosyncratic, but a degree of temporal stability in functioning is maintained such that the ecosystem services they underpin would also be stable during decadal and longer-term changes.

  7. Discrete modelling of bacterial conjugation dynamics

    CERN Document Server

    Goni-Moreno, Angel

    2012-01-01

    In bacterial populations, cells are able to cooperate in order to yield complex collective functionalities. Interest in population-level cellular behaviour is increasing, due to both our expanding knowledge of the underlying biological principles, and the growing range of possible applications for engineered microbial consortia. Researchers in the field of synthetic biology - the application of engineering principles to living systems - have, for example, recently shown how useful decision-making circuits may be distributed across a bacterial population. The ability of cells to interact through small signalling molecules (a mechanism known as it quorum sensing) is the basis for the majority of existing engineered systems. However, horizontal gene transfer (or conjugation) offers the possibility of cells exchanging messages (using DNA) that are much more information-rich. The potential of engineering this conjugation mechanism to suit specific goals will guide future developments in this area. Motivated by a l...

  8. Bacterial microbiome of lungs in COPD.

    Science.gov (United States)

    Sze, Marc A; Hogg, James C; Sin, Don D

    2014-01-01

    Chronic obstructive pulmonary disease (COPD) is currently the third leading cause of death in the world. Although smoking is the main risk factor for this disease, only a minority of smokers develop COPD. Why this happens is largely unknown. Recent discoveries by the human microbiome project have shed new light on the importance and richness of the bacterial microbiota at different body sites in human beings. The microbiota plays a particularly important role in the development and functional integrity of the immune system. Shifts or perturbations in the microbiota can lead to disease. COPD is in part mediated by dysregulated immune responses to cigarette smoke and other environmental insults. Although traditionally the lung has been viewed as a sterile organ, by using highly sensitive genomic techniques, recent reports have identified diverse bacterial communities in the human lung that may change in COPD. This review summarizes the current knowledge concerning the lung microbiota in COPD and its potential implications for pathogenesis of the disease.

  9. Educational achievement and economic self-sufficiency in adults after childhood bacterial meningitis

    DEFF Research Database (Denmark)

    Roed-Petersen, Casper; Omland, Lars Haukali; Skinhoj, Peter;

    2013-01-01

    To our knowledge, no previous study has examined functioning in adult life among persons who had bacterial meningitis in childhood.......To our knowledge, no previous study has examined functioning in adult life among persons who had bacterial meningitis in childhood....

  10. Bacterial adaptation to the gut environment favors successful colonization

    Science.gov (United States)

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

    2011-01-01

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

  11. Exploring the diversity of protein modifications: special bacterial phosphorylation systems

    DEFF Research Database (Denmark)

    Mijakovic, Ivan; Grangeasse, Christophe; Turgay, Kürşad

    2016-01-01

    that has been most thoroughly investigated. Unlike in eukarya, a large diversity of enzyme families has been shown to phosphorylate and dephosphorylate proteins on various amino acids with different chemical properties in bacteria. In this review, after a brief overview of the known bacterial...... phosphorylation systems, we focus on more recently discovered and less widely known kinases and phosphatases. Namely, we describe in detail tyrosine- and arginine-phosphorylation together with some examples of unusual serine-phosphorylation systems and discuss their potential role and function in bacterial...... physiology, and regulatory networks. Investigating these unusual bacterial kinase and phosphatases is not only important to understand their role in bacterial physiology but will help to generally understand the full potential and evolution of protein phosphorylation for signal transduction, protein...

  12. Application of Sub-Micrometer Vibrations to Mitigate Bacterial Adhesion

    Directory of Open Access Journals (Sweden)

    Will R. Paces

    2014-03-01

    Full Text Available As a prominent concern regarding implantable devices, eliminating the threat of opportunistic bacterial infection represents a significant benefit to both patient health and device function. Current treatment options focus on chemical approaches to negate bacterial adhesion, however, these methods are in some ways limited. The scope of this study was to assess the efficacy of a novel means of modulating bacterial adhesion through the application of vibrations using magnetoelastic materials. Magnetoelastic materials possess unique magnetostrictive property that can convert a magnetic field stimulus into a mechanical deformation. In vitro experiments demonstrated that vibrational loads generated by the magnetoelastic materials significantly reduced the number of adherent bacteria on samples exposed to Escherichia coli, Staphylococcus epidermidis and Staphylococcus aureus suspensions. These experiments demonstrate that vibrational loads from magnetoelastic materials can be used as a post-deployment activated means to deter bacterial adhesion and device infection.

  13. Positioning of bacterial chemoreceptors.

    Science.gov (United States)

    Jones, Christopher W; Armitage, Judith P

    2015-05-01

    For optimum growth, bacteria must adapt to their environment, and one way that many species do this is by moving towards favourable conditions. To do so requires mechanisms to both physically drive movement and provide directionality to this movement. The pathways that control this directionality comprise chemoreceptors, which, along with an adaptor protein (CheW) and kinase (CheA), form large hexagonal arrays. These arrays can be formed around transmembrane receptors, resulting in arrays embedded in the inner membrane, or they can comprise soluble receptors, forming arrays in the cytoplasm. Across bacterial species, chemoreceptor arrays (both transmembrane and soluble) are localised to a variety of positions within the cell; some species with multiple arrays demonstrate this variety within individual cells. In many cases, the positioning pattern of the arrays is linked to the need for segregation of arrays between daughter cells on division, ensuring the production of chemotactically competent progeny. Multiple mechanisms have evolved to drive this segregation, including stochastic self-assembly, cellular landmarks, and the utilisation of ParA homologues. The variety of mechanisms highlights the importance of chemotaxis to motile species.

  14. 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.

  15. 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.

  16. Bacterial microbiome of lungs in COPD

    Directory of Open Access Journals (Sweden)

    Sze MA

    2014-02-01

    Full Text Available Marc A Sze,1 James C Hogg,2 Don D Sin1 1Department of Medicine, 2Department of Pathology and Laboratory Medicine, The James Hogg Research Centre, Providence Heart-Lung Institute, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada Abstract: Chronic obstructive pulmonary disease (COPD is currently the third leading cause of death in the world. Although smoking is the main risk factor for this disease, only a minority of smokers develop COPD. Why this happens is largely unknown. Recent discoveries by the human microbiome project have shed new light on the importance and richness of the bacterial microbiota at different body sites in human beings. The microbiota plays a particularly important role in the development and functional integrity of the immune system. Shifts or perturbations in the microbiota can lead to disease. COPD is in part mediated by dysregulated immune responses to cigarette smoke and other environmental insults. Although traditionally the lung has been viewed as a sterile organ, by using highly sensitive genomic techniques, recent reports have identified diverse bacterial communities in the human lung that may change in COPD. This review summarizes the current knowledge concerning the lung microbiota in COPD and its potential implications for pathogenesis of the disease. Keywords: chronic obstructive pulmonary disease, bacterial microbiome, lungs

  17. Bacterial Communities: Interactions to Scale

    Science.gov (United States)

    Stubbendieck, Reed M.; Vargas-Bautista, Carol; Straight, Paul D.

    2016-01-01

    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. PMID:27551280

  18. 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.

  19. Diagnosis of bacterial hepatic abscess by CT

    Institute of Scientific and Technical Information of China (English)

    Cheng-Lin Wang; Xue-Jun Guo; Shui-Bo Qiu; Yi Lei; Zhi-Dong Yuan; Han-Bin Dong; Hui-An Liu

    2007-01-01

    BACKGROUND: Bacterial hepatic abscess usually is acute and progressive, often resulting in sepsis, impairment of liver function and disseminated intravascular coagulation. The mortality rate was as high as 80%in the past. For the purpose of early diagnosis and differential diagnosis of this disease, we probed the imaging manifestations and their characteristics in bacterial hepatic abscesses by CT scan. METHODS:Twenty-four lesions from 21 patients with bacterial hepatic abscesses that were conifrmed by clinical features, puncture and culture were reviewed for CT manifestations. Fourteen patients were male and 7 were female, with an average age of 56.2 years. All lesions underwent CT plain scan and three-phase enhanced scan and 15 patients underwent delayed-phase imaging. Three senior radiologists read the iflms in accordance with a standard. RESULTS: Among 24 lesions, 18 (75%) were situated in the right liver with diameters of 1.4-9.3 cm (average 4.5 cm). Nineteen (79.2%) lesions were round or sub-round in shape, and 22 (91.7%) had smooth, uninterrupted and sharp edges. All lesions showed low attenuation of less than 20 Hu. Twenty-two enhanced lesions (91.7%) had rim-shaped enhancement in the abscess wall, and 13 (54.2%) showed single or double-ring signs. Eighteen (75%) displayed honeycomb-like, grid-like or strip-like enhancement. Eighteen (75%) were regionally enhanced in the surroundings or upper or lower layers. Only 2 (8.3%) displayed a gas-liquid surface sign. CONCLUSIONS:  The CT ifndings of bacterial hepatic abscess are usually typical, and the diagnosis of the abscess is not dififcult. To precisely diagnose atypical cases, it is necessary to combine CT with clinical observations and follow-up.

  20. Meningitis bacteriana Bacterial meningitis

    Directory of Open Access Journals (Sweden)

    Ana Teresa Alvarado Guevara

    2006-03-01

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

  1. Bacterial Culture of Neonatal Sepsis

    OpenAIRE

    AH Movahedian; R Moniri; Z Mosayebi

    2006-01-01

    Neonatal bacterial sepsis is one of the major cause of morbidity and mortality in neonates. This retrospective study was performed to determine the incidence of bacterial sepsis with focus on Gram negative organisms in neonates admitted at Beheshti Hospital in Kashan, during a 3-yr period, from September 2002 to September 2005. Blood culture was performed on all neonates with risk factors or signs of suggestive sepsis. Blood samples were cultured using brain heart infusion (BHI) broth accordi...

  2. Mast cells in bacterial infections

    OpenAIRE

    Rönnberg, Elin

    2014-01-01

    Mast cells are implicated in immunity towards bacterial infection, but the molecular mechanisms by which mast cells contribute to the host response are only partially understood. Previous studies have examined how mast cells react to purified bacterial cell wall components, such as peptidoglycan and lipopolysaccharide. To investigate how mast cells react to live bacteria we co-cultured mast cells and the gram-positive bacteria Streptococcus equi (S. equi) and Staphylococcus aureus (S. aureus)...

  3. Bacterial Alkaloids Prevent Amoebal Predation.

    Science.gov (United States)

    Klapper, Martin; Götze, Sebastian; Barnett, Robert; Willing, Karsten; Stallforth, Pierre

    2016-07-25

    Bacterial defense mechanisms have evolved to protect bacteria against predation by nematodes, predatory bacteria, or amoebae. We identified novel bacterial alkaloids (pyreudiones A-D) that protect the producer, Pseudomonas fluorescens HKI0770, against amoebal predation. Isolation, structure elucidation, total synthesis, and a proposed biosynthetic pathway for these structures are presented. The generation of P. fluorescens gene-deletion mutants unable to produce pyreudiones rendered the bacterium edible to a variety of soil-dwelling amoebae. PMID:27294402

  4. Bacterial cellulose/boehmite composites

    International Nuclear Information System (INIS)

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

  5. 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.

  6. 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. PMID:22099187

  7. 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.

  8. Increasing complexity of the bacterial cytoskeleton

    DEFF Research Database (Denmark)

    Møller-Jensen, Jakob; Löwe, Jan

    2005-01-01

    Bacteria contain cytoskeletal elements involved in major cellular processes including DNA segregation and cell morphogenesis and division. Distant bacterial homologues of tubulin (FtsZ) and actin (MreB and ParM) not only resemble their eukaryotic counterparts structurally but also show similar...... functional characteristics, assembling into filamentous structures in a nucleotide-dependent fashion. Recent advances in fluorescence microscopic imaging have revealed that FtsZ and MreB form highly dynamic helical structures that encircle the cells along the inside of the cell membrane. With the discovery...

  9. Spatial Scales of Bacterial Diversity in Cold-Water Coral Reef Ecosystems

    OpenAIRE

    Sandra Schöttner; Christian Wild; Friederike Hoffmann; Antje Boetius; Alban Ramette

    2012-01-01

    Background: Cold-water coral reef ecosystems are recognized as biodiversity hotspots in the deep sea, but insights into their associated bacterial communities are still limited. Deciphering principle patterns of bacterial community variation over multiple spatial scales may however prove critical for a better understanding of factors contributing to cold-water coral reef stability and functioning. Methodology/Principal Findings: Bacterial community structure, as determined by Automated Riboso...

  10. Soil bacterial community responses to global changes

    DEFF Research Database (Denmark)

    Bergmark, Lasse

    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......’ of climate change manipulations on soil microorganisms and nutrient availability in a Danish heathland, where the samples were taken shortly after a prolonged pre-summer drought. The major findings in the study are that warming increased measures of fungi and bacteria and drought might shift/change...... 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...

  11. Positively regulated bacterial expression systems.

    Science.gov (United States)

    Brautaset, Trygve; Lale, Rahmi; Valla, Svein

    2009-01-01

    Regulated promoters are useful tools for many aspects related to recombinant gene expression in bacteria, including for high-level expression of heterologous proteins and for expression at physiological levels in metabolic engineering applications. In general, it is common to express the genes of interest from an inducible promoter controlled either by a positive regulator or by a repressor protein. In this review, we discuss established and potentially useful positively regulated bacterial promoter systems, with a particular emphasis on those that are controlled by the AraC-XylS family of transcriptional activators. The systems function in a wide range of microorganisms, including enterobacteria, soil bacteria, lactic bacteria and streptomycetes. The available systems that have been applied to express heterologous genes are regulated either by sugars (L-arabinose, L-rhamnose, xylose and sucrose), substituted benzenes, cyclohexanone-related compounds, ε-caprolactam, propionate, thiostrepton, alkanes or peptides. It is of applied interest that some of the inducers require the presence of transport systems, some are more prone than others to become metabolized by the host and some have been applied mainly in one or a limited number of species. Based on bioinformatics analyses, the AraC-XylS family of regulators contains a large number of different members (currently over 300), but only a small fraction of these, the XylS/Pm, AraC/P(BAD), RhaR-RhaS/rhaBAD, NitR/PnitA and ChnR/Pb regulator/promoter systems, have so far been explored for biotechnological applications.

  12. The Bacterial Cytoskeleton

    Science.gov (United States)

    Watters, Christopher

    2006-01-01

    For a eukaryotic cell biologist, learning new things about old, familiar subjects (such as the differences between eukaryotes and prokaryotes) is one of the pleasures of teaching introductory biology courses. Such learning usually entails examining how bacteria function, in ways other than how they replicate and transcribe DNA and how they…

  13. Impairment of the bacterial biofilm stability by triclosan.

    Directory of Open Access Journals (Sweden)

    Helen V Lubarsky

    Full Text Available The accumulation of the widely-used antibacterial and antifungal compound triclosan (TCS in freshwaters raises concerns about the impact of this harmful chemical on the biofilms that are the dominant life style of microorganisms in aquatic systems. However, investigations to-date rarely go beyond effects at the cellular, physiological or morphological level. The present paper focuses on bacterial biofilms addressing the possible chemical impairment of their functionality, while also examining their substratum stabilization potential as one example of an important ecosystem service. The development of a bacterial assemblage of natural composition--isolated from sediments of the Eden Estuary (Scotland, UK--on non-cohesive glass beads (<63 µm and exposed to a range of triclosan concentrations (control, 2-100 µg L(-1 was monitored over time by Magnetic Particle Induction (MagPI. In parallel, bacterial cell numbers, division rate, community composition (DGGE and EPS (extracellular polymeric substances: carbohydrates and proteins secretion were determined. While the triclosan exposure did not prevent bacterial settlement, biofilm development was increasingly inhibited by increasing TCS levels. The surface binding capacity (MagPI of the assemblages was positively correlated to the microbial secreted EPS matrix. The EPS concentrations and composition (quantity and quality were closely linked to bacterial growth, which was affected by enhanced TCS exposure. Furthermore, TCS induced significant changes in bacterial community composition as well as a significant decrease in bacterial diversity. The impairment of the stabilization potential of bacterial biofilm under even low, environmentally relevant TCS levels is of concern since the resistance of sediments to erosive forces has large implications for the dynamics of sediments and associated pollutant dispersal. In addition, the surface adhesive capacity of the biofilm acts as a sensitive measure of

  14. 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.

  15. Bacterial tactic responses.

    Science.gov (United States)

    Armitage, J P

    1999-01-01

    Many, if not most, bacterial species swim. The synthesis and operation of the flagellum, the most complex organelle of a bacterium, takes a significant percentage of cellular energy, particularly in the nutrient limited environments in which many motile species are found. It is obvious that motility accords cells a survival advantage over non-motile mutants under normal, poorly mixed conditions and is an important determinant in the development of many associations between bacteria and other organisms, whether as pathogens or symbionts and in colonization of niches and the development of biofilms. This survival advantage is the result of sensory control of swimming behaviour. Although too small to sense a gradient along the length of the cell, and unable to swim great distances because of buffetting by Brownian motion and the curvature resulting from a rotating flagellum, bacteria can bias their random swimming direction towards a more favourable environment. The favourable environment will vary from species to species and there is now evidence that in many species this can change depending on the current physiological growth state of the cell. In general, bacteria sense changes in a range of nutrients and toxins, compounds altering electron transport, acceptors or donors into the electron transport chain, pH, temperature and even the magnetic field of the Earth. The sensory signals are balanced, and may be balanced with other sensory pathways such as quorum sensing, to identify the optimum current environment. The central sensory pathway in this process is common to most bacteria and most effectors. The environmental change is sensed by a sensory protein. In most species examined this is a transmembrane protein, sensing the external environment, but there is increasing evidence for additional cytoplasmic receptors in many species. All receptors, whether sensing sugars, amino acids or oxygen, share a cytoplasmic signalling domain that controls the activity of a

  16. New Treatments for Bacterial Keratitis

    Directory of Open Access Journals (Sweden)

    Raymond L. M. Wong

    2012-01-01

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

  17. TBK1 protects vacuolar integrity during intracellular bacterial infection.

    Directory of Open Access Journals (Sweden)

    Andrea L Radtke

    2007-03-01

    Full Text Available TANK-binding kinase-1 (TBK1 is an integral component of Type I interferon induction by microbial infection. The importance of TBK1 and Type I interferon in antiviral immunity is well established, but the function of TBK1 in bacterial infection is unclear. Upon infection of murine embryonic fibroblasts with Salmonella enterica serovar Typhimurium (Salmonella, more extensive bacterial proliferation was observed in tbk1(-/- than tbk1(+/+ cells. TBK1 kinase activity was required for restriction of bacterial infection, but interferon regulatory factor-3 or Type I interferon did not contribute to this TBK1-dependent function. In tbk1(-/-cells, Salmonella, enteropathogenic Escherichia coli, and Streptococcus pyogenes escaped from vacuoles into the cytosol where increased replication occurred, which suggests that TBK1 regulates the integrity of pathogen-containing vacuoles. Knockdown of tbk1 in macrophages and epithelial cells also resulted in increased bacterial localization in the cytosol, indicating that the role of TBK1 in maintaining vacuolar integrity is relevant in different cell types. Taken together, these data demonstrate a requirement for TBK1 in control of bacterial infection distinct from its established role in antiviral immunity.

  18. Bacterial phylogeny structures soil resistomes across habitats

    Science.gov (United States)

    Forsberg, Kevin J.; Patel, Sanket; Gibson, Molly K.; Lauber, Christian L.; Knight, Rob; Fierer, Noah; Dantas, Gautam

    2014-05-01

    Ancient and diverse antibiotic resistance genes (ARGs) have previously been identified from soil, including genes identical to those in human pathogens. Despite the apparent overlap between soil and clinical resistomes, factors influencing ARG composition in soil and their movement between genomes and habitats remain largely unknown. General metagenome functions often correlate with the underlying structure of bacterial communities. However, ARGs are proposed to be highly mobile, prompting speculation that resistomes may not correlate with phylogenetic signatures or ecological divisions. To investigate these relationships, we performed functional metagenomic selections for resistance to 18 antibiotics from 18 agricultural and grassland soils. The 2,895 ARGs we discovered were mostly new, and represent all major resistance mechanisms. We demonstrate that distinct soil types harbour distinct resistomes, and that the addition of nitrogen fertilizer strongly influenced soil ARG content. Resistome composition also correlated with microbial phylogenetic and taxonomic structure, both across and within soil types. Consistent with this strong correlation, mobility elements (genes responsible for horizontal gene transfer between bacteria such as transposases and integrases) syntenic with ARGs were rare in soil by comparison with sequenced pathogens, suggesting that ARGs may not transfer between soil bacteria as readily as is observed between human pathogens. Together, our results indicate that bacterial community composition is the primary determinant of soil ARG content, challenging previous hypotheses that horizontal gene transfer effectively decouples resistomes from phylogeny.

  19. The bacterial genus Collimonas mycophagy, weathering, and other adaptive solutions to life in oligotrophic soil environments

    NARCIS (Netherlands)

    Leveau, J.H.J.; Uroz, S.; De Boer, W.

    2010-01-01

    This minireview provides a synopsis of past and present research on the biology and ecology of members of the bacterial genus Collimonas. From the distribution, abundance and functional behaviours of these so-called collimonads emerges a general picture of bacterial adaptation to low-nutrient soil e

  20. Softness of the bacterial cell wall of Streptococcus mitis as probed by micro-electrophoresis

    NARCIS (Netherlands)

    Vadillo-Rodriguez, V.; Busscher, H.J.; Norde, W.; Mei, van der H.C.

    2002-01-01

    Chemical and structural complexity of bacterial cell surfaces complicate accurate quantification of cell surfaces properties. The presence of fibrils, fimbriae or other surface appendages on bacterial cell surfaces largely influence those properties and would therefore play a major function in inter

  1. Properties of bacterial endophytes and their proposed role in plant growth

    NARCIS (Netherlands)

    Hardoim, Pablo R.; van Overbeek, Leo S.; van Elsas, Jan Dirk

    2008-01-01

    Bacterial endophytes live inside plants for at least part of their life cycle. Studies of the interaction of endophytes with their host plants and their function within their hosts are important to address the ecological relevance of endophytes. The modulation of ethylene levels in plants by bacteri

  2. Purple Bacterial Light-harvesting Complexes: From Dreams to Structures.

    Science.gov (United States)

    Cogdell, Richard J; Hashimoto, Hideki; Gardiner, Alastair T

    2004-01-01

    This paper describes the main stages involved in the research efforts designed to try and understand the structure and function of purple bacterial antenna complexes. Wherever possible the work has been illustrated by pictures of the major people who carried it out.

  3. Bacterial peroxide forming enzymes

    OpenAIRE

    Madeira, Joaquim Paulo Curre

    2015-01-01

    Dissertação de mestrado, Engenharia Biológica, Faculdade de Ciências e Tecnologia, Universidade do Algarve; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2015 Lignin, after cellulose, is the most abundant organic polymer on Earth and has vital functions as a constituent of plant cell walls including structural resistance and protection against pathogens and hydrolysis. Notwithstanding lignin degradation by microbes represents a key-step in the co...

  4. Antibiotic resistance of bacterial biofilms

    DEFF Research Database (Denmark)

    Hoiby, N.; Bjarnsholt, T.; Givskov, M.;

    2010-01-01

    A biofilm is a structured consortium of bacteria embedded in a self-produced polymer matrix consisting of polysaccharide, protein and DNA. Bacterial biofilms cause chronic infections because they show increased tolerance to antibiotics and disinfectant chemicals as well as resisting phagocytosis...... and other components of the body's defence system. The persistence of, for example, staphylococcal infections related to foreign bodies is due to biofilm formation. Likewise, chronic Pseudomonas aeruginosa lung infection in cystic fibrosis patients is caused by biofilm-growing mucoid strains....... Characteristically, gradients of nutrients and oxygen exist from the top to the bottom of biofilms and these gradients are associated with decreased bacterial metabolic activity and increased doubling times of the bacterial cells; it is these more or less dormant cells that are responsible for some of the tolerance...

  5. Clinical applications of bacterial glycoproteins.

    Science.gov (United States)

    Fulton, Kelly M; Smith, Jeffrey C; Twine, Susan M

    2016-01-01

    There is an ongoing race between bacterial evolution and medical advances. Pathogens have the advantages of short generation times and horizontal gene transfer that enable rapid adaptation to new host environments and therapeutics that currently outpaces clinical research. Antibiotic resistance, the growing impact of nosocomial infections, cancer-causing bacteria, the risk of zoonosis, and the possibility of biowarfare all emphasize the increasingly urgent need for medical research focussed on bacterial pathogens. Bacterial glycoproteins are promising targets for alternative therapeutic intervention since they are often surface exposed, involved in host-pathogen interactions, required for virulence, and contain distinctive glycan structures. The potential exists to exploit these unique structures to improve clinical prevention, diagnosis, and treatment strategies. Translation of the potential in this field to actual clinical impact is an exciting prospect for fighting infectious diseases. PMID:26971465

  6. Bacterial Artificial Chromosome Mutagenesis Using Recombineering

    Directory of Open Access Journals (Sweden)

    Kumaran Narayanan

    2011-01-01

    Full Text Available Gene expression from bacterial artificial chromosome (BAC clones has been demonstrated to facilitate physiologically relevant levels compared to viral and nonviral cDNA vectors. BACs are large enough to transfer intact genes in their native chromosomal setting together with flanking regulatory elements to provide all the signals for correct spatiotemporal gene expression. Until recently, the use of BACs for functional studies has been limited because their large size has inherently presented a major obstacle for introducing modifications using conventional genetic engineering strategies. The development of in vivo homologous recombination strategies based on recombineering in E. coli has helped resolve this problem by enabling facile engineering of high molecular weight BAC DNA without dependence on suitably placed restriction enzymes or cloning steps. These techniques have considerably expanded the possibilities for studying functional genetics using BACs in vitro and in vivo.

  7. An assessment of bacterial small RNA target prediction programs

    OpenAIRE

    Pain, Adrien; Ott, Alban; Amine, Hamza; Rochat, Tatiana; Bouloc, Philippe; Gautheret, Daniel

    2015-01-01

    Most bacterial regulatory RNAs exert their function through base-pairing with target RNAs. Computational prediction of targets is a busy research field that offers biologists a variety of web sites and software. However, it is difficult for a non-expert to evaluate how reliable those programs are. Here, we provide a simple benchmark for bacterial sRNA target prediction based on trusted E. coli sRNA/target pairs. We use this benchmark to assess the most recent RNA target predictors as well as ...

  8. Scale-Invariant Correlations in Dynamic Bacterial Clusters

    Science.gov (United States)

    Chen, Xiao; Dong, Xu; Be'er, Avraham; Swinney, Harry L.; Zhang, H. P.

    2012-04-01

    In Bacillus subtilis colonies, motile bacteria move collectively, spontaneously forming dynamic clusters. These bacterial clusters share similarities with other systems exhibiting polarized collective motion, such as bird flocks or fish schools. Here we study experimentally how velocity and orientation fluctuations within clusters are spatially correlated. For a range of cell density and cluster size, the correlation length is shown to be 30% of the spatial size of clusters, and the correlation functions collapse onto a master curve after rescaling the separation with correlation length. Our results demonstrate that correlations of velocity and orientation fluctuations are scale invariant in dynamic bacterial clusters.

  9. Taking root: enduring effect of rhizosphere bacterial colonization in mangroves.

    Directory of Open Access Journals (Sweden)

    Newton C M Gomes

    Full Text Available BACKGROUND: Mangrove forests are of global ecological and economic importance, but are also one of the world's most threatened ecosystems. Here we present a case study examining the influence of the rhizosphere on the structural composition and diversity of mangrove bacterial communities and the implications for mangrove reforestation approaches using nursery-raised plants. METHODOLOGY/PRINCIPAL FINDINGS: A barcoded pyrosequencing approach was used to assess bacterial diversity in the rhizosphere of plants in a nursery setting, nursery-raised transplants and native (non-transplanted plants in the same mangrove habitat. In addition to this, we also assessed bacterial composition in the bulk sediment in order to ascertain if the roots of mangrove plants affect sediment bacterial composition. We found that mangrove roots appear to influence bacterial abundance and composition in the rhizosphere. Due to the sheer abundance of roots in mangrove habitat, such an effect can have an important impact on the maintenance of bacterial guilds involved in nutrient cycling and other key ecosystem functions. Surprisingly, we also noted a marked impact of initial nursery conditions on the rhizosphere bacterial composition of replanted mangrove trees. This result is intriguing because mangroves are periodically inundated with seawater and represent a highly dynamic environment compared to the more controlled nursery environment. CONCLUSIONS/SIGNIFICANCE: In as far as microbial diversity and composition influences plant growth and health, this study indicates that nursery conditions and early microbial colonization patterns of the replants are key factors that should be considered during reforestation projects. In addition to this, our results provide information on the role of the mangrove rhizosphere as a habitat for bacteria from estuarine sediments.

  10. 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...

  11. 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.

  12. A Program Against Bacterial Bioterrorism

    DEFF Research Database (Denmark)

    Kemp, Michael; Dargis, Rimtas; Andresen, Keld;

    2012-01-01

    In 2002 it was decided to establish laboratory facilities in Denmark for diagnosing agents associated with bioterrorism in order to make an immediate appropriate response to the release of such agents possible. Molecular assays for detection of specific agents and molecular and proteomic techniques...... for bacterial infections not associated with bioterrorism that are difficult to culture or identify....

  13. Molecular Mechanisms Underlying Bacterial Persisters

    DEFF Research Database (Denmark)

    Maisonneuve, Etienne; Gerdes, Kenn

    2014-01-01

    technological advances in microfluidics and reporter genes have improved this scenario. Here, we summarize recent progress in the field, revealing the ubiquitous bacterial stress alarmone ppGpp as an emerging central regulator of multidrug tolerance and persistence, both in stochastically and environmentally...

  14. Magnetotactic Bacterial Cages as Safe and Smart Gene Delivery Vehicles

    KAUST Repository

    Alsaiari, Shahad K.

    2016-07-27

    In spite of the huge advances in the area of synthetic carriers, their efficiency still poorly compares to natural vectors. Herein, we report the use of unmodified magnetotactic bacteria as a guidable delivery vehicle for DNA functionalized gold nanoparticles (AuNPs). High cargo loading is established under anaerobic conditions (bacteria is alive) through endocytosis where AuNPs are employed as transmembrane proteins mimics (facilitate endocytosis) as well as imaging agents to verify and quantify loading and release. The naturally bio-mineralized magnetosomes, within the bacteria, induce heat generation inside bacteria through magnetic hyperthermia. Most importantly after exposing the system to air (bacteria is dead) the cell wall stays intact providing an efficient bacterial vessel. Upon incubation with THP-1 cells, the magnetotactic bacterial cages (MBCs) adhere to the cell wall and are directly engulfed through the phagocytic activity of these cells. Applying magnetic hyperthermia leads to the dissociation of the bacterial microcarrier and eventual release of cargo.

  15. Mast cells: multitalented facilitators of protection against bacterial pathogens

    Science.gov (United States)

    Trivedi, Nikita H; Guentzel, M Neal; Rodriguez, Annette R; Yu, Jieh-Juen; Forsthuber, Thomas G; Arulanandam, Bernard P

    2014-01-01

    Mast cells are crucial effector cells evoking immune responses against bacterial pathogens. The positioning of mast cells at the host–environment interface, and the multitude of pathogen-recognition receptors and preformed mediator granules make these cells potentially the earliest to respond to an invading pathogen. In this review, the authors summarize the receptors used by mast cells to recognize invading bacteria and discuss the function of immune mediators released by mast cells in control of bacterial infection. The interaction of mast cells with other immune cells, including macrophages, dendritic cells and T cells, to induce protective immunity is highlighted. The authors also discuss mast cell-based vaccine strategies and the potential application in control of bacterial disease. PMID:23390944

  16. Labelling Bacterial Nanocages with Photo-switchable Fluorophores.

    Science.gov (United States)

    Putri, Rindia M; Fredy, Jean Wilfried; Cornelissen, Jeroen J L M; Koay, Melissa S T; Katsonis, Nathalie

    2016-06-17

    The robustness and biocompatibility of bacterial nanocages holds promise for bio-nanotechnologies. The propensity of these nano-carriers to penetrate cells has been demonstrated, which calls for the development of tracking strategies, both in vitro and in vivo. Here, we label bacterial nanocages with photo-switchable fluorophores, to facilitate their imaging by super-resolution microscopy. We demonstrate the functionalization of the encapsulin from Brevibacterium linens with a spiropyran, which is not fluorescent, by covalent attachment to the amine residues at the outer encapsulin shell. Upon alternating irradiation with ultraviolet and visible light, the spiropyran switches forth and back to its fluorescent merocyanine photo-isomer and thus the fluorescence can be switched on and off, reversibly. We also show that the bacterial compartments preserve their structural integrity upon covalent modification and over at least five irradiation cycles. PMID:26854330

  17. A Common Fold Mediates Vertebrate Defense and Bacterial Attack

    Energy Technology Data Exchange (ETDEWEB)

    Rosado, Carlos J.; Buckle, Ashley M.; Law, Ruby H.P.; Butcher, Rebecca E.; Kan, Wan-Ting; Bird, Catherina H.; Ung, Kheng; Browne, Kylie A.; Baran, Katherine; Bashtannyk-Puhalovich, Tanya A.; Faux, Noel G.; Wong, Wilson; Porter, Corrine J.; Pike, Robert N.; Ellisdon, Andrew M.; Pearce, Mary C.; Bottomley, Stephen P.; Emsley, Jonas; Smith, A. Ian; Rossjohn, Jamie; Hartland, Elizabeth L.; Voskoboinik, Ilia; Trapani, Joseph A.; Bird, Phillip I.; Dunstone, Michelle A.; Whisstock, James C. (PMCI-A); (Monash); (Nottingham)

    2008-10-02

    Proteins containing membrane attack complex/perforin (MACPF) domains play important roles in vertebrate immunity, embryonic development, and neural-cell migration. In vertebrates, the ninth component of complement and perforin form oligomeric pores that lyse bacteria and kill virus-infected cells, respectively. However, the mechanism of MACPF function is unknown. We determined the crystal structure of a bacterial MACPF protein, Plu-MACPF from Photorhabdus luminescens, to 2.0 angstrom resolution. The MACPF domain reveals structural similarity with poreforming cholesterol-dependent cytolysins (CDCs) from Gram-positive bacteria. This suggests that lytic MACPF proteins may use a CDC-like mechanism to form pores and disrupt cell membranes. Sequence similarity between bacterial and vertebrate MACPF domains suggests that the fold of the CDCs, a family of proteins important for bacterial pathogenesis, is probably used by vertebrates for defense against infection.

  18. Microhabitat heterogeneity across leaves and flower organs promotes bacterial diversity.

    Science.gov (United States)

    Junker, Robert R; Keller, Alexander

    2015-09-01

    Eukaryote-associated microbiomes interact with their hosts in multiple manners, thereby affecting the hosts' phenotype, physical condition and behaviour. In plants, bacteria have numerous functions, with variable net effects, both in natural and agricultural systems. However, information about the composition and diversity of the bacterial communities associated with different aboveground plant organs, particularly flowers, is lacking. In addition, the relative effects of microhabitat and environmental conditions on community establishment require further attention. Here, using culture-independent methods, we determine that leaves and three floral microhabitats (nectar, stamina and styles) of Metrosideros polymorpha (Myrtaceae), a tree endemic to Hawai'i, host unique indicator communities composed of relatively abundant bacterial taxa. These indicator communities are accompanied by a large number of ubiquitous or rare bacteria with lower abundances. In our study system, the strong effect of microhabitat filtering on plant-associated community composition and bacterial richness and diversity strongly exceeds the influence of environmental effects such as precipitation, altitude, substrate age and geographic distance. Thus, the bacterial richness of aboveground plant organs is strongly underestimated when only one microhabitat, e.g. leaves, is considered. Our study represents a first step towards a comprehensive characterization of the distribution, composition and underlying factors, of plant bacterial communities, with implications for future basic and applied research on plant health, pollination and reproduction. PMID:26253507

  19. Leaf morphology of 40 evergreen and deciduous broadleaved subtropical tree species and relationships to functional ecophysiological traits.

    Science.gov (United States)

    Kröber, W; Heklau, H; Bruelheide, H

    2015-03-01

    We explored potential of morphological and anatomical leaf traits for predicting ecophysiological key functions in subtropical trees. We asked whether the ecophysiological parameters stomatal conductance and xylem cavitation vulnerability could be predicted from microscopy leaf traits. We investigated 21 deciduous and 19 evergreen subtropical tree species, using individuals of the same age and from the same environment in the Biodiversity-Ecosystem Functioning experiment at Jiangxi (BEF-China). Information-theoretic linear model selection was used to identify the best combination of morphological and anatomical predictors for ecophysiological functions. Leaf anatomy and morphology strongly depended on leaf habit. Evergreen species tended to have thicker leaves, thicker spongy and palisade mesophyll, more palisade mesophyll layers and a thicker subepidermis. Over 50% of all evergreen species had leaves with multi-layered palisade parenchyma, while only one deciduous species (Koelreuteria bipinnata) had this. Interactions with leaf habit were also included in best multi-predictor models for stomatal conductance (gs ) and xylem cavitation vulnerability. In addition, maximum gs was positively related to log ratio of palisade to spongy mesophyll thickness. Vapour pressure deficit (vpd) for maximum gs increased with the log ratio of palisade to spongy mesophyll thickness in species having leaves with papillae. In contrast, maximum specific hydraulic conductivity and xylem pressure at which 50% loss of maximum specific xylem hydraulic conductivity occurred (Ψ50 ) were best predicted by leaf habit and density of spongy parenchyma. Evergreen species had lower Ψ50 values and lower maximum xylem hydraulic conductivities. As hydraulic leaf and wood characteristics were reflected in structural leaf traits, there is high potential for identifying further linkages between morphological and anatomical leaf traits and ecophysiological responses.

  20. The Human Microbiome during Bacterial Vaginosis.

    Science.gov (United States)

    Onderdonk, Andrew B; Delaney, Mary L; Fichorova, Raina N

    2016-04-01

    Bacterial vaginosis (BV) is the most commonly reported microbiological syndrome among women of childbearing age. BV is characterized by a shift in the vaginal flora from the dominant Lactobacillus to a polymicrobial flora. BV has been associated with a wide array of health issues, including preterm births, pelvic inflammatory disease, increased susceptibility to HIV infection, and other chronic health problems. A number of potential microbial pathogens, singly and in combinations, have been implicated in the disease process. The list of possible agents continues to expand and includes members of a number of genera, including Gardnerella, Atopobium, Prevotella, Peptostreptococcus, Mobiluncus, Sneathia, Leptotrichia, Mycoplasma, and BV-associated bacterium 1 (BVAB1) to BVAB3. Efforts to characterize BV using epidemiological, microscopic, microbiological culture, and sequenced-based methods have all failed to reveal an etiology that can be consistently documented in all women with BV. A careful analysis of the available data suggests that what we term BV is, in fact, a set of common clinical signs and symptoms that can be provoked by a plethora of bacterial species with proinflammatory characteristics, coupled to an immune response driven by variability in host immune function. PMID:26864580

  1. Steps in the bacterial flagellar motor.

    Directory of Open Access Journals (Sweden)

    Thierry Mora

    2009-10-01

    Full Text Available The bacterial flagellar motor is a highly efficient rotary machine used by many bacteria to propel themselves. It has recently been shown that at low speeds its rotation proceeds in steps. Here we propose a simple physical model, based on the storage of energy in protein springs, that accounts for this stepping behavior as a random walk in a tilted corrugated potential that combines torque and contact forces. We argue that the absolute angular position of the rotor is crucial for understanding step properties and show this hypothesis to be consistent with the available data, in particular the observation that backward steps are smaller on average than forward steps. We also predict a sublinear speed versus torque relationship for fixed load at low torque, and a peak in rotor diffusion as a function of torque. Our model provides a comprehensive framework for understanding and analyzing stepping behavior in the bacterial flagellar motor and proposes novel, testable predictions. More broadly, the storage of energy in protein springs by the flagellar motor may provide useful general insights into the design of highly efficient molecular machines.

  2. The neglected intrinsic resistome of bacterial pathogens.

    Directory of Open Access Journals (Sweden)

    Alicia Fajardo

    Full Text Available Bacteria with intrinsic resistance to antibiotics are a worrisome health problem. It is widely believed that intrinsic antibiotic resistance of bacterial pathogens is mainly the consequence of cellular impermeability and activity of efflux pumps. However, the analysis of transposon-tagged Pseudomonas aeruginosa mutants presented in this article shows that this phenotype emerges from the action of numerous proteins from all functional categories. Mutations in some genes make P. aeruginosa more susceptible to antibiotics and thereby represent new targets. Mutations in other genes make P. aeruginosa more resistant and therefore define novel mechanisms for mutation-driven acquisition of antibiotic resistance, opening a new research field based in the prediction of resistance before it emerges in clinical environments. Antibiotics are not just weapons against bacterial competitors, but also natural signalling molecules. Our results demonstrate that antibiotic resistance genes are not merely protective shields and offer a more comprehensive view of the role of antibiotic resistance genes in the clinic and in nature.

  3. Cognitive outcome in adults after bacterial meningitis.

    NARCIS (Netherlands)

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

    2007-01-01

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

  4. Distributions of Bacterial Generalists among the Guts of Birds, Fish, and Mammals - abstract

    Science.gov (United States)

    Complex distributions of bacterial taxa within diverse animal microbiomes have inspired ecological and biogeographical approaches to revealing the functions of taxa that may be most important for host health. Of particular interest are bacteria that find many diverse habitats sui...

  5. Filtration properties of bacterial cellulose membranes

    OpenAIRE

    Lehtonen, Janika

    2015-01-01

    Bacterial cellulose has the same molecular formula as cellulose from plant origin, but it is characterized by several unique properties including high purity, crystallinity and mechanical strength. These properties are dependent on parameters such as the bacterial strain used, the cultivation conditions and post-growth processing. The possibility to achieve bacterial cellulose membranes with different properties by varying these parameters could make bacterial cellulose an interesting materi...

  6. Synthesis of Multifunctional Cellulose Nanocrystals for Lectin Recognition and Bacterial Imaging

    OpenAIRE

    Zhou, Juan; Butchosa, Núria; Jayawardena, H. Surangi N.; Park, JaeHyeung; Zhou, Qi; Yan, Mingdi; Ramström, Olof

    2015-01-01

    Multifunctional cellulose nanocrystals have been synthesized and applied as a new type of glyconanomaterial in lectin binding and bacterial imaging. The cellulose nanocrystals were prepared by TEMPO-mediated oxidation and acidic hydrolysis, followed by functionalization with a quinolone fluorophore and carbohydrate ligands. The cellulose nanocrystals were subsequently applied in interaction studies with carbohydrate-binding proteins and in bacterial imaging. The results show that the function...

  7. Distribution of Triplet Separators in Bacterial Genomes

    Institute of Scientific and Technical Information of China (English)

    HU Rui; ZHENG Wei-Mou

    2001-01-01

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

  8. Bacterial Cellulose From Rice Waste Water With Addition Chitosan, Glycerol, And Silver Nanoparticle

    Directory of Open Access Journals (Sweden)

    Eli Rohaeti

    2016-05-01

    Full Text Available This study aimed to prepare silver nanoparticles chemically, deposite silver nanoparticles on bacterial cellulose-chitosan-glycerol composite based rice waste water, as well as test the antibacterial activity of bacterial cellulose and its composite. Preparation of silver nanoparticles was conducted by chemical reduction of silver nitrate solution, as well as trisodium citrate as the reductor. Bacterial cellulose from rice waste water is fermented by the bacteria Acetobacter xylinum for 7 days. The dried bacterial cellulose was composited with chitosan and glycerol by immersion method on 2% of chitosan solution and 0.5% of glycerol solution. UV-Vis spectroscopy is used to determine the formation of silvernanoparticles and Particle Size Analyzer to test the size and particle size distribution. Characterization was conducted to bacterial cellulose and its composite included functional groups by FTIR, the mechanical properties by Tensile Tester, crystallinity by XRD, surface photograph by SEM, and antibacterial test against S. aureus and E. coli by the shake flask turbidimetry method. Silver nanoparticle characterization indicated that silver nanoparticles are formed at a wavelength of 421.80 nm, yellow, diameter particle size of 61.8 nm. SEM images showed that the surface of bacterial cellulose had deposited silver nanoparticles and antibacterial test showed an inhibitory effect of bacterial cellulose, bacterial cellulose-chitosan composite, and bacterial cellulose-chitosan-glycerol composite which are deposited silver nanoparticles against the growth of S. aureus and E. coli bacteria.

  9. Soil bacterial communities respond to mowing and nutrient addition in a steppe ecosystem.

    Science.gov (United States)

    Zhang, Ximei; Chen, Quansheng; Han, Xingguo

    2013-01-01

    In many grassland ecosystems, nitrogen (N) and phosphorus (P) are added to improve plant productivity, and the aboveground plant biomass is mowed and stored as hay for the bullamacow. Nutrient addition and mowing affect the biodiversity and ecosystem functioning, and most of the previous studies have primarily focused on their effects on macro-organisms, neglecting the responses of soil microbial communities. In this study, we examined the changes in three community attributes (abundance, richness, and composition) of the entire bacterial kingdom and 16 dominant bacterial phyla/classes in response to mowing, N addition, P addition, and their combinations, by conducting a 5-year experiment in a steppe ecosystem in Inner Mongolia, China. Overall, N addition had a greater effect than mowing and P addition on most of these bacterial groups, as indicated by changes in the abundance, richness and composition in response to these treatments. N addition affected these soil bacterial groups primarily through reducing soil pH and increasing available N content. Meanwhile, the 16 bacterial phyla/classes responded differentially to these experimental treatments, with Acidobacteria, Acidimicrobidae, Deltaproteobacteria, and Gammaproteobacteria being the most sensitive. The changes in the abundance, richness, and composition of various bacterial groups could imply some potential shift in their ecosystem functions. Furthermore, the important role of decreased soil pH caused by N addition in affecting soil bacterial communities suggests the importance of restoring acidified soil to maintain soil bacterial diversity. PMID:24391915

  10. 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.

  11. Bacterial survival in Martian conditions

    CERN Document Server

    D'Alessandro, Giuseppe Galletta; Giulio Bertoloni; Maurizio

    2010-01-01

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

  12. [Bacterial vaginal fluor in intrauterine contraception].

    Science.gov (United States)

    Feichter, G E; Nohlen, M; Tauber, P F

    1979-11-01

    Vaginal swabs obtained from 100 IUD-users were examined bacteriologically. Fifty-one women had vaginal discharge and 49 women used as control group had no complaints originating either from the IUD or from the genital tract. In the group of IUD-users with vaginal discharge the number of bacterial isolates was higher and the cultures were more diversified. The nulliparous patients in this group exhibited more anaerobic cultures than the IUD-users without discharge. The significance of vaginal discharge in IUD-users is its function as a pool for pathogenic bacteria which may provoke and/or maintain inflammatory diseases of the female genital tract. IUD-users with vaginal discharge do therefore need not only bacteriologic diagnosis, but also consequent treatment of the discharge.

  13. Describing the structural robustness landscape of bacterial small RNAs

    Directory of Open Access Journals (Sweden)

    Rodrigo Guillermo

    2012-04-01

    Full Text Available Abstract Background The potential role of RNA molecules as gene expression regulators has led to a new perspective on the intracellular control and genome organization. Because secondary structures are crucial for their regulatory role, we sought to investigate their robustness to mutations and environmental changes. Results Here, we dissected the structural robustness landscape of the small non-coding RNAs (sncRNAs encoded in the genome of the bacterium Escherichia coli. We found that bacterial sncRNAs are not significantly robust to both mutational and environmental perturbations when compared against artificial, unbiased sequences. However, we found that, on average, bacterial sncRNAs tend to be significantly plastic, and that mutational and environmental robustness strongly correlate. We further found that, on average, epistasis in bacterial sncRNAs is significantly antagonistic, and positively correlates with plasticity. Moreover, the evolution of robustness is likely dependent upon the environmental stability of the cell, with more fluctuating environments leading to the emergence and fixation of more robust molecules. Mutational robustness also appears to be correlated with structural functionality and complexity. Conclusion Our study provides a deep characterization of the structural robustness landscape of bacterial sncRNAs, suggesting that evolvability could be evolved as a consequence of selection for more plastic molecules. It also supports that environmental fluctuations could promote mutational robustness. As a result, plasticity emerges to link robustness, functionality and evolvability.

  14. Differentiation of regions with atypical oligonucleotide composition in bacterial genomes

    Directory of Open Access Journals (Sweden)

    Reva Oleg N

    2005-10-01

    Full Text Available Abstract Background Complete sequencing of bacterial genomes has become a common technique of present day microbiology. Thereafter, data mining in the complete sequence is an essential step. New in silico methods are needed that rapidly identify the major features of genome organization and facilitate the prediction of the functional class of ORFs. We tested the usefulness of local oligonucleotide usage (OU patterns to recognize and differentiate types of atypical oligonucleotide composition in DNA sequences of bacterial genomes. Results A total of 163 bacterial genomes of eubacteria and archaea published in the NCBI database were analyzed. Local OU patterns exhibit substantial intrachromosomal variation in bacteria. Loci with alternative OU patterns were parts of horizontally acquired gene islands or ancient regions such as genes for ribosomal proteins and RNAs. OU statistical parameters, such as local pattern deviation (D, pattern skew (PS and OU variance (OUV enabled the detection and visualization of gene islands of different functional classes. Conclusion A set of approaches has been designed for the statistical analysis of nucleotide sequences of bacterial genomes. These methods are useful for the visualization and differentiation of regions with atypical oligonucleotide composition prior to or accompanying gene annotation.

  15. Bacterial communication and group behavior

    OpenAIRE

    Greenberg, E. Peter

    2003-01-01

    The existence of species-specific and interspecies bacterial cell-cell communication and group organization was only recently accepted. Researchers are now realizing that the ability of these microbial teams to communicate and form structures, known as biofilms, at key times during the establishment of infection significantly increases their ability to evade both host defenses and antibiotics. This Perspective series discusses the known signaling mechanisms, the roles they play in both chroni...

  16. The problem of bacterial diarrhoea.

    Science.gov (United States)

    Harries, J T

    1976-01-01

    The reported incidence of "pathogenic" bacteria, as judged by serotype, in the stools of children with acute diarrhoea has varied from 4 to 33% over the last twenty years. Techniques such as tissue culture provide a means for detecting enterotoxin-producing strains of bacteria, strains which often do not possess "pathogenic" serotypes. "Pathogenicity" requires redefinition, and the aetiological importance of bacteria in diarrhoea is probably considerably greater than previous reports have indicated. Colonization of the bowel by a pathogen will result in structural and/or mucosal abnormalities, and will depend on a series of complex interactions between the external environment, the pathogen, and the host and its resident bacterial flora. Enteropathogenic bacteria may be broadly classified as (i) invasive (e.g. Shigella, Salmonella and some Escherichia coli) which predominantly affect the distal bowel, or (ii) non-invasive (e.g. Vibrio cholerae and E. coli) which affect the proximal bowel. V. cholerae and E. coli elaborate heat-labile enterotoxins which activate adenylate cyclase and induce small intestinal secretion; the secretory effects of heat-stable E. coli and heat-labile Shigella dysenteriae enterotoxins are not accompanied by cyclase activation. The two major complications of acute diarrhoea are (i) hypernatraemic dehydration with its attendant neurological, renal and vascular lesions, and (ii) protracted diarrhoea which may lead to severe malnutrition. Deconjugation of bile salts and colonization of the small bowel with toxigenic strains of E. coli may be important in the pathophysiology of the protracted diarrhoea syndrome. The control of bacterial diarrhoea requires a corrdinated political, educational, social, public health and scientific attack. Bacterial diarrhoea is a major health problem throughout the world, and carries an appreciable morbidity and mortality. This is particularly the case during infancy, and in those developing parts of the world

  17. Bacterial survival in Martian conditions

    OpenAIRE

    Galletta, Giuseppe; Bertoloni, Giulio; D'Alessandro, Maurizio

    2010-01-01

    We shortly discuss the observable consequences of the two hypotheses about the origin of life on Earth and Mars: the Lithopanspermia (Mars to Earth or viceversa) and the origin from a unique progenitor, that for Earth is called LUCA (the LUCA hypothesis). To test the possibility that some lifeforms similar to the terrestrial ones may survive on Mars, we designed and built two simulators of Martian environments where to perform experiments with different bacterial strains: LISA and mini-LISA. ...

  18. Small intestinal bacterial overgrowth syndrome

    Institute of Scientific and Technical Information of China (English)

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

    2010-01-01

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

  19. Population dynamics of bacterial persistence

    OpenAIRE

    Patra, Pintu

    2014-01-01

    The life of microorganisms is characterized by two main tasks, rapid growth under conditions permitting growth and survival under stressful conditions. The environments, in which microorganisms dwell, vary in space and time. The microorganisms innovate diverse strategies to readily adapt to the regularly fluctuating environments. Phenotypic heterogeneity is one such strategy, where an isogenic population splits into subpopulations that respond differently under identical environments. Bacteri...

  20. Immunization by a bacterial aerosol

    OpenAIRE

    Garcia-Contreras, Lucila; Wong, Yun-Ling; Muttil, Pavan; Padilla, Danielle; Sadoff, Jerry; DeRousse, Jessica; Germishuizen, Willem Andreas; Goonesekera, Sunali; Elbert, Katharina; Bloom, Barry R.; Miller, Rich; Fourie, P. Bernard; Hickey, Anthony; Edwards, David

    2008-01-01

    By manufacturing a single-particle system in two particulate forms (i.e., micrometer size and nanometer size), we have designed a bacterial vaccine form that exhibits improved efficacy of immunization. Microstructural properties are adapted to alter dispersive and aerosol properties independently. Dried “nanomicroparticle” vaccines possess two axes of nanoscale dimensions and a third axis of micrometer dimension; the last one permits effective micrometer-like physical dispersion, and the form...

  1. Rheumatoid arthritis and bacterial infections

    OpenAIRE

    N L Prokopjeva; N N Vesikova; I M Marusenko; V A Ryabkov

    2008-01-01

    To study features of bacterial infections course in pts with rheumatoid arthritis (RA) and changes of laboratory measures after focus of infection sanation. Material and methods. 46 pts with definite rheumatoid arthritis were examined at the time of comorbid infection (Cl) detection and after infection focus sanation. Bacteriological test with evaluation of flora sensitivity to antibiotics by disco-diffusion method was performed at baseline and after the course of antibacterial therapy to ass...

  2. Molecular approaches for bacterial azoreductases

    OpenAIRE

    Montira Leelakriangsak

    2013-01-01

    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...

  3. Bacterial meningitis by streptococcus agalactiae

    OpenAIRE

    Villarreal-Velásquez Tatiana Paola; Cortés-Daza César Camilo

    2012-01-01

    Introduction: bacterial meningitis is an infectious disease considered a medicalemergency. The timely management has an important impact on the evolution of thedisease. Streptococcus agalactiae, a major causative agent of severe infections innewborns can colonize different tissues, including the central nervous system.Case report: Male patient 47 years old from rural areas, with work activity as amilker of cattle, referred to tertiary care, with disorientation, neck stiffness, and grandmal se...

  4. Panamanian frog species host unique skin bacterial communities

    Directory of Open Access Journals (Sweden)

    Lisa K. Belden

    2015-10-01

    Full Text Available Vertebrates, including amphibians, host diverse symbiotic microbes that contribute to host disease resistance. Globally, and especially in montane tropical systems, many amphibian species are threatened by a chytrid fungus, Batrachochytrium dendrobatidis (Bd, that causes a lethal skin disease. Bd therefore may be a strong selective agent on the diversity and function of the microbial communities inhabiting amphibian skin. In Panamá, amphibian population declines and the spread of Bd have been tracked. In 2012, we completed a field survey in Panamá to examine frog skin microbiota in the context of Bd infection. We focused on three frog species and collected two skin swabs per frog from a total of 136 frogs across four sites that varied from west to east in the time since Bd arrival. One swab was used to assess bacterial community structure using 16S rRNA amplicon sequencing and to determine Bd infection status, and one was used to assess metabolite diversity, as the bacterial production of anti-fungal metabolites is an important disease resistance function. The skin microbiota of the three Panamanian frog species differed in OTU (operational taxonomic unit, ~bacterial species community composition and metabolite profiles, although the pattern was less strong for the metabolites. Comparisons between frog skin bacterial communities from Panamá and the US suggest broad similarities at the phylum level, but key differences at lower taxonomic levels. In our field survey in Panamá, across all four sites, only 35 individuals (~26% were Bd infected. There was no clustering of OTUs or metabolite profiles based on Bd infection status and no clear pattern of west-east changes in OTUs or metabolite profiles across the four sites. Overall, our field survey data suggest that different bacterial communities might be producing broadly similar sets of metabolites across frog hosts and sites. Community structure and function may not be as tightly coupled in

  5. 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.

  6. Cytochemical Differences in Bacterial Glycocalyx

    Science.gov (United States)

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

    2005-02-01

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

  7. Effects of Plant Biomass, Plant Diversity, and Water Content on Bacterial Communities in Soil Lysimeters: Implications for the Determinants of Bacterial Diversity▿ †

    OpenAIRE

    Zul, Delita; Denzel, Sabine; Kotz, Andrea; Overmann, Jörg

    2007-01-01

    Soils may comprise tens of thousands to millions of bacterial species. It is still unclear whether this high level of diversity is governed by functional redundancy or by a multitude of ecological niches. In order to address this question, we analyzed the reproducibility of bacterial community composition after different experimental manipulations. Soil lysimeters were planted with four different types of plant communities, and the water content was adjusted. Group-specific phylogenetic finge...

  8. The study of the extreme radiation tolerance mechanisms of the bacterium Deinococcus deserti by a functional genomics approach; Etude des mecanismes de l'extreme tolerance aux radiations de la bacterie Deinococcus deserti par une approche de genomique fonctionnelle

    Energy Technology Data Exchange (ETDEWEB)

    Dulermo, R.

    2009-12-15

    The genome of Deinococcus deserti, a highly radiation-tolerant bacterium, was analyzed and compared to those of D. radiodurans and D. geothermalis. About 230 proteins are specifically conserved in these 3 species, including IrrE, a regulator protein essential for radio tolerance. D.deserti has several supplementary DNA repair genes, like imuY and dnaE2 (trans-lesion DNA polymerases). Moreover, D. deserti has 3 recA that code for 2 different RecA proteins (RecAC et RecAP). To study these genes, genetic tools were developed for D. deserti. Different results suggest that IrrE, required for the induction of several genes after irradiation, has peptidase activity. The 2 RecA proteins are functional for DNA repair. D. deserti is mutable by UV, which requires ImuY, DnaE2 and RecAC, but not RecAP. (author)

  9. Molecular cloning, bacterial expression and functional characterisation of cytochrome P450 monooxygenase, CYP97C27, and NADPH-cytochrome P450 reductase, CPR I, from Croton stellatopilosus Ohba.

    Science.gov (United States)

    Sintupachee, Siriluk; Ngamrojanavanich, Nattaya; Sitthithaworn, Worapan; De-Eknamkul, Wanchai

    2014-12-01

    The cDNAs for cytochrome P450 monooxygenase (designated as CYP97C27 by D. Nelson's group) and NADPH-cytochrome P450 reductase (designated as CPR I based on its classification) were isolated from Croton stellatopilosus leaves, which actively biosynthesise plaunotol (18-OH geranylgeraniol). CYP97C27 and CPR I contain open reading frames encoding proteins of 471 and 711 amino acids with predicted molecular masses of 53 and 79kDa, respectively. By aligning the deduced sequences of CYP97C27 and CPR I with other plant species, all functional domains of CYP97C27 (heme and oxygen binding) and CPR I (CYP- and FMN, FAD, and NADPH cofactor binding) were identified. Amino acid sequence comparison indicated that both CYP97C27 (85-93%) and CPR I (79-83%) share high sequence identities with homologous proteins in other plant species, suggesting that CYP97C27 belongs to the CYP97C subfamily and that CPR I belongs to class I of the dicotyledonous CPR. Functional characterisation of both enzymes, produced in Escherichia coli (pET32a/BL21(DE3)) as recombinant proteins, showed that simultaneous incubation of CYP97C27 and CPR I with the substrate geranylgeraniol (GGOH) and coenzyme NADPH led to formation of the product plaunotol. In C. stellatopilosus, the levels of the CYP97C27 and CPR I transcripts were highly correlated with those of several mRNAs involved in the plaunotol biosynthetic pathway, suggesting that CYP97C27 and CPR I are the enzymes that catalyse the last hydroxylation step of the pathway.

  10. Functional expression of a putative geraniol 8-hydroxylase by reconstitution of bacterially expressed plant CYP76F45 and NADPH-cytochrome P450 reductase CPR I from Croton stellatopilosus Ohba.

    Science.gov (United States)

    Sintupachee, Siriluk; Promden, Worrawat; Ngamrojanavanich, Nattaya; Sitthithaworn, Worapan; De-Eknamkul, Wanchai

    2015-10-01

    While attempting to isolate the enzyme geranylgeraniol 18-hydroxylase, which is involved in plaunotol biosynthesis in Croton stellatopilosus (Cs), the cDNAs for a cytochrome P450 monooxygenase(designated as CYP76F45) and an NADPH-cytochrome P450 reductase (designated as CPR I based on its classification) were isolated from the leaf. The CYP76F45 and CsCPR I genes have open reading frames (ORFs) encoding 507- and 711-amino acid proteins with predicted relative molecular weights of 56.7 and 79.0 kDa,respectively. Amino acid sequence comparison showed that both CYP76F45 (63–73%) and CsCPR I (79–83%) share relatively high sequence identities with homologous proteins in other plant species.Phylogenetic tree analysis confirmed that CYP76F45 belongs to the CYP76 family and that CsCPR I belongs to Class I of dicotyledonous CPRs, with both being closely related to Ricinus communis genes. Functional characterization of both enzymes, each expressed separately in Escherichia coli as recombinant proteins,showed that only simultaneous incubation of the membrane bound proteins with the substrate geraniol (GOH) and the coenzyme NADPH could form 8-hydroxygeraniol. The enzyme mixture could also utilize acyclic sesquiterpene farnesol (FOH) with a comparable substrate preference ratio (GOH:FOH) of 54:46. The levelsof the CYP76F45 and CsCPR I transcripts in the shoots, leaves and twigs of C. stellatopilosus were correlated with the levels of a major monoterpenoid indole alkaloid, identified tentatively as 19-Evallesamine,that accumulated in these plant parts. These results suggested that CYP76F45 and CPR I function as the enzyme geraniol-8-hydroxylase (G8H), which is likely to be involved in the biosynthesis of the indole alkaloid in C. stellatopilosus [corrected].

  11. Bacterial adhesion and biofilms on surfaces

    Institute of Scientific and Technical Information of China (English)

    Trevor Roger Garrett; Manmohan Bhakoo; Zhibing Zhang

    2008-01-01

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

  12. Bacterial migration through punctured surgical gloves under real surgical conditions

    Directory of Open Access Journals (Sweden)

    Heidecke Claus-Dieter

    2010-07-01

    Full Text Available Abstract Background The aim of this study was to confirm recent results from a previous study focussing on the development of a method to measure the bacterial translocation through puncture holes in surgical gloves under real surgical conditions. Methods An established method was applied to detect bacterial migration from the operating site through the punctured glove. Biogel™ double-gloving surgical gloves were used during visceral surgeries over a 6-month period. A modified Gaschen-bag method was used to retrieve organisms from the inner glove, and thus-obtained bacteria were compared with micro-organisms detected by an intra-operative swab. Results In 20 consecutive procedures, 194 gloves (98 outer gloves, 96 inner gloves were examined. The rate of micro-perforations of the outer surgical glove was 10% with a median wearing time of 100 minutes (range: 20-175 minutes. Perforations occurred in 81% on the non-dominant hand, with the index finger most frequently (25% punctured. In six cases, bacterial migration could be demonstrated microbiologically. In 5% (5/98 of outer gloves and in 1% (1/96 of the inner gloves, bacterial migration through micro-perforations was observed. For gloves with detected micro-perforations (n = 10 outer layers, the calculated migration was 50% (n = 5. The minimum wearing time was 62 minutes, with a calculated median wearing time of 71 minutes. Conclusions This study confirms previous results that bacterial migration through unnoticed micro-perforations in surgical gloves does occur under real practical surgical conditions. Undetected perforation of surgical gloves occurs frequently. Bacterial migration from the patient through micro-perforations on the hand of surgeons was confirmed, limiting the protective barrier function of gloves if worn over longer periods.

  13. Bacterial community diversity in municipal waste landfill sites.

    Science.gov (United States)

    Song, Liyan; Wang, Yangqing; Tang, Wei; Lei, Yu

    2015-09-01

    Little is known about the bacterial diversity of landfills and how environmental factors impact the diversity. In this study, PCR-based 454 pyrosequencing was used to investigate the bacterial communities of ten landfill leachate samples from five landfill sites in China. A total of 137 K useable sequences from the V3-V6 regions of the 16S rRNA gene were retrieved from 205 K reads. These sequences revealed the presence of a large number of operational taxonomic units (OTUs) in the landfills (709-1599 OTUs per sample). The most predominant bacterial representatives in the landfills investigated, regardless of geographic area, included Gammaproteobacteria, Firmicutes, and Bacteroidetes. The phyla Fusobacteria and Tenericutes were also found for the first time to be predominant in the landfills. The phylum Fusobacteria predominated (51.5 and 48.8%) in two semi-arid landfills, and the phylum Tenericutes dominated (30.6%) at one humid, subtropical landfill. Further, a large number of Pseudomonas was detected in most samples, comprising the dominant group and accounting for 40.9 to 92.4% of the total abundance. Principal component analysis (PCA) and cluster analysis based on OTU abundance showed that the abundant taxa separated the bacterial community. Canonical correlation analysis (CCA) suggested that precipitation and landfilling age significantly impact on the bacterial community structure. The bacterial community function (e.g., cellulolytic bacteria, sulfate-reducing bacteria (SRB), sulfate-oxidizing bacteria, and xenobiotic organic compound (XOC)-degrading bacteria) was also diverse, but the pattern is unclear.

  14. Genefish: an alternate metagenomic approach for capturing targeted bacterial diversity in an engineered recipient E. coli strain

    OpenAIRE

    Lombard, Nathalie; Faugier, Aurélie; Lavire, Céline; Jacquiod, Samuel; Philippot, Laurent; Zhang, Xiaojun; Lazzaroni, Jean-Claude; Simonet, Pascal; Franqueville, Laure

    2009-01-01

    The metagenomic approach, defined as the direct recovery and cloning of bacterial DNA from the environment in domesticated bacterial hosts has been widely used to study bacterial populations and their functional genes in numerous environments. The advantage of this approach over conventional culture based techniques is that it encompasses a wider range of bacteria by bypassing the bias of uncultivability of more than 99% of the bacteria in soil. However, in complex and rich environments such ...

  15. Molecular evolution of bacterial indoleamine 2,3-dioxygenase.

    Science.gov (United States)

    Yuasa, Hajime J; Ushigoe, Akiko; Ball, Helen J

    2011-10-01

    Indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO) are tryptophan-degrading enzymes that catalyze the first step in L-Trp catabolism via the kynurenine pathway. In mammals, TDO is mainly expressed in the liver and primarily supplies nicotinamide adenine dinucleotide (NAD(+)). TDO is widely distributed from mammals to bacteria. Active IDO enzymes have been reported only in vertebrates and fungi. In mammals, IDO activity plays a significant role in the immune system while in fungal species, IDO is constitutively expressed and supplies NAD(+), like mammalian TDO. A search of genomic databases reveals that some bacterial species also have a putative IDO gene. A phylogenetic analysis clustered bacterial IDOs into two groups, group I or group II bacterial IDOs. The catalytic efficiencies of group I bacterial IDOs were very low and they are suspected not to contribute significantly to L-Trp metabolism. The bacterial species bearing the group I bacterial IDO are scattered across a few phyla and no phylogenetically close relationship is observed between them. This suggests that the group I bacterial IDOs might be acquired by horizontal gene transmission that occurred in each lineage independently. In contrast, group II bacterial IDOs showed rather high catalytic efficiency. Particularly, the enzymatic characteristics (K(m), V(max) and inhibitor selectivity) of the Gemmatimonas aurantiaca IDO are comparable to those of mammalian IDO1, although comparison of the IDO sequences does not suggest a close evolutionary relationship. In several bacteria, TDO and the kynureninase gene (kynU) are clustered on their chromosome suggesting that these genes could be transcribed in an operon. Interestingly, G. aurantiaca has no TDO, and the IDO is clustered with kynU on its chromosome. Although the G. aurantiaca also has NadA and NadB to synthesize a quinolinic acid (a precursor of NAD(+)) via the aspartate pathway, the high activity of the G. aurantiaca IDO flanking

  16. Prolonged inhibition of bacterial protein synthesis abolishes Salmonella invasion.

    OpenAIRE

    MacBeth, K J; Lee, C. A.

    1993-01-01

    We have found that prolonged inhibition of bacterial protein synthesis abolishes the ability of Salmonella typhimurium to enter HEp-2 cells. Our results suggest that an essential invasion factor has a functional half-life that is seen as a gradual loss of invasiveness in the absence of protein synthesis. Therefore, Salmonella invasiveness appears to be a transient phenotype that is lost unless protein synthesis is maintained. This finding may explain why salmonellae grown to stationary phase ...

  17. Molecular Architecture of the Bacterial Flagellar Motor in Cells

    OpenAIRE

    Zhao, Xiaowei; Norris, Steven J; Liu, Jun

    2014-01-01

    The flagellum is one of the most sophisticated self-assembling molecular machines in bacteria. Powered by the proton-motive force, the flagellum rapidly rotates in either a clockwise or counterclockwise direction, which ultimately controls bacterial motility and behavior. Escherichia coli and Salmonella enterica have served as important model systems for extensive genetic, biochemical, and structural analysis of the flagellum, providing unparalleled insights into its structure, function, and ...

  18. System-level design of bacterial cell cycle control

    OpenAIRE

    McAdams, Harley H.; Shapiro, Lucy

    2009-01-01

    Understanding of the cell cycle control logic in Caulobacter has progressed to the point where we now have an integrated view of the operation of an entire bacterial cell cycle system functioning as a state machine. Oscillating levels of a few temporally-controlled master regulator proteins in a cyclical circuit drive cell cycle progression. To a striking degree, the cell cycle regulation is a whole cell phenomenon. Phospho-signaling proteins and proteases dynamically deployed to specific loc...

  19. FbsA-Driven Fibrinogen Polymerization: A Bacterial ``Deceiving Strategy''

    Science.gov (United States)

    Pierno, Matteo; Maravigna, Laura; Piazza, Roberto; Visai, Livia; Speziale, Pietro

    2006-01-01

    We show that FbsA, a cell wall protein of the bacterium Streptococcus agalactiae, promotes large-scale aggregation of human plasma fibrinogen, leading to the formation of a semiflexible polymerlike network. This extensive aggregation process takes place not only in solution, but also on FbsA-functionalized colloidal particles, and leads to the formation of a thick layer on the bacterial cell wall itself, which becomes an efficient mask against phagocytosis.

  20. Control of intestinal bacterial proliferation in regulation of lifespan in Caenorhabditis elegans

    Directory of Open Access Journals (Sweden)

    Portal-Celhay Cynthia

    2012-03-01

    Full Text Available Abstract Background A powerful approach to understanding complex processes such as aging is to use model organisms amenable to genetic manipulation, and to seek relevant phenotypes to measure. Caenorhabditis elegans is particularly suited to studies of aging, since numerous single-gene mutations have been identified that affect its lifespan; it possesses an innate immune system employing evolutionarily conserved signaling pathways affecting longevity. As worms age, bacteria accumulate in the intestinal tract. However, quantitative relationships between worm genotype, lifespan, and intestinal lumen bacterial load have not been examined. We hypothesized that gut immunity is less efficient in older animals, leading to enhanced bacterial accumulation, reducing longevity. To address this question, we evaluated the ability of worms to control bacterial accumulation as a functional marker of intestinal immunity. Results We show that as adult worms age, several C. elegans genotypes show diminished capacity to control intestinal bacterial accumulation. We provide evidence that intestinal bacterial load, regulated by gut immunity, is an important causative factor of lifespan determination; the effects are specified by bacterial strain, worm genotype, and biologic age, all acting in concert. Conclusions In total, these studies focus attention on the worm intestine as a locus that influences longevity in the presence of an accumulating bacterial population. Further studies defining the interplay between bacterial species and host immunity in C. elegans may provide insights into the general mechanisms of aging and age-related diseases.

  1. Channel-forming bacterial toxins in biosensing and macromolecule delivery.

    Science.gov (United States)

    Gurnev, Philip A; Nestorovich, Ekaterina M

    2014-08-21

    To intoxicate cells, pore-forming bacterial toxins are evolved to allow for the transmembrane traffic of different substrates, ranging from small inorganic ions to cell-specific polypeptides. Recent developments in single-channel electrical recordings, X-ray crystallography, protein engineering, and computational methods have generated a large body of knowledge about the basic principles of channel-mediated molecular transport. These discoveries provide a robust framework for expansion of the described principles and methods toward use of biological nanopores in the growing field of nanobiotechnology. This article, written for a special volume on "Intracellular Traffic and Transport of Bacterial Protein Toxins", reviews the current state of applications of pore-forming bacterial toxins in small- and macromolecule-sensing, targeted cancer therapy, and drug delivery. We discuss the electrophysiological studies that explore molecular details of channel-facilitated protein and polymer transport across cellular membranes using both natural and foreign substrates. The review focuses on the structurally and functionally different bacterial toxins: gramicidin A of Bacillus brevis, α-hemolysin of Staphylococcus aureus, and binary toxin of Bacillus anthracis, which have found their "second life" in a variety of developing medical and technological applications.

  2. Update and actual trends on bacterial infections following liver transplantation

    Institute of Scientific and Technical Information of China (English)

    Jose Luis del Pozo

    2008-01-01

    Recent advances in effective antimicrobial prophylactic strategies have led to a decline in the incidence of opportunistic infections in liver transplant recipients.However, morbidity and mortality due to infectious diseases remain as major problems. Bacterial infections occurring early after transplant are mainly related to the technical aspects of the procedure. By contrast,after the first postoperative days and beyond, the nature and variety of infectious complications change.Opportunistic bacterial infections are uncommon after 6 mo in patients receiving stable and reduced maintenance doses of immunosuppression with good graft function and little is documented about these cases in the literature. Transplant recipients may be more susceptible to some pathogens, such as the Nocardia species, Legionella species, Listeria monocytogenes , Mycoplasma species, Salmonella species or Rhodococcus equi. Respiratory infections due to capsulated bacteria, such as Streptococcus pneumoniae and Haemophilus influenza, can be lifethreatening if not promptly treated in this population.These late bacterial infections may be very difficult to recognize and treat in this population. In this article,we review what has been described in the literature with regards to late bacterial infections following liver transplantation.

  3. Channel-Forming Bacterial Toxins in Biosensing and Macromolecule Delivery

    Directory of Open Access Journals (Sweden)

    Philip A. Gurnev

    2014-08-01

    Full Text Available To intoxicate cells, pore-forming bacterial toxins are evolved to allow for the transmembrane traffic of different substrates, ranging from small inorganic ions to cell-specific polypeptides. Recent developments in single-channel electrical recordings, X-ray crystallography, protein engineering, and computational methods have generated a large body of knowledge about the basic principles of channel-mediated molecular transport. These discoveries provide a robust framework for expansion of the described principles and methods toward use of biological nanopores in the growing field of nanobiotechnology. This article, written for a special volume on “Intracellular Traffic and Transport of Bacterial Protein Toxins”, reviews the current state of applications of pore-forming bacterial toxins in small- and macromolecule-sensing, targeted cancer therapy, and drug delivery. We discuss the electrophysiological studies that explore molecular details of channel-facilitated protein and polymer transport across cellular membranes using both natural and foreign substrates. The review focuses on the structurally and functionally different bacterial toxins: gramicidin A of Bacillus brevis, α-hemolysin of Staphylococcus aureus, and binary toxin of Bacillus anthracis, which have found their “second life” in a variety of developing medical and technological applications.

  4. Surface display of proteins by Gram-negative bacterial autotransporters

    Directory of Open Access Journals (Sweden)

    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.

  5. Assembly of the bacterial type III secretion machinery.

    Science.gov (United States)

    Diepold, Andreas; Wagner, Samuel

    2014-07-01

    Many bacteria that live in contact with eukaryotic hosts, whether as symbionts or as pathogens, have evolved mechanisms that manipulate host cell behaviour to their benefit. One such mechanism, the type III secretion system, is employed by Gram-negative bacterial species to inject effector proteins into host cells. This function is reflected by the overall shape of the machinery, which resembles a molecular syringe. Despite the simplicity of the concept, the type III secretion system is one of the most complex known bacterial nanomachines, incorporating one to more than hundred copies of up to twenty different proteins into a multi-MDa transmembrane complex. The structural core of the system is the so-called needle complex that spans the bacterial cell envelope as a tripartite ring system and culminates in a needle protruding from the bacterial cell surface. Substrate targeting and translocation are accomplished by an export machinery consisting of various inner membrane embedded and cytoplasmic components. The formation of such a multimembrane-spanning machinery is an intricate task that requires precise orchestration. This review gives an overview of recent findings on the assembly of type III secretion machines, discusses quality control and recycling of the system and proposes an integrated assembly model.

  6. Normal flora and bacterial vaginosis in pregnancy: an overview.

    Science.gov (United States)

    Redelinghuys, Mathys Jacobus; Ehlers, Marthie Magdaleen; Dreyer, Andries William; Kock, Marleen Magdalena

    2016-05-01

    The female genital tract is an intricate, yet balanced ecosystem that hosts a variety of different residential microflora. The physiological changes that occur during pregnancy may disrupt this balanced ecosystem and predispose women to a potentially pathogenic microbiota. Bacteria that are associated with bacterial vaginosis (BV) are opportunistic pathogens that frequently form part of this microbiota. The overgrowth of and infections with these bacteria are linked to poor obstetric outcomes and increased transmission of other reproductive tract infections (RTIs). These infections increase women's susceptibility of acquiring HIV, the rates of HIV shedding and the development of acquired immune deficiency syndrome (AIDS) in HIV-infected patients. It is unknown how the plethora of bacterial species associated with BV contributes to the dynamics of this condition. The use of high-throughput methods have led to the in-depth investigation of different BV-related bacterial species and the functional capabilities of these species. However, the pathogenesis of BV is still poorly defined and the role of individual BV-related bacterial species in specific pregnancy complications is unclear and controversial. The majority of BV infections are asymptomatic and successful diagnosis is complicated by the lack of reliable and standardized diagnostic tests. PMID:25834920

  7. A new experimental approach for studying bacterial genomic island evolution identifies island genes with bacterial host-specific expression patterns

    Directory of Open Access Journals (Sweden)

    Nickerson Cheryl A

    2006-01-01

    Full Text Available Abstract Background Genomic islands are regions of bacterial genomes that have been acquired by horizontal transfer and often contain blocks of genes that function together for specific processes. Recently, it has become clear that the impact of genomic islands on the evolution of different bacterial species is significant and represents a major force in establishing bacterial genomic variation. However, the study of genomic island evolution has been mostly performed at the sequence level using computer software or hybridization analysis to compare different bacterial genomic sequences. We describe here a novel experimental approach to study the evolution of species-specific bacterial genomic islands that identifies island genes that have evolved in such a way that they are differentially-expressed depending on the bacterial host background into which they are transferred. Results We demonstrate this approach by using a "test" genomic island that we have cloned from the Salmonella typhimurium genome (island 4305 and transferred to a range of Gram negative bacterial hosts of differing evolutionary relationships to S. typhimurium. Systematic analysis of the expression of the island genes in the different hosts compared to proper controls allowed identification of genes with genera-specific expression patterns. The data from the analysis can be arranged in a matrix to give an expression "array" of the island genes in the different bacterial backgrounds. A conserved 19-bp DNA site was found upstream of at least two of the differentially-expressed island genes. To our knowledge, this is the first systematic analysis of horizontally-transferred genomic island gene expression in a broad range of Gram negative hosts. We also present evidence in this study that the IS200 element found in island 4305 in S. typhimurium strain LT2 was inserted after the island had already been acquired by the S. typhimurium lineage and that this element is likely not

  8. Regulation of bacterial communities through antimicrobial activity by the coral holobiont.

    Science.gov (United States)

    Kvennefors, E Charlotte E; Sampayo, Eugenia; Kerr, Caroline; Vieira, Genyess; Roff, George; Barnes, Andrew C

    2012-04-01

    Interactions between corals and associated bacteria and amongst these bacterial groups are likely to play a key role in coral health. However, the complexity of these interactions is poorly understood. We investigated the functional role of specific coral-associated bacteria in maintaining microbial communities on the coral Acropora millepora (Ehrenberg 1834) and the ability of coral mucus to support or inhibit bacterial growth. Culture-independent techniques were used to assess bacterial community structures whilst bacterial culture was employed to assess intra- and inter-specific antimicrobial activities of bacteria. Members of Pseudoalteromonas and ribotypes closely related to Vibrio coralliilyticus displayed potent antimicrobial activity against a range of other cultured isolates and grew readily on detached coral mucus. Although such bacterial ribotypes would be expected to have a competitive advantage, they were rare or absent on intact and healthy coral colonies growing in situ (analysed using denaturing gradient gel electrophoresis and 16S rRNA gene sequencing). The most abundant bacterial ribotypes found on healthy corals were Gammaproteobacteria, previously defined as type A coral associates. Our results indicate that this group of bacteria and specific members of the Alphaproteobacteria described here as 'type B associates' may be important functional groups for coral health. We suggest that bacterial communities on coral are kept in check by a combination of host-derived and microbial interactions and that the type A associates in particular may play a key role in maintaining stability of microbial communities on healthy coral colonies. PMID:21984347

  9. Periodontal diseases as bacterial infection

    Directory of Open Access Journals (Sweden)

    A. Bascones Martínez

    2005-12-01

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

  10. Bacterial mutagenicity assays: test methods.

    Science.gov (United States)

    Gatehouse, David

    2012-01-01

    The most widely used assays for detecting chemically induced gene mutations are those employing bacteria. The plate incorporation assay using various Salmonella typhimurium LT2 and E. coli WP2 strains is a short-term bacterial reverse mutation assay specifically designed to detect a wide range of chemical substances capable of causing DNA damage leading to gene mutations. The test is used worldwide as an initial screen to determine the mutagenic potential of new chemicals and drugs.The test uses several strains of S. typhimurium which carry different mutations in various genes of the histidine operon, and E. coli which carry the same AT base pair at the critical mutation site within the trpE gene. These mutations act as hot spots for mutagens that cause DNA damage via different mechanisms. When these auxotrophic bacterial strains are grown on a minimal media agar plates containing a trace of the required amino-acid (histidine or tryptophan), only those bacteria that revert to amino-acid independence (His(+) or Tryp(+)) will grow to form visible colonies. The number of spontaneously induced revertant colonies per plate is relatively constant. However, when a mutagen is added to the plate, the number of revertant colonies per plate is increased, usually in a dose-related manner.This chapter provides detailed procedures for performing the test in the presence and absence of a metabolic activation system (S9-mix), including advice on specific assay variations and any technical problems. PMID:22147566

  11. BACTERIAL DESEASES IN SEA FISH

    Directory of Open Access Journals (Sweden)

    Ivančica Strunjak-Perović

    1997-10-01

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

  12. Bioinformatic Comparison of Bacterial Secretomes

    Institute of Scientific and Technical Information of China (English)

    Catharine Song; Aseem Kumar; Mazen Saleh

    2009-01-01

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

  13. Bacterial Culture of Neonatal Sepsis

    Directory of Open Access Journals (Sweden)

    AH Movahedian

    2006-08-01

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

  14. Immunization by a bacterial aerosol.

    Science.gov (United States)

    Garcia-Contreras, Lucila; Wong, Yun-Ling; Muttil, Pavan; Padilla, Danielle; Sadoff, Jerry; Derousse, Jessica; Germishuizen, Willem Andreas; Goonesekera, Sunali; Elbert, Katharina; Bloom, Barry R; Miller, Rich; Fourie, P Bernard; Hickey, Anthony; Edwards, David

    2008-03-25

    By manufacturing a single-particle system in two particulate forms (i.e., micrometer size and nanometer size), we have designed a bacterial vaccine form that exhibits improved efficacy of immunization. Microstructural properties are adapted to alter dispersive and aerosol properties independently. Dried "nanomicroparticle" vaccines possess two axes of nanoscale dimensions and a third axis of micrometer dimension; the last one permits effective micrometer-like physical dispersion, and the former provides alignment of the principal nanodimension particle axes with the direction of airflow. Particles formed with this combination of nano- and micrometer-scale dimensions possess a greater ability to aerosolize than particles of standard spherical isotropic shape and of similar geometric diameter. Here, we demonstrate effective application of this biomaterial by using the live attenuated tuberculosis vaccine bacille Calmette-Guérin (BCG). Prepared as a spray-dried nanomicroparticle aerosol, BCG vaccine exhibited high-efficiency delivery and peripheral lung targeting capacity from a low-cost and technically simple delivery system. Aerosol delivery of the BCG nanomicroparticle to normal guinea pigs subsequently challenged with virulent Mycobacterium tuberculosis significantly reduced bacterial burden and lung pathology both relative to untreated animals and to control animals immunized with the standard parenteral BCG. PMID:18344320

  15. Effect of aerosolization on subsequent bacterial survival.

    OpenAIRE

    Walter, M V; Marthi, B; Fieland, V P; Ganio, L M

    1990-01-01

    To determine whether aerosolization could impair bacterial survival, Pseudomonas syringae and Erwinia herbicola were aerosolized in a greenhouse, the aerosol was sampled at various distances from the site of release by using all-glass impingers, and bacterial survival was followed in the impingers for 6 h. Bacterial survival subsequent to aerosolization of P. syringae and E. herbicola was not impaired 1 m from the site of release. P. syringae aerosolized at 3 to 15 m from the site of release ...

  16. Drag Reduction of Bacterial Cellulose Suspensions

    OpenAIRE

    Ogata, Satoshi; Numakawa, Tetsuya; Kubo, Takuya

    2010-01-01

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

  17. Drag Reduction of Bacterial Cellulose Suspensions

    OpenAIRE

    Satoshi Ogata; Tetsuya Numakawa; Takuya Kubo

    2011-01-01

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

  18. Bacterial translocation - impact on the adipocyte compartment.

    Science.gov (United States)

    Kruis, Tassilo; Batra, Arvind; Siegmund, Britta

    2014-01-01

    Over the last decade it became broadly recognized that adipokines and thus the fat tissue compartment exert a regulatory function on the immune system. Our own group described the pro-inflammatory function of the adipokine leptin within intestinal inflammation in a variety of animal models. Following-up on this initial work, the aim was to reveal stimuli and mechanisms involved in the activation of the fat tissue compartment and the subsequent release of adipokines and other mediators paralleled by the infiltration of immune cells. This review will summarize the current literature on the possible role of the mesenteric fat tissue in intestinal inflammation with a focus on Crohn's disease (CD). CD is of particular interest in this context since the transmural intestinal inflammation has been associated with a characteristic hypertrophy of the mesenteric fat, a phenomenon called "creeping fat." The review will address three consecutive questions: (i) What is inducing adipocyte activation, (ii) which factors are released after activation and what are the consequences for the local fat tissue compartment and infiltrating cells; (iii) do the answers generated before allow for an explanation of the role of the mesenteric fat tissue within intestinal inflammation? With this review we will provide a working model indicating a close interaction in between bacterial translocation, activation of the adipocytes, and subsequent direction of the infiltrating immune cells. In summary, the models system mesenteric fat indicates a unique way how adipocytes can directly interact with the immune system.

  19. An overview of the role of bacterial infection in male infertility

    Directory of Open Access Journals (Sweden)

    Hamed Fanaei

    2013-03-01

    Full Text Available An important cause of male infertility is the bacterial infections of the genitourinary tract. These infections affect sperm cell function and whole spermatogenesis and also cause deterioration in spermatogenesis, obstruction of the seminal tract, and impairment of spermatozoa function. The most important bacteria associated with genitourinary tract infections include chlamydia trachomatis, Neisseria gonorrhoeae, and genital mycoplasma species. Inappropriate or delayed therapy of the bacterial infections of the genitourinary tract will lead to reduced fertility and, subsequently in severe cases, infertility. In other words, a good understanding of the interaction between bacterial infections and the reproductive system plays an important role in the treatment of infertile men. In this review article, we will discuss clinical and laboratory findings related to the bacterial infection of the genitourinary tract and its effects on male infertility.

  20. Bacterial successions in the Broiler Gastrointestinal tract

    DEFF Research Database (Denmark)

    Ranjitkar, Samir; Lawley, Blair; Tannock, Gerald;

    2016-01-01

    of crop, gizzard, ileum and ceca in relation to the feeding strategy and age (8, 15, 22, 25, 29 and 36 days). Of the four dietary treatments, bacterial diversity was analyzed for MBF and CKMS-30 by 454-pyrosequencing of 16S rRNA gene. Since there was no significant influence of diets on bacterial...... diversity, data were pooled for downstream analysis. With increasing age, a clear succession of bacterial communities and an increased bacterial diversity was observed. Lactobacillaceae (mainly Lactobacillus) represented most of the Firmicutes at all ages and in all segments of the gut except the ceca...

  1. CRISPR-Cas systems: new players in gene regulation and bacterial physiology

    OpenAIRE

    Sampson, Timothy R.; Weiss, David S.

    2014-01-01

    CRISPR-Cas systems are bacterial defenses against foreign nucleic acids derived from bacteriophages, plasmids or other sources. These systems are targeted in an RNA-dependent, sequence-specific manner, and are also adaptive, providing protection against previously encountered foreign elements. In addition to their canonical function in defense against foreign nucleic acid, their roles in various aspects of bacterial physiology are now being uncovered. We recently revealed a role for a Cas9-ba...

  2. Can we estimate bacterial growth rates from ribosomal RNA content?

    Energy Technology Data Exchange (ETDEWEB)

    Kemp, P.F.

    1995-12-31

    Several studies have demonstrated a strong relationship between the quantity of RNA in bacterial cells and their growth rate under laboratory conditions. It may be possible to use this relationship to provide information on the activity of natural bacterial communities, and in particular on growth rate. However, if this approach is to provide reliably interpretable information, the relationship between RNA content and growth rate must be well-understood. In particular, a requisite of such applications is that the relationship must be universal among bacteria, or alternately that the relationship can be determined and measured for specific bacterial taxa. The RNA-growth rate relationship has not been used to evaluate bacterial growth in field studies, although RNA content has been measured in single cells and in bulk extracts of field samples taken from coastal environments. These measurements have been treated as probable indicators of bacterial activity, but have not yet been interpreted as estimators of growth rate. The primary obstacle to such interpretations is a lack of information on biological and environmental factors that affect the RNA-growth rate relationship. In this paper, the available data on the RNA-growth rate relationship in bacteria will be reviewed, including hypotheses regarding the regulation of RNA synthesis and degradation as a function of growth rate and environmental factors; i.e. the basic mechanisms for maintaining RNA content in proportion to growth rate. An assessment of the published laboratory and field data, the current status of this research area, and some of the remaining questions will be presented.

  3. Impact of CO2 leakage from sub-seabed carbon dioxide capture and storage (CCS) reservoirs on benthic virus-prokaryote interactions and functions.

    Science.gov (United States)

    Rastelli, Eugenio; Corinaldesi, Cinzia; Dell'Anno, Antonio; Amaro, Teresa; Queirós, Ana M; Widdicombe, Stephen; Danovaro, Roberto

    2015-01-01

    Atmospheric CO2 emissions are a global concern due to their predicted impact on biodiversity, ecosystems functioning, and human life. Among the proposed mitigation strategies, CO2 capture and storage, primarily the injection of CO2 into marine deep geological formations has been suggested as a technically practical option for reducing emissions. However, concerns have been raised that possible leakage from such storage sites, and the associated elevated levels of pCO2 could locally impact the biodiversity and biogeochemical processes in the sediments above these reservoirs. Whilst a number of impact assessment studies have been conducted, no information is available on the specific responses of viruses and virus-host interactions. In the present study, we tested the impact of a simulated CO2 leakage on the benthic microbial assemblages, with specific focus on microbial activity and virus-induced prokaryotic mortality (VIPM). We found that exposure to levels of CO2 in the overlying seawater from 1,000 to 20,000 ppm for a period up to 140 days, resulted in a marked decrease in heterotrophic carbon production and organic matter degradation rates in the sediments, associated with lower rates of VIPM, and a progressive accumulation of sedimentary organic matter with increasing CO2 concentrations. These results suggest that the increase in seawater pCO2 levels that may result from CO2 leakage, can severely reduce the rates of microbial-mediated recycling of the sedimentary organic matter and viral infections, with major consequences on C cycling and nutrient regeneration, and hence on the functioning of benthic ecosystems.

  4. Effect of heavy metals on bacterial transport

    Science.gov (United States)

    Zhang, H.; Olson, M. S.

    2010-12-01

    Adsorption of metals onto bacteria and soil takes place as stormwater runoff infiltrates into the subsurface. Changes in both bacterial surfaces and soil elemental content have been observed, and may alter the attachment of bacteria to soil surfaces. In this study, scanning electron microscopy (SEM) and Energy Dispersive X-ray Spectrometry (EDS) analyses were performed on soil samples equilibrated with synthetic stormwater amended with copper, lead and zinc. The results demonstrate the presence of copper and zinc on soil surfaces. To investigate bacterial attachment behavior, sets of batch sorption experiments were conducted on Escherichia Coli (E. coli) under different chemical conditions by varying solution compositions (nutrient solution vs synthetic stormwater). The adsorption data is best described using theoretical linear isotherms. The equilibrium coefficient (Kd) of E. coli is higher in synthetic stormwater than in nutrient solution without heavy metals. The adsorption of heavy metals onto bacterial surfaces significantly decreases their negative surface charge as determined via zeta potential measurements (-17.0±5.96mv for E. coli equilibrated with synthetic stormwater vs -21.6±5.45mv for E. coli equilibrated with nutrient solution), indicating that bacterial attachment may increase due to the attachment of metals onto bacterial surfaces and their subsequent change in surface charge. The attachment efficiency (α) of bacteria was also calculated and compared for both solution chemistries. Bacterial attachment efficiency (α) in synthetic stormwater is 0.997, which is twice as high as that in nutrient solution(α 0.465). The ratio of bacterial diameter : collector diameter suggests minimal soil straining during bacterial transport. Results suggest that the presence of metals in synthetic stormwater leads to an increase in bacterial attachment to soil surfaces. In terms of designing stormwater infiltration basins, the presence of heavy metals seems to

  5. Bacterial community structure and diversity in a black soil as affected by long-term fertilization

    Institute of Scientific and Technical Information of China (English)

    WEI Dan; YANG Qian; ZHANG Jun-Zheng; WANG Shuang; CHEN Xue-Li; ZHANG Xi-Lin; LI Wei-Qun

    2008-01-01

    Black soil (Mollisol) is one of the main soil types in northeastern China.Biolog and polymerase chain reactiondenaturing gradient gel electrophoresis (PCR-DGGE) methods were used to examine the influence of various fertilizer combinations on the structure and function of the bacterial community in a black soil collected from Harbin,Heilongjiang Province.Biolog results showed that substrate richness and catabolic diversity of the soil bacterial community were the greatest in the chemical fertilizer and chemical fertilizer+manure treatments.The metabolic ability of the bacterial community in the manure treatment was similar to the control.DGGE fingerprinting indicated similarity in the distribution of most 16S rDNA bands among all treatments,suggesting that microorganisms with those bands were stable and not influenced by fertilization.However,chemical fertilizer increased the diversity of soil bacterial community.Principal component analysis of Biolog and DGGE data revealed that the structure and function of the bacterial community were similar in the control and manure treatments,suggesting that the application of manure increased the soil microbial population,but had no effect on the bacterial community structure.Catabolic function was similar in the chemical fertilizer and chemical fertilizer+manure treatments,but the composition structure of the soil microbes differed between them.The use of chemical fertilizers could result in a decline in the catabolic activity of fast-growing or eutrophic bacteria.

  6. Temporal dynamics of sediment bacterial communities in monospecific stands of Juncus maritimus and Spartina maritima.

    Science.gov (United States)

    Cleary, D F R; Polónia, A R M; Sousa, A I; Lillebø, A I; Queiroga, H; Gomes, N C M

    2016-09-01

    In the present study, we used 16S rRNA barcoded pyrosequencing to investigate to what extent monospecific stands of different salt marsh plant species (Juncus maritimus and Spartina maritima), sampling site and temporal variation affect sediment bacterial communities. We also used a bioinformatics tool, PICRUSt, to predict metagenome gene functional content. Our results showed that bacterial community composition from monospecific stands of both plant species varied temporally, but both host plant species maintained compositionally distinct communities of bacteria. Juncus sediment was characterised by higher abundances of Alphaproteobacteria, Myxococcales, Rhodospirillales, NB1-j and Ignavibacteriales, while Spartina sediment was characterised by higher abundances of Anaerolineae, Synechococcophycidae, Desulfobacterales, SHA-20 and Rhodobacterales. The differences in composition and higher taxon abundance between the sediment bacterial communities of stands of both plant species may be expected to affect overall metabolic diversity. In line with this expectation, there were also differences in the predicted enrichment of selected metabolic pathways. In particular, bacterial communities of Juncus sediment were predicted to be enriched for pathways related to the degradation of various (xenobiotic) compounds. Bacterial communities of Spartina sediment in turn were predicted to be enriched for pathways related to the biosynthesis of various bioactive compounds. Our study highlights the differences in composition and predicted functions of sediment-associated bacterial communities from two different salt marsh plant species. Loss of salt marsh habitat may thus be expected to both adversely affect microbial diversity and ecosystem functioning and have consequences for environmental processes such as nutrient cycling and pollutant remediation. PMID:27061465

  7. Cooperative Model of Bacterial Sensing

    CERN Document Server

    Shi, Y; Shi, Yu; Duke, Thomas

    1998-01-01

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

  8. Unexpected versatility in bacterial riboswitches.

    Science.gov (United States)

    Mellin, J R; Cossart, Pascale

    2015-03-01

    Bacterial riboswitches are elements present in the 5'-untranslated regions (UTRs) of mRNA molecules that bind to ligands and regulate the expression of downstream genes. Riboswitches typically regulate the expression of protein-coding genes. However, mechanisms of riboswitch-mediated regulation have recently been shown to be more diverse than originally thought, with reports showing that riboswitches can regulate the expression of noncoding RNAs and control the access of proteins, such as transcription termination factor Rho and RNase E, to a nascent RNA. Riboswitches are also increasingly used in biotechnology, with advances in the engineering of synthetic riboswitches and the development of riboswitch-based sensors. In this review we address the emerging roles and mechanisms of riboswitch-mediated regulation in natura and recent progress in the development of riboswitch-based technology. PMID:25708284

  9. Circuit architecture explains functional similarity of bacterial heat shock responses

    CERN Document Server

    Inoue, Masayo; Trusina, Ala

    2012-01-01

    Heat shock response is a stress response to temperature changes and a consecutive increase in amounts of unfolded proteins. To restore homeostasis, cells upregulate chaperones facilitating protein folding by means of transcription factors (TF). We here investigate two heat shock systems: one characteristic to gram negative bacteria, mediated by transcriptional activator sigma32 in E. coli, and another characteristic to gram positive bacteria, mediated by transcriptional repressor HrcA in L. lactis. We construct simple mathematical model of the two systems focusing on the negative feedbacks, where free chaperons suppress sigma32 activation in the former, while they activate HrcA repression in the latter. We demonstrate that both systems, in spite of the difference at the TF regulation level, are capable of showing very similar heat shock dynamics. We find that differences in regulation impose distinct constrains on chaperone-TF binding affinities: the binding constant of free sigma32 to chaperon DnaK, known to...

  10. Functional organization of a multimodular bacterial chemosensory apparatus.

    Directory of Open Access Journals (Sweden)

    Audrey Moine

    2014-03-01

    Full Text Available Chemosensory systems (CSS are complex regulatory pathways capable of perceiving external signals and translating them into different cellular behaviors such as motility and development. In the δ-proteobacterium Myxococcus xanthus, chemosensing allows groups of cells to orient themselves and aggregate into specialized multicellular biofilms termed fruiting bodies. M. xanthus contains eight predicted CSS and 21 chemoreceptors. In this work, we systematically deleted genes encoding components of each CSS and chemoreceptors and determined their effects on M. xanthus social behaviors. Then, to understand how the 21 chemoreceptors are distributed among the eight CSS, we examined their phylogenetic distribution, genomic organization and subcellular localization. We found that, in vivo, receptors belonging to the same phylogenetic group colocalize and interact with CSS components of the respective phylogenetic group. Finally, we identified a large chemosensory module formed by three interconnected CSS and multiple chemoreceptors and showed that complex behaviors such as cell group motility and biofilm formation require regulatory apparatus composed of multiple interconnected Che-like systems.

  11. Functional bacterial amyloid increases Pseudomonas biofilm hydrophobicity and stiffness

    DEFF Research Database (Denmark)

    Zeng, Guanghong; Vad, Brian S; Dueholm, Morten S;

    2015-01-01

    The success of Pseudomonas species as opportunistic pathogens derives in great part from their ability to form stable biofilms that offer protection against chemical and mechanical attack. The extracellular matrix of biofilms contains numerous biomolecules, and it has recently been discovered...... stiffness 20-fold. Deletion of any one of the individual members of in the fap operon (except the putative chaperone FapA) abolishes this ability to increase biofilm stiffness and correlates with the loss of amyloid. We conclude that amyloid makes major contributions to biofilm mechanical robustness....

  12. Circuit architecture explains functional similarity of bacterial heat shock responses

    International Nuclear Information System (INIS)

    Heat shock response is a stress response to temperature changes and a consecutive increase in amounts of unfolded proteins. To restore homeostasis, cells upregulate chaperones facilitating protein folding by means of transcription factors (TFs). We here investigate two heat shock systems: one characteristic to gram negative bacteria, mediated by transcriptional activator σ32 in E. coli, and another characteristic to gram positive bacteria, mediated by transcriptional repressor HrcA in L. lactis. We construct simple mathematical models of the two systems focusing on the negative feedbacks, where free chaperones suppress σ32 activation in the former, while they activate HrcA repression in the latter. We demonstrate that both systems, in spite of the difference at the TF regulation level, are capable of showing very similar heat shock dynamics. We find that differences in regulation impose distinct constraints on chaperone–TF binding affinities: the binding constant of free σ32 to chaperone DnaK, known to be in 100 nM range, set the lower limit of amount of free chaperone that the system can sense the change at the heat shock, while the binding affinity of HrcA to chaperone GroE set the upper limit and have to be rather large extending into the micromolar range. (paper)

  13. A functional gene array for detection of bacterial virulence elements

    Energy Technology Data Exchange (ETDEWEB)

    Jaing, C

    2007-11-01

    We report our development of the first of a series of microarrays designed to detect pathogens with known mechanisms of virulence and antibiotic resistance. By targeting virulence gene families as well as genes unique to specific biothreat agents, these arrays will provide important data about the pathogenic potential and drug resistance profiles of unknown organisms in environmental samples. To validate our approach, we developed a first generation array targeting genes from Escherichia coli strains K12 and CFT073, Enterococcus faecalis and Staphylococcus aureus. We determined optimal probe design parameters for microorganism detection and discrimination, measured the required target concentration, and assessed tolerance for mismatches between probe and target sequences. Mismatch tolerance is a priority for this application, due to DNA sequence variability among members of gene families. Arrays were created using the NimbleGen Maskless Array Synthesizer at Lawrence Livermore National Laboratory. Purified genomic DNA from combinations of one or more of the four target organisms, pure cultures of four related organisms, and environmental aerosol samples with spiked-in genomic DNA were hybridized to the arrays. Based on the success of this prototype, we plan to design further arrays in this series, with the goal of detecting all known virulence and antibiotic resistance gene families in a greatly expanded set of organisms.

  14. Biosynthesis of a Fully Functional Cyclotide inside Living Bacterial Cells

    Energy Technology Data Exchange (ETDEWEB)

    Camarero, J A; Kimura, R H; Woo, Y; Cantor, J; Shekhtman, A

    2007-04-05

    The cyclotide MCoTI-II is a powerful trypsin inhibitor recently isolated from the seeds of Momordica cochinchinensis, a plant member of cucurbitaceae family. We report for the first time the in vivo biosynthesis of natively-folded MCoTI-II inside live E. coli cells. Our biomimetic approach involves the intracellular backbone cyclization of a linear cyclotide-intein fusion precursor mediated by a modified protein splicing domain. The cyclized peptide then spontaneously folds into its native conformation. The use of genetically engineered E. coli cells containing mutations in the glutathione and thioredoxin reductase genes considerably improves the production of folded MCoTI-II in vivo. Biochemical and structural characterization of the recombinant MCoTI-II confirmed its identity. Biosynthetic access to correctly-folded cyclotides allows the possibility of generating cell-based combinatorial libraries that can be screened inside living cells for their ability to modulate or inhibit cellular processes.

  15. PPARγ in Bacterial Infections: A Friend or Foe?

    Science.gov (United States)

    2016-01-01

    Peroxisome proliferator-activated receptor γ (PPARγ) is now recognized as an important modulator of leukocyte inflammatory responses and function. Its immunoregulatory function has been studied in a variety of contexts, including bacterial infections of the lungs and central nervous system, sepsis, and conditions such as chronic granulomatous disease. Although it is generally believed that PPARγ activation is beneficial for the host during bacterial infections via its anti-inflammatory and antibacterial properties, PPARγ agonists have also been shown to dampen the host immune response and in some cases exacerbate infection by promoting leukocyte apoptosis and interfering with leukocyte migration and infiltration. In this review we discuss the role of PPARγ and its activation during bacterial infections, with focus on the potential of PPARγ agonists and perhaps antagonists as novel therapeutic modalities. We conclude that adjustment in the dosage and timing of PPARγ agonist administration, based on the competence of host antimicrobial defenses and the extent of inflammatory response and tissue injury, is critical for achieving the essential balance between pro- and anti-inflammatory effects on the immune system.

  16. Pattern Formation of Bacterial Colonies by Escherichia coli

    Science.gov (United States)

    Tokita, Rie; Katoh, Takaki; Maeda, Yusuke; Wakita, Jun-ichi; Sano, Masaki; Matsuyama, Tohey; Matsushita, Mitsugu

    2009-07-01

    We have studied the morphological diversity and change in bacterial colonies, using the bacterial species Escherichia coli, as a function of both agar concentration Ca and nutrient concentration Cn. We observed various colony patterns, classified them into four types by pattern characteristics and established a morphological diagram by dividing it into four regions. They are regions A [diffusion-limited aggregation (DLA)-like], B (Eden-like), C (concentric-ring), and D (fluid-spreading). In particular, we have observed a concentric-ring colony growth for E. coli. We focused on the periodic growth in region C and obtained the following results: (i) A colony grows cyclically with the growing front repeating an advance (migration phase) and a momentary rest (consolidation phase) alternately. (ii) The growth width L and the bulge width W in one cycle decrease asymptotically to certain values, when Ca is increased. (iii) L does not depend on Cn, while W is an increasing function of Cn. Plausible mechanisms are proposed to explain the experimental results, by comparing them with those obtained for other bacterial species such as Proteus mirabilis and Bacillus subtilis.

  17. A Molecularly Complete Planar Bacterial Outer Membrane Platform.

    Science.gov (United States)

    Hsia, Chih-Yun; Chen, Linxiao; Singh, Rohit R; DeLisa, Matthew P; Daniel, Susan

    2016-01-01

    The bacterial outer membrane (OM) is a barrier containing membrane proteins and liposaccharides that fulfill crucial functions for Gram-negative bacteria. With the advent of drug-resistant bacteria, it is necessary to understand the functional role of this membrane and its constituents to enable novel drug designs. Here we report a simple method to form an OM-like supported bilayer (OM-SB), which incorporates native lipids and membrane proteins of gram-negative bacteria from outer membrane vesicles (OMVs). We characterize the formation of OM-SBs using quartz crystal microbalance with dissipation (QCM-D) and fluorescence microscopy. We show that the orientation of proteins in the OM-SB matches the native bacterial membrane, preserving the characteristic asymmetry of these membranes. As a demonstration of the utility of the OM-SB platform, we quantitatively measure antibiotic interactions between OM-SBs and polymyxin B, a cationic peptide used to treat Gram-negative infections. This data enriches understanding of the antibacterial mechanism of polymyxin B, including disruption kinetics and changes in membrane mechanical properties. Combining OM-SBs with microfluidics will enable higher throughput screening of antibiotics. With a broader view, we envision that a molecularly complete membrane-scaffold could be useful for cell-free applications employing engineered membrane proteins in bacterial membranes for myriad technological purposes. PMID:27600663

  18. Diversity and abundance of the bacterial community of the red Macroalga Porphyra umbilicalis: did bacterial farmers produce macroalgae?

    Directory of Open Access Journals (Sweden)

    Lilibeth N Miranda

    Full Text Available Macroalgae harbor microbial communities whose bacterial biodiversity remains largely uncharacterized. The goals of this study were 1 to examine the composition of the bacterial community associated with Porphyra umbilicalis Kützing from Schoodic Point, ME, 2 determine whether there are seasonal trends in species diversity but a core group of bacteria that are always present, and 3 to determine how the microbial community associated with a laboratory strain (P.um.1 established in the presence of antibiotics has changed. P. umbilicalis blades (n = 5, fall 2010; n = 5, winter 2011; n = 2, clonal P.um.1 were analyzed by pyrosequencing over two variable regions of the 16 S rDNA (V5-V6 and V8; 147,880 total reads. The bacterial taxa present were classified at an 80% confidence threshold into eight phyla (Bacteroidetes, Proteobacteria, Planctomycetes, Chloroflexi, Actinobacteria, Deinococcus-Thermus, Firmicutes, and the candidate division TM7. The Bacteroidetes comprised the majority of bacterial sequences on both field and lab blades, but the Proteobacteria (Alphaproteobacteria, Gammaproteobacteria were also abundant. Sphingobacteria (Bacteroidetes and Flavobacteria (Bacteroidetes had inverse abundances on natural versus P.um.1 blades. Bacterial communities were richer and more diverse on blades sampled in fall compared to winter. Significant differences were observed between microbial communities among all three groups of blades examined. Only two OTUs were found on all 12 blades, and only one of these, belonging to the Saprospiraceae (Bacteroidetes, was abundant. Lewinella (as 66 OTUs was found on all field blades and was the most abundant genus. Bacteria from the Bacteroidetes, Proteobacteria and Planctomycetes that are known to digest the galactan sulfates of red algal cell walls were well-represented. Some of these taxa likely provide essential morphogenetic and beneficial nutritive factors to P. umbilicalis and may have had

  19. Use of Bacteriophages to control bacterial pathogens

    Science.gov (United States)

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

  20. Plant Natural Products Targeting Bacterial Virulence Factors.

    Science.gov (United States)

    Silva, Laura Nunes; Zimmer, Karine Rigon; Macedo, Alexandre José; Trentin, Danielle Silva

    2016-08-24

    Decreased antimicrobial efficiency has become a global public health issue. The paucity of new antibacterial drugs is evident, and the arsenal against infectious diseases needs to be improved urgently. The selection of plants as a source of prototype compounds is appropriate, since plant species naturally produce a wide range of secondary metabolites that act as a chemical line of defense against microorganisms in the environment. Although traditional approaches to combat microbial infections remain effective, targeting microbial virulence rather than survival seems to be an exciting strategy, since the modulation of virulence factors might lead to a milder evolutionary pressure for the development of resistance. Additionally, anti-infective chemotherapies may be successfully achieved by combining antivirulence and conventional antimicrobials, extending the lifespan of these drugs. This review presents an updated discussion of natural compounds isolated from plants with chemically characterized structures and activity against the major bacterial virulence factors: quorum sensing, bacterial biofilms, bacterial motility, bacterial toxins, bacterial pigments, bacterial enzymes, and bacterial surfactants. Moreover, a critical analysis of the most promising virulence factors is presented, highlighting their potential as targets to attenuate bacterial virulence. The ongoing progress in the field of antivirulence therapy may therefore help to translate this promising concept into real intervention strategies in clinical areas. PMID:27437994

  1. Bacterial cell division proteins as antibiotic targets

    NARCIS (Netherlands)

    T. den Blaauwen; J.M. Andreu; O. Monasterio

    2014-01-01

    Proteins involved in bacterial cell division often do not have a counterpart in eukaryotic cells and they are essential for the survival of the bacteria. The genetic accessibility of many bacterial species in combination with the Green Fluorescence Protein revolution to study localization of protein

  2. Recent advances in bacterial heme protein biochemistry

    OpenAIRE

    Mayfield, Jeffery A.; Dehner, Carolyn A.; Dubois, Jennifer L.

    2011-01-01

    Recent progress in genetics, fed by the burst in genome sequence data, has led to the identification of a host of novel bacterial heme proteins that are now being characterized in structural and mechanistic terms. The following short review highlights very recent work with bacterial heme proteins involved in the uptake, biosynthesis, degradation, and use of heme in respiration and sensing.

  3. Multiple bacterial species reside in chronic wounds

    DEFF Research Database (Denmark)

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

    2006-01-01

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

  4. Bacterial biofilms: prokaryotic adventures in multicellularity

    DEFF Research Database (Denmark)

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

    2003-01-01

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

  5. Barriers to bacterial motility on unsaturated surfaces

    DEFF Research Database (Denmark)

    Dechesne, Arnaud; Smets, Barth F.

    2013-01-01

    and their isogenic mutants unable to express various type of motility we aimed to quantify the physical limits of bacterial motility. Our results demonstrate how hydration controls bacterial motility under unsaturated conditions. They can form the base of improved biodegradation models that include microbial...

  6. Sustainable strategies for treatment of bacterial infections

    DEFF Research Database (Denmark)

    Molin, Søren

    2014-01-01

    not in a foreseeable future develop novel approaches and strategies to combat bacterial infections, many people will be at risk of dying from even trivial infections for which we until recently had highly effective antibiotics. We have for a number of years investigated chronic bacterial lung infections in patients...

  7. Prolonged inhibition of bacterial protein synthesis abolishes Salmonella invasion.

    Science.gov (United States)

    MacBeth, K J; Lee, C A

    1993-01-01

    We have found that prolonged inhibition of bacterial protein synthesis abolishes the ability of Salmonella typhimurium to enter HEp-2 cells. Our results suggest that an essential invasion factor has a functional half-life that is seen as a gradual loss of invasiveness in the absence of protein synthesis. Therefore, Salmonella invasiveness appears to be a transient phenotype that is lost unless protein synthesis is maintained. This finding may explain why salmonellae grown to stationary phase lose their ability to enter cultured cells. In addition, a short-lived capacity to enter cells may be important during infection so that bacterial invasiveness is limited to certain times and host sites during pathogenesis. PMID:8454361

  8. Bacterial iron-sulfur cluster sensors in mammalian pathogens

    Science.gov (United States)

    Miller, Halie K.; Auerbuch, Victoria

    2015-01-01

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

  9. Harnessing CRISPR-Cas systems for bacterial genome editing.

    Science.gov (United States)

    Selle, Kurt; Barrangou, Rodolphe

    2015-04-01

    Manipulation of genomic sequences facilitates the identification and characterization of key genetic determinants in the investigation of biological processes. Genome editing via clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) constitutes a next-generation method for programmable and high-throughput functional genomics. CRISPR-Cas systems are readily reprogrammed to induce sequence-specific DNA breaks at target loci, resulting in fixed mutations via host-dependent DNA repair mechanisms. Although bacterial genome editing is a relatively unexplored and underrepresented application of CRISPR-Cas systems, recent studies provide valuable insights for the widespread future implementation of this technology. This review summarizes recent progress in bacterial genome editing and identifies fundamental genetic and phenotypic outcomes of CRISPR targeting in bacteria, in the context of tool development, genome homeostasis, and DNA repair.

  10. A Replisome's journey through the bacterial chromosome.

    Science.gov (United States)

    Beattie, Thomas R; Reyes-Lamothe, Rodrigo

    2015-01-01

    Genome duplication requires the coordinated activity of a multi-component machine, the replisome. In contrast to the background of metabolic diversity across the bacterial domain, the composition and architecture of the bacterial replisome seem to have suffered few changes during evolution. This immutability underlines the replisome's efficiency in copying the genome. It also highlights the success of various strategies inherent to the replisome for responding to stress and avoiding problems during critical stages of DNA synthesis. Here we summarize current understanding of bacterial replisome architecture and highlight the known variations in different bacterial taxa. We then look at the mechanisms in place to ensure that the bacterial replisome is assembled appropriately on DNA, kept together during elongation, and disassembled upon termination. We put forward the idea that the architecture of the replisome may be more flexible that previously thought and speculate on elements of the replisome that maintain its stability to ensure a safe journey from origin to terminus. PMID:26097470

  11. AN EXPERIMENTAL ANALYSIS OF BACTERIAL ALLERGY.

    Science.gov (United States)

    Zinsser, H; Tamiya, T

    1926-11-30

    Our experiments have confirmed the fact that the so called bacterial allergies are dependent upon a mechanism which differs materially from that determining true protein anaphylaxis. Anaphylaxis to protein substances of the bacteria probably occurs but plays a relatively unimportant rôle in the phenomena of infection. The bacterial allergies, however, are of great importance since they develop rapidly and render the infected animal highly vulnerable to products of the bacterial growth which are relatively innocuous for the normal animal. Neither the type-specific carbohydrate "residue antigens" (the "soluble specific substances" of Avery and Heidelberger) nor the antibodies reacting with them play any part whatever in bacterial allergy, and since these type-specific substances represent the haptophore groups of the whole bacteria by which they react with the agglutinins, precipitins, sensitizers, etc., of immune serum, allergy, as previously determined by Mackenzie and Woo, is in no way related to that phase of resistance which is determined by these antibodies. This does not, however, preclude the possibility that allergic hypersusceptibility may not in some way be related to other factors of resistance more definitely associated with cellular rather than with intravascular reactions. Our previous studies with Jennings and Ward in tuberculosis point in this direction (20). Guinea pigs can be actively sensitized with all the bacteria with which we have worked when repeated injections of whole bacteria or of the protein (nucleoprotein) fraction are administered. Large amounts of the latter are necessary since these materials are indifferent antigens, possibly because of the severe manipulations necessary in their production. Sensitiveness develops usually within 10 days after the first dose and increases with continued treatment for 3 or 4 weeks. Sensitiveness is relatively specific, by which we mean that there is a definite specificity which, however, in highly

  12. Effects of grazing on leaf traits and ecosystem functioning in Inner Mongolia grasslands: scaling from species to community

    Directory of Open Access Journals (Sweden)

    S. X. Zheng

    2010-03-01

    Full Text Available Understanding the mechanistic links between environmental drivers, human disturbance, plant functional traits, and ecosystem properties is a fundamental aspect of biodiversity-ecosystem functioning research. Recent studies have focused mostly on leaf-level traits or community-level weighted traits to predict species responses to grazing and the consequent change in ecosystem functioning. However, studies of leaf-level traits or community-level weighted traits seldom identify the mechanisms linking grazing impact on leaf traits to ecosystem functioning. Here, using a multi-organization-level approach, we examined the effects of grazing on leaf traits (i.e., leaf area, leaf dry mass and specific leaf area and ecosystem functioning across six communities of three vegetation types along a soil moisture gradient in the Xilin River Basin of Inner Mongolia grassland, China. Our results showed that the effects of grazing on leaf traits differed substantially when scaling up from leaf-level to species, functional group (i.e., life forms and water ecotype types, and community levels; and they also varied with vegetation type or site conditions. The effects of grazing on leaf traits diminished progressively along the hierarchy of organizational levels in the meadow, whereas the impacts were predominantly negative and the magnitude of the effects increased considerably at higher organizational levels in the typical steppe. Soil water and nutrient availability, functional trade-offs between leaf size and number of leaves per individual, and differentiation in avoidance and tolerance strategies among coexisting species are likely to be responsible for the observed responses of leaf traits to grazing at different levels of organization and among vegetation types. Our findings also demonstrate that, at both the functional group and community levels, standing aboveground biomass increased with leaf area and specific leaf area. Compared with the large changes in

  13. Effects of grazing on leaf traits and ecosystem functioning in Inner Mongolia grasslands: scaling from species to community

    Science.gov (United States)

    Zheng, S. X.; Ren, H. Y.; Lan, Z. C.; Li, W. H.; Wang, K. B.; Bai, Y. F.

    2010-03-01

    Understanding the mechanistic links between environmental drivers, human disturbance, plant functional traits, and ecosystem properties is a fundamental aspect of biodiversity-ecosystem functioning research. Recent studies have focused mostly on leaf-level traits or community-level weighted traits to predict species responses to grazing and the consequent change in ecosystem functioning. However, studies of leaf-level traits or community-level weighted traits seldom identify the mechanisms linking grazing impact on leaf traits to ecosystem functioning. Here, using a multi-organization-level approach, we examined the effects of grazing on leaf traits (i.e., leaf area, leaf dry mass and specific leaf area) and ecosystem functioning across six communities of three vegetation types along a soil moisture gradient in the Xilin River Basin of Inner Mongolia grassland, China. Our results showed that the effects of grazing on leaf traits differed substantially when scaling up from leaf-level to species, functional group (i.e., life forms and water ecotype types), and community levels; and they also varied with vegetation type or site conditions. The effects of grazing on leaf traits diminished progressively along the hierarchy of organizational levels in the meadow, whereas the impacts were predominantly negative and the magnitude of the effects increased considerably at higher organizational levels in the typical steppe. Soil water and nutrient availability, functional trade-offs between leaf size and number of leaves per individual, and differentiation in avoidance and tolerance strategies among coexisting species are likely to be responsible for the observed responses of leaf traits to grazing at different levels of organization and among vegetation types. Our findings also demonstrate that, at both the functional group and community levels, standing aboveground biomass increased with leaf area and specific leaf area. Compared with the large changes in leaf traits and

  14. Chronic Liver Disease Impairs Bacterial Clearance in a Human Model of Induced Bacteremia

    OpenAIRE

    Ashare, Alix; Stanford, Clark; Hancock, Patricia; Stark, Donna; Lilli, Kathleen; Birrer, Emily; Nymon, Amanda; Doerschug, Kevin C.; Hunninghake, Gary W.

    2009-01-01

    Sepsis often causes impaired hepatic function. Patients with liver disease have an increased risk of bacteremia. This is thought to be secondary to impaired reticuloendothelial system function. However, this has not been demonstrated clinically. Since transient bacteremia occurs following toothbrushing, we hypothesized that subjects with cirrhosis would have impaired bacterial clearance following toothbrushing compared with subjects with pulmonary disease and healthy controls. After baseline ...

  15. Impact of CRISPR immunity on the emergence and virulence of bacterial pathogens

    OpenAIRE

    Hatoum-Aslan, Asma; Marraffini, Luciano A.

    2013-01-01

    CRISPR-Cas systems protect prokaryotes from viruses and plasmids and function primarily as an adaptive immune system in these organisms. Recent discoveries, however, revealed unexpected roles for CRISPR loci as barriers to horizontal gene transfer and as modulators of gene expression. We review how both of these functions of CRISPR-Cas systems can affect the emergence and virulence of human bacterial pathogens.

  16. 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.

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

    Science.gov (United States)

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

    2016-01-01

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

  18. Characterization of Bacterial Communities in Deep-Sea Hydrothermal Vents from Three Oceanic Regions.

    Science.gov (United States)

    He, Tianliang; Zhang, Xiaobo

    2016-04-01

    Deep-sea hydrothermal vents are considered to be one of the most spectacular ecosystems on Earth. Microorganisms form the basis of the food chain in vents controlling the vent communities. However, the diversity of bacterial communities in deep-sea hydrothermal vents from different oceans remains largely unknown. In this study, the pyrosequencing of 16S rRNA gene was used to characterize the bacterial communities of the venting sulfide, seawater, and tubeworm trophosome from East Pacific Rise, South Atlantic Ridge, and Southwest Indian Ridge, respectively. A total of 23,767 operational taxonomic units (OTUs) were assigned into 42 different phyla. Although Proteobacteria, Actinobacteria, and Bacteroidetes were the predominant phyla in all vents, differences of bacterial diversity were observed among different vents from three oceanic regions. The sulfides of East Pacific Rise possessed the most diverse bacterial communities. The bacterial diversities of venting seawater were much lower than those of vent sulfides. The symbiotic bacteria of tubeworm Ridgeia piscesae were included in the bacterial community of vent sulfides, suggesting their significant ecological functions as the primary producers in the deep-sea hydrothermal vent ecosystems. Therefore, our study presented a comprehensive view of bacterial communities in deep-sea hydrothermal vents from different oceans. PMID:26626941

  19. Characterization of Bacterial Communities in Deep-Sea Hydrothermal Vents from Three Oceanic Regions.

    Science.gov (United States)

    He, Tianliang; Zhang, Xiaobo

    2016-04-01

    Deep-sea hydrothermal vents are considered to be one of the most spectacular ecosystems on Earth. Microorganisms form the basis of the food chain in vents controlling the vent communities. However, the diversity of bacterial communities in deep-sea hydrothermal vents from different oceans remains largely unknown. In this study, the pyrosequencing of 16S rRNA gene was used to characterize the bacterial communities of the venting sulfide, seawater, and tubeworm trophosome from East Pacific Rise, South Atlantic Ridge, and Southwest Indian Ridge, respectively. A total of 23,767 operational taxonomic units (OTUs) were assigned into 42 different phyla. Although Proteobacteria, Actinobacteria, and Bacteroidetes were the predominant phyla in all vents, differences of bacterial diversity were observed among different vents from three oceanic regions. The sulfides of East Pacific Rise possessed the most diverse bacterial communities. The bacterial diversities of venting seawater were much lower than those of vent sulfides. The symbiotic bacteria of tubeworm Ridgeia piscesae were included in the bacterial community of vent sulfides, suggesting their significant ecological functions as the primary producers in the deep-sea hydrothermal vent ecosystems. Therefore, our study presented a comprehensive view of bacterial communities in deep-sea hydrothermal vents from different oceans.

  20. Mass Spectrometry-Based Bacterial Proteomics: Focus on Dermatologic Microbial Pathogens.

    Science.gov (United States)

    Soufi, Youcef; Soufi, Boumediene

    2016-01-01

    The composition of human skin acts as a natural habitat for various bacterial species that function in a commensal and symbiotic fashion. In a healthy individual, bacterial flora serves to protect the host. Under certain conditions such as minor trauma, impaired host immunity, or environmental factors, the risk of developing skin infections is increased. Although a large majority of bacterial associated skin infections are common, a portion can potentially manifest into clinically significant morbidity. For example, Gram-positive species that typically reside on the skin such as Staphylococcus and Streptococcus can cause numerous epidermal (impetigo, ecthyma) and dermal (cellulitis, necrotizing fasciitis, erysipelas) skin infections. Moreover, the increasing incidence of bacterial antibiotic resistance represents a serious challenge to modern medicine and threatens the health care system. Therefore, it is critical to develop tools and strategies that can allow us to better elucidate the nature and mechanism of bacterial virulence. To this end, mass spectrometry (MS)-based proteomics has been revolutionizing biomedical research, and has positively impacted the microbiology field. Advances in MS technologies have paved the way for numerous bacterial proteomes and their respective post translational modifications (PTMs) to be accurately identified and quantified in a high throughput and robust fashion. This technological platform offers critical information with regards to signal transduction, adherence, and microbial-host interactions associated with bacterial pathogenesis. This mini-review serves to highlight the current progress proteomics has contributed toward the understanding of bacteria that are associated with skin related diseases, infections, and antibiotic resistance.