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  1. Toxin-Antitoxin Systems in Clinical Pathogens

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    Laura Fernández-García

    2016-07-01

    Full Text Available Toxin-antitoxin (TA systems are prevalent in bacteria and archaea. Although not essential for normal cell growth, TA systems are implicated in multiple cellular functions associated with survival under stress conditions. Clinical strains of bacteria are currently causing major human health problems as a result of their multidrug resistance, persistence and strong pathogenicity. Here, we present a review of the TA systems described to date and their biological role in human pathogens belonging to the ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. and others of clinical relevance (Escherichia coli, Burkholderia spp., Streptococcus spp. and Mycobacterium tuberculosis. Better understanding of the mechanisms of action of TA systems will enable the development of new lines of treatment for infections caused by the above-mentioned pathogens.

  2. Toxin-Antitoxin Systems of Staphylococcus aureus.

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    Schuster, Christopher F; Bertram, Ralph

    2016-05-05

    Toxin-antitoxin (TA) systems are small genetic elements found in the majority of prokaryotes. They encode toxin proteins that interfere with vital cellular functions and are counteracted by antitoxins. Dependent on the chemical nature of the antitoxins (protein or RNA) and how they control the activity of the toxin, TA systems are currently divided into six different types. Genes comprising the TA types I, II and III have been identified in Staphylococcus aureus. MazF, the toxin of the mazEF locus is a sequence-specific RNase that cleaves a number of transcripts, including those encoding pathogenicity factors. Two yefM-yoeB paralogs represent two independent, but auto-regulated TA systems that give rise to ribosome-dependent RNases. In addition, omega/epsilon/zeta constitutes a tripartite TA system that supposedly plays a role in the stabilization of resistance factors. The SprA1/SprA1AS and SprF1/SprG1 systems are post-transcriptionally regulated by RNA antitoxins and encode small membrane damaging proteins. TA systems controlled by interaction between toxin protein and antitoxin RNA have been identified in S. aureus in silico, but not yet experimentally proven. A closer inspection of possible links between TA systems and S. aureus pathophysiology will reveal, if these genetic loci may represent druggable targets. The modification of a staphylococcal TA toxin to a cyclopeptide antibiotic highlights the potential of TA systems as rather untapped sources of drug discovery.

  3. Toxin-Antitoxin Systems of Staphylococcus aureus

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    Christopher F. Schuster

    2016-05-01

    Full Text Available Toxin-antitoxin (TA systems are small genetic elements found in the majority of prokaryotes. They encode toxin proteins that interfere with vital cellular functions and are counteracted by antitoxins. Dependent on the chemical nature of the antitoxins (protein or RNA and how they control the activity of the toxin, TA systems are currently divided into six different types. Genes comprising the TA types I, II and III have been identified in Staphylococcus aureus. MazF, the toxin of the mazEF locus is a sequence-specific RNase that cleaves a number of transcripts, including those encoding pathogenicity factors. Two yefM-yoeB paralogs represent two independent, but auto-regulated TA systems that give rise to ribosome-dependent RNases. In addition, omega/epsilon/zeta constitutes a tripartite TA system that supposedly plays a role in the stabilization of resistance factors. The SprA1/SprA1AS and SprF1/SprG1 systems are post-transcriptionally regulated by RNA antitoxins and encode small membrane damaging proteins. TA systems controlled by interaction between toxin protein and antitoxin RNA have been identified in S. aureus in silico, but not yet experimentally proven. A closer inspection of possible links between TA systems and S. aureus pathophysiology will reveal, if these genetic loci may represent druggable targets. The modification of a staphylococcal TA toxin to a cyclopeptide antibiotic highlights the potential of TA systems as rather untapped sources of drug discovery.

  4. A regulatory role for Staphylococcus aureus toxin-antitoxin system PemIKSa.

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    Bukowski, Michal; Lyzen, Robert; Helbin, Weronika M; Bonar, Emilia; Szalewska-Palasz, Agnieszka; Wegrzyn, Grzegorz; Dubin, Grzegorz; Dubin, Adam; Wladyka, Benedykt

    2013-01-01

    Toxin-antitoxin systems were shown to be involved in plasmid maintenance when they were initially discovered, but other roles have been demonstrated since. Here we identify and characterize a novel toxin-antitoxin system (pemIKSa) located on Staphylococcus aureus plasmid pCH91. The toxin (PemKSa) is a sequence-specific endoribonuclease recognizing the tetrad sequence U↓AUU, and the antitoxin (PemISa) inhibits toxin activity by physical interaction. Although the toxin-antitoxin system is responsible for stable plasmid maintenance our data suggest the participation of pemIKSa in global regulation of staphylococcal virulence by alteration of the translation of large pools of genes. We propose a common mechanism of reversible activation of toxin-antitoxin systems based on antitoxin transcript resistance to toxin cleavage. Elucidation of this mechanism is particularly interesting because reversible activation is a prerequisite for the proposed general regulatory role of toxin-antitoxin systems.

  5. Prokaryotic toxin-antitoxin systems: novel regulations of the toxins.

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    Otsuka, Yuichi

    2016-05-01

    Toxin-antitoxin (TA) systems are widely conserved in prokaryotic plasmids and chromosomes and are linked to many roles in cell physiology, including plasmid maintenance, stress response, persistence and protection from phage infection. A TA system is composed of a stable toxin and a labile antitoxin that inhibits a harmful effect of the cognate toxin. When gene expression from the TA loci is repressed under certain conditions such as nutrient starvation, the toxin is freed from the rapidly degrading antitoxin and obstructs an essential cellular process, such as DNA replication, translation and peptidoglycan synthesis, which subsequently causes growth arrest. TA systems are classified into five types according to the nature and the function of antitoxins, and the activity of toxins is tightly regulated in a variety of ways. This short-review highlights several novel regulatory mechanisms for Escherichia coli toxins that we recently discovered.

  6. Bacterial toxin-antitoxin gene system as containment control in yeast cells

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    Kristoffersen, P.; Jensen, G. B.; Gerdes, K.;

    2000-01-01

    The potential of a bacterial toxin-antitoxin gene system for use in containment control in eukaryotes was explored. The Escherichia coli relE and relB genes were expressed in the yeast Saccharomyces cerevisiae, Expression of the relE gene was highly toxic to yeast cells. However, expression...... of the relB gene counteracted the effect of relE to some extent, suggesting that toxin-antitoxin interaction also occurs in S. cerevisiae, Thus, bacterial toxin-antitoxin gene systems also have potential applications in the control of cell proliferation in eukaryotic cells, especially in those industrial...

  7. Toxin-Antitoxin Systems as Multilevel Interaction Systems

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    Goeders, Nathalie; Van Melderen, Laurence

    2014-01-01

    Toxin-antitoxin (TA) systems are small genetic modules usually composed of a toxin and an antitoxin counteracting the activity of the toxic protein. These systems are widely spread in bacterial and archaeal genomes. TA systems have been assigned many functions, ranging from persistence to DNA stabilization or protection against mobile genetic elements. They are classified in five types, depending on the nature and mode of action of the antitoxin. In type I and III, antitoxins are RNAs that either inhibit the synthesis of the toxin or sequester it. In type II, IV and V, antitoxins are proteins that either sequester, counterbalance toxin activity or inhibit toxin synthesis. In addition to these interactions between the antitoxin and toxin components (RNA-RNA, protein-protein, RNA-protein), TA systems interact with a variety of cellular factors, e.g., toxins target essential cellular components, antitoxins are degraded by RNAses or ATP-dependent proteases. Hence, TA systems have the capacity to interact with each other at different levels. In this review, we will discuss the different interactions in which TA systems are involved and their implications in TA system functions and evolution. PMID:24434905

  8. Prokaryotic toxin-antitoxin systems--the role in bacterial physiology and application in molecular biology.

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    Bukowski, Michal; Rojowska, Anna; Wladyka, Benedykt

    2011-01-01

    Bacteria have developed multiple complex mechanisms ensuring an adequate response to environmental changes. In this context, bacterial cell division and growth are subject to strict control to ensure metabolic balance and cell survival. A plethora of studies cast light on toxin-antitoxin (TA) systems as metabolism regulators acting in response to environmental stress conditions. Many of those studies suggest direct relations between the TA systems and the pathogenic potential or antibiotic resistance of relevant bacteria. Other studies point out that TA systems play a significant role in ensuring stability of mobile genetic material. The evolutionary origin and relations between various TA systems are still a subject of a debate. The impact of toxin-antitoxin systems on bacteria physiology prompted their application in molecular biology as tools allowing cloning of some hard-to-maintain genes, plasmid maintenance and production of recombinant proteins.

  9. Repurposing a Prokaryotic Toxin-Antitoxin System for the Selective Killing of Oncogenically Stressed Human Cells.

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    Preston, Mark A; Pimentel, Belén; Bermejo-Rodríguez, Camino; Dionne, Isabelle; Turnbull, Alice; de la Cueva-Méndez, Guillermo

    2016-07-15

    Prokaryotes express intracellular toxins that pass unnoticed to carrying cells until coexpressed antitoxin partners are degraded in response to stress. Although not evolved to function in eukaryotes, one of these toxins, Kid, induces apoptosis in mammalian cells, an effect that is neutralized by its cognate antitoxin, Kis. Here we engineered this toxin-antitoxin pair to create a synthetic system that becomes active in human cells suffering a specific oncogenic stress. Inspired by the way Kid becomes active in bacterial cells, we produced a Kis variant that is selectively degraded in human cells expressing oncoprotein E6. The resulting toxin-antitoxin system functions autonomously in human cells, distinguishing those that suffer the oncogenic insult, which are killed by Kid, from those that do not, which remain protected by Kis. Our results provide a framework for developing personalized anticancer strategies avoiding off-target effects, a challenge that has been hardly tractable by other means thus far.

  10. Identification and characterization of toxin-antitoxin systems in strains of Lactobacillus rhamnosus isolated from humans.

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    Klimina, K M; Kjasova, D K; Poluektova, E U; Krügel, H; Leuschner, Y; Saluz, H-P; Danilenko, V N

    2013-08-01

    The toxin-antitoxin gene systems (TASs) are present in the genomes of the overwhelming majority of bacteria and archaea. These systems are involved in various cellular regulatory processes (including stress response), and have not been previously investigated in Lactobacilli. We identified 6 putative TASs with toxins belonging to the MazE and RelE superfamilies (PemK1-А1Lrh, PemK2-А2Lrh, PemK3-RelB2Lrh, RelE1Lrh, RelB3-RelE3Lrh, and YefM-YoeBLrh) in the genomes of annotated strains of Lactobacillus rhamnosus. PCR analyses revealed that all systems were found in the genomes of 15 strains of L. rhamnosus isolated from humans in central Russia. These strains were highly heterogeneous with respect to the presence of TASs, as well as their nucleotide and amino acid sequences. In three cases, the relE1 genes contained IS3 elements. TAS heterogeneity may be used to reveal inter-genus differences between strains. Cloning of the toxin genes of 3 TASs inhibited Escherichia coli growth, thus confirming their functionality. Cell growth arrest caused by expression of the toxin genes could be reverted by the expression of a cognate antitoxins. Transcription of toxin-antitoxin loci in L. rhamnosus was shown by RT-PCR. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. A common origin for the bacterial toxin-antitoxin systems parD and ccd, suggested by analyses of toxin/target and toxin/antitoxin interactions.

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    Andrew B Smith

    Full Text Available Bacterial toxin-antitoxin (TA systems encode two proteins, a potent inhibitor of cell proliferation (toxin and its specific antidote (antitoxin. Structural data has revealed striking similarities between the two model TA toxins CcdB, a DNA gyrase inhibitor encoded by the ccd system of plasmid F, and Kid, a site-specific endoribonuclease encoded by the parD system of plasmid R1. While a common structural fold seemed at odds with the two clearly different modes of action of these toxins, the possibility of functional crosstalk between the parD and ccd systems, which would further point to their common evolutionary origin, has not been documented. Here, we show that the cleavage of RNA and the inhibition of protein synthesis by the Kid toxin, two activities that are specifically counteracted by its cognate Kis antitoxin, are altered, but not inhibited, by the CcdA antitoxin. In addition, Kis was able to inhibit the stimulation of DNA gyrase-mediated cleavage of DNA by CcdB, albeit less efficiently than CcdA. We further show that physical interactions between the toxins and antitoxins of the different systems do occur and define the stoichiometry of the complexes formed. We found that CcdB did not degrade RNA nor did Kid have any reproducible effect on the tested DNA gyrase activities, suggesting that these toxins evolved to reach different, rather than common, cellular targets.

  12. Horizontal gene transfer of chromosomal Type II toxin-antitoxin systems of Escherichia coli.

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    Ramisetty, Bhaskar Chandra Mohan; Santhosh, Ramachandran Sarojini

    2016-02-01

    Type II toxin-antitoxin systems (TAs) are small autoregulated bicistronic operons that encode a toxin protein with the potential to inhibit metabolic processes and an antitoxin protein to neutralize the toxin. Most of the bacterial genomes encode multiple TAs. However, the diversity and accumulation of TAs on bacterial genomes and its physiological implications are highly debated. Here we provide evidence that Escherichia coli chromosomal TAs (encoding RNase toxins) are 'acquired' DNA likely originated from heterologous DNA and are the smallest known autoregulated operons with the potential for horizontal propagation. Sequence analyses revealed that integration of TAs into the bacterial genome is unique and contributes to variations in the coding and/or regulatory regions of flanking host genome sequences. Plasmids and genomes encoding identical TAs of natural isolates are mutually exclusive. Chromosomal TAs might play significant roles in the evolution and ecology of bacteria by contributing to host genome variation and by moderation of plasmid maintenance.

  13. Proteomic profiling of Mycobacterium tuberculosis identifies nutrient-starvation-responsive toxin-antitoxin systems

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    Albrethsen, Jakob; Agner, Jeppe; Piersma, Sander R

    2013-01-01

    In order to successfully enter the latent stage, Mycobacterium tuberculosis must adapt to conditions such as nutrient limitation and hypoxia. In vitro models that mimic latent infection are valuable tools for describing the changes in metabolism that occur when the bacterium exists in a non......-growing form. We used two complementary proteomic approaches, label-free LC-MS/MS analysis and two-dimensional difference gel electrophoresis, to determine the proteome profile of extracellular proteins from M. tuberculosis cultured under nutrient starvation. Through the label-free LC-MS/MS analysis......, significant differences in the overall metabolism during nutrient starvation were detected. Notably, members of the toxin-antitoxin systems were present in larger quantities in nutrient-starved cultures, supporting a role for these global modules as M. tuberculosis switches its metabolism into dormancy...

  14. A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism.

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    Dy, Ron L; Przybilski, Rita; Semeijn, Koen; Salmond, George P C; Fineran, Peter C

    2014-04-01

    Bacterial abortive infection (Abi) systems are 'altruistic' cell death systems that are activated by phage infection and limit viral replication, thereby providing protection to the bacterial population. Here, we have used a novel approach of screening Abi systems as a tool to identify and characterize toxin-antitoxin (TA)-acting Abi systems. We show that AbiE systems are encoded by bicistronic operons and function via a non-interacting (Type IV) bacteriostatic TA mechanism. The abiE operon was negatively autoregulated by the antitoxin, AbiEi, a member of a widespread family of putative transcriptional regulators. AbiEi has an N-terminal winged-helix-turn-helix domain that is required for repression of abiE transcription, and an uncharacterized bi-functional C-terminal domain, which is necessary for transcriptional repression and sufficient for toxin neutralization. The cognate toxin, AbiEii, is a predicted nucleotidyltransferase (NTase) and member of the DNA polymerase β family. AbiEii specifically bound GTP, and mutations in conserved NTase motifs (I-III) and a newly identified motif (IV), abolished GTP binding and subsequent toxicity. The AbiE systems can provide phage resistance and enable stabilization of mobile genetic elements, such as plasmids. Our study reveals molecular insights into the regulation and function of the widespread bi-functional AbiE Abi-TA systems and the biochemical properties of both toxin and antitoxin proteins.

  15. Type II Toxin-Antitoxin Systems in the Unicellular Cyanobacterium Synechocystis sp. PCC 6803.

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    Kopfmann, Stefan; Roesch, Stefanie K; Hess, Wolfgang R

    2016-07-21

    Bacterial toxin-antitoxin (TA) systems are genetic elements, which are encoded by plasmid as well as chromosomal loci. They mediate plasmid and genomic island maintenance through post-segregational killing mechanisms but may also have milder effects, acting as mobile stress response systems that help certain cells of a population in persisting adverse growth conditions. Very few cyanobacterial TA system have been characterized thus far. In this work, we focus on the cyanobacterium Synechocystis 6803, a widely used model organism. We expand the number of putative Type II TA systems from 36 to 69 plus seven stand-alone components. Forty-seven TA pairs are located on the chromosome and 22 are plasmid-located. Different types of toxins are associated with various antitoxins in a mix and match principle. According to protein domains and experimental data, 81% of all toxins in Synechocystis 6803 likely exhibit RNase activity, suggesting extensive potential for toxicity-related RNA degradation and toxin-mediated transcriptome remodeling. Of particular interest is the Ssr8013-Slr8014 system encoded on plasmid pSYSG, which is part of a larger defense island or the pSYSX system Slr6056-Slr6057, which is linked to a bacterial ubiquitin-like system. Consequently, Synechocystis 6803 is one of the most prolific sources of new information about these genetic elements.

  16. Heterologous Expression of Toxins from Bacterial Toxin-Antitoxin Systems in Eukaryotic Cells: Strategies and Applications

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    Chew Chieng Yeo

    2016-02-01

    Full Text Available Toxin-antitoxin (TA systems are found in nearly all prokaryotic genomes and usually consist of a pair of co-transcribed genes, one of which encodes a stable toxin and the other, its cognate labile antitoxin. Certain environmental and physiological cues trigger the degradation of the antitoxin, causing activation of the toxin, leading either to the death or stasis of the host cell. TA systems have a variety of functions in the bacterial cell, including acting as mediators of programmed cell death, the induction of a dormant state known as persistence and the stable maintenance of plasmids and other mobile genetic elements. Some bacterial TA systems are functional when expressed in eukaryotic cells and this has led to several innovative applications, which are the subject of this review. Here, we look at how bacterial TA systems have been utilized for the genetic manipulation of yeasts and other eukaryotes, for the containment of genetically modified organisms, and for the engineering of high expression eukaryotic cell lines. We also examine how TA systems have been adopted as an important tool in developmental biology research for the ablation of specific cells and the potential for utility of TA systems in antiviral and anticancer gene therapies.

  17. Heterologous Expression of Toxins from Bacterial Toxin-Antitoxin Systems in Eukaryotic Cells: Strategies and Applications.

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    Yeo, Chew Chieng; Abu Bakar, Fauziah; Chan, Wai Ting; Espinosa, Manuel; Harikrishna, Jennifer Ann

    2016-02-19

    Toxin-antitoxin (TA) systems are found in nearly all prokaryotic genomes and usually consist of a pair of co-transcribed genes, one of which encodes a stable toxin and the other, its cognate labile antitoxin. Certain environmental and physiological cues trigger the degradation of the antitoxin, causing activation of the toxin, leading either to the death or stasis of the host cell. TA systems have a variety of functions in the bacterial cell, including acting as mediators of programmed cell death, the induction of a dormant state known as persistence and the stable maintenance of plasmids and other mobile genetic elements. Some bacterial TA systems are functional when expressed in eukaryotic cells and this has led to several innovative applications, which are the subject of this review. Here, we look at how bacterial TA systems have been utilized for the genetic manipulation of yeasts and other eukaryotes, for the containment of genetically modified organisms, and for the engineering of high expression eukaryotic cell lines. We also examine how TA systems have been adopted as an important tool in developmental biology research for the ablation of specific cells and the potential for utility of TA systems in antiviral and anticancer gene therapies.

  18. Evolution of the SpoIISABC Toxin-Antitoxin-Antitoxin System in Bacilli

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    Marek Gabriško

    2016-06-01

    Full Text Available Programmed cell death in bacteria is generally associated with two-component toxin-antitoxin systems. The SpoIISABC system, originally identified in Bacillus subtilis, consists of three components: a SpoIISA toxin and the SpoIISB and SpoIISC antitoxins. SpoIISA is a membrane-bound protein, while SpoIISB and SpoIISC are small cytosolic antitoxins, which are able to bind SpoIISA and neutralize its toxicity. In the presented bioinformatics analysis, a taxonomic distribution of the genes of the SpoIISABC system is investigated; their conserved regions and residues are identified; and their phylogenetic relationships are inferred. The SpoIISABC system is part of the core genome in members of the Bacillus genus of the Firmicutes phylum. Its presence in some non-bacillus species is likely the result of horizontal gene transfer. The SpoIISB and SpoIISC antitoxins originated by gene duplications, which occurred independently in the B. subtilis and B. cereus lineages. In the B. cereus lineage, the SpoIIS module is present in two different architectures.

  19. Evolution of the SpoIISABC Toxin-Antitoxin-Antitoxin System in Bacilli

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    Gabriško, Marek; Barák, Imrich

    2016-01-01

    Programmed cell death in bacteria is generally associated with two-component toxin-antitoxin systems. The SpoIISABC system, originally identified in Bacillus subtilis, consists of three components: a SpoIISA toxin and the SpoIISB and SpoIISC antitoxins. SpoIISA is a membrane-bound protein, while SpoIISB and SpoIISC are small cytosolic antitoxins, which are able to bind SpoIISA and neutralize its toxicity. In the presented bioinformatics analysis, a taxonomic distribution of the genes of the SpoIISABC system is investigated; their conserved regions and residues are identified; and their phylogenetic relationships are inferred. The SpoIISABC system is part of the core genome in members of the Bacillus genus of the Firmicutes phylum. Its presence in some non-bacillus species is likely the result of horizontal gene transfer. The SpoIISB and SpoIISC antitoxins originated by gene duplications, which occurred independently in the B. subtilis and B. cereus lineages. In the B. cereus lineage, the SpoIIS module is present in two different architectures. PMID:27294956

  20. Toxins of Prokaryotic Toxin-Antitoxin Systems with Sequence-Specific Endoribonuclease Activity

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    Masuda, Hisako; Inouye, Masayori

    2017-01-01

    Protein translation is the most common target of toxin-antitoxin system (TA) toxins. Sequence-specific endoribonucleases digest RNA in a sequence-specific manner, thereby blocking translation. While past studies mainly focused on the digestion of mRNA, recent analysis revealed that toxins can also digest tRNA, rRNA and tmRNA. Purified toxins can digest single-stranded portions of RNA containing recognition sequences in the absence of ribosome in vitro. However, increasing evidence suggests that in vivo digestion may occur in association with ribosomes. Despite the prevalence of recognition sequences in many mRNA, preferential digestion seems to occur at specific positions within mRNA and also in certain reading frames. In this review, a variety of tools utilized to study the nuclease activities of toxins over the past 15 years will be reviewed. A recent adaptation of an RNA-seq-based technique to analyze entire sets of cellular RNA will be introduced with an emphasis on its strength in identifying novel targets and redefining recognition sequences. The differences in biochemical properties and postulated physiological roles will also be discussed. PMID:28420090

  1. Type II toxin-antitoxin systems are unevenly distributed among Escherichia coli phylogroups.

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    Fiedoruk, Krzysztof; Daniluk, Tamara; Swiecicka, Izabela; Sciepuk, Malgorzata; Leszczynska, Katarzyna

    2015-01-01

    Type II toxin-antitoxin systems (TAs) are bicistronic operons ubiquitous in prokaryotic genomes, displaying multilevel association with cell physiology. Various possible functions have been assigned to TAs, ranging from beneficial for their hosts, such as a stress response, dormancy and protection against genomic parasites, to detrimental or useless functions, such as selfish alleles. As there is a link between several Escherichia coli features (e.g. virulence, lifestyle) and the phylogeny of this species, we hypothesized a similar association with TAs. Using PCR we studied the distribution of 15 chromosomal and plasmidic type II TA loci in 84 clinical E. coli isolates in relation to their main phylogenetic groups (A, B1, B2 and D). In addition, we performed in silico searching of these TA loci in 60 completely sequenced E. coli genomes deposited in GenBank. The highest number of TA loci per strain was observed in group A (mean 8.2, range 5-12) and the lowest in group B2 (mean 4.2, range 2-8). Moreover, significant differences in the prevalence of nine chromosomal TAs among E. coli phylogroups were noted. In conclusion, the presence of some chromosomal TAs in E. coli is phylogroup-related rather than a universal feature of the species. In addition, their limited collection in group B2 clearly distinguish it from the other E. coli phylogroups.

  2. Automated discovery and phylogenetic analysis of new toxin-antitoxin systems

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    Milinkovitch Michel C

    2008-06-01

    Full Text Available Abstract Background Although often viewed as elements "at the service of" bacteria, plasmids exhibit replication and maintenance mechanisms that make them purely "selfish DNA" candidates. Toxin-antitoxin (TA systems are a spectacular example of such mechanisms: a gene coding for a cytotoxic stable protein is preceded by a gene coding for an unstable antitoxin. The toxin being more stable than the antitoxin, absence of the operon causes a reduction of the amount of the latter relative to the amount of the former. Thus, a cell exhibiting a TA system on a plasmid is 'condemned' either not to loose it or to die. Results Different TA systems have been described and classified in several families, according to similarity and functional parameters. However, given the small size and large divergence among TA system sequences, it is likely that many TA systems are not annotated as such in the rapidly accumulating NCBI database. To detect these putative TA systems, we developed an algorithm that searches public databases on the basis of predefined similarity and TA-specific structural constraints. This approach, using a single starting query sequence for each of the ParE, Doc, and VapC families, and two starting sequences for the MazF/CcdB family, identified over 1,500 putative TA systems. These groups of sequences were analyzed phylogenetically for a better classification and understanding of TA systems evolution. Conclusion The phylogenetic distributions of the newly uncovered TA systems are very different within the investigated families. The resulting phylogenetic trees are available for browsing and searching through a java program available at http://ueg.ulb.ac.be/tiq/.

  3. What is the link between stringent response, endoribonuclease encoding type II toxin-antitoxin systems and persistence?

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    Ramisetty, B. C. M.; Ghosh, Debabrata; Chowdhury, M. R.

    2016-01-01

    Persistence is a transient and non-inheritable tolerance to antibiotics by a small fraction of a bacterial population. One of the proposed determinants of bacterial persistence is toxin-antitoxin systems (TASs) which are also implicated in a wide range of stress-related phenomena. Maisonneuve E....... The decrease in the concentration of antitoxins supposedly activated the toxin to increase in the number of persisters during antibiotic treatment. In this study, we show that inorganic polyphosphate is not required for transcriptional activation of yefM/yoeB TAS, which is an indirect indication of Lon...

  4. Keeping the wolves at bay: antitoxins of prokaryotic type II toxin-antitoxin systems

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    Wai Ting eChan

    2016-03-01

    Full Text Available In their initial stages of discovery, prokaryotic toxin-antitoxin (TA systems were confined to bacterial plasmids where they function to mediate the maintenance and stability of usually low- to medium-copy number plasmids through the post-segregational killing of any plasmid-free daughter cells that developed. Their eventual discovery as nearly ubiquitous and repetitive elements in bacterial chromosomes led to a wealth of knowledge and scientific debate as to their diversity and functionality in the prokaryotic lifestyle. Currently categorized into six different types designated types I – VI, type II TA systems are the best characterized. These generally comprised of two genes encoding a proteic toxin and its corresponding proteic antitoxin, respectively. Under normal growth conditions, the stable toxin is prevented from exerting its lethal effect through tight binding with the less stable antitoxin partner, forming a non-lethal TA protein complex. Besides binding with its cognate toxin, the antitoxin also plays a role in regulating the expression of the type II TA operon by binding to the operator site, thereby repressing transcription from the TA promoter. In most cases, full repression is observed in the presence of the TA complex as binding of the toxin enhances the DNA binding capability of the antitoxin. TA systems have been implicated in a gamut of prokaryotic cellular functions such as being mediators of programmed cell death as well as persistence or dormancy, biofilm formation, as defensive weapons against bacteriophage infections and as virulence factors in pathogenic bacteria. It is thus apparent that these antitoxins, as DNA-binding proteins, play an essential role in modulating the prokaryotic lifestyle whilst at the same time preventing the lethal action of the toxins under normal growth conditions, i.e., keeping the proverbial wolves at bay. In this review, we will cover the diversity and characteristics of various type II TA

  5. Is the mazEF toxin-antitoxin system responsible for vancomycin resistance in clinical isolates of Enterococcus faecalis?

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    Sadeghifard, Nourkhoda

    2014-03-01

    Full Text Available [english] The current study was conducted to investigate the relationship between vancomycin-resistant (VRE and the presence of toxin-antitoxin (TA system, which may be useful as target for novel antimicrobial therapy concepts. The susceptibility of was determined by MIC, and the presence of the TA system was evaluated by PCR. Among 200 isolates 39.5% showed resistance to vancomycin (VRE, while 60.5% were susceptible strains (VSE. The TA system was positive in all VRE isolates (100%, but less prevalent (38/121, 31.4% among the 121 VSE strains. In conclusion, our study demonstrated a positive relationship between the presence of vancomycin resistance and TA system. This observation may introduce therapeutic options against a novel antimicrobial target in enterococci.

  6. Discovery of functional toxin/antitoxin systems in bacteria by shotgun cloning

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    Sberro, Hila; Leavitt, Azita; Kiro, Ruth; Koh, Eugene; Peleg, Yoav; Qimron, Udi; Sorek, Rotem

    2013-04-01

    Toxin-antitoxin (TA) modules, composed of a toxic protein and a counteracting antitoxin, play important roles in bacterial physiology. We examined the experimental insertion of 1.5 million genes from 388 microbial genomes into an Escherichia coli host using over 8.5 million random clones. This revealed hundreds of genes (toxins) that could only be cloned when the neighboring gene (antitoxin) was present on the same clone. Clustering of these genes revealed TA families widespread in bacterial genomes, some of which deviate from the classical characteristics previously described for such modules. Introduction of these genes into E. coli validated that the toxin toxicity is mitigated by the antitoxin. Infection experiments with T7 phage showed that two of the new modules can provide resistance against phage. Moreover, our experiments revealed an 'anti-defense' protein in phage T7 that neutralizes phage resistance. Our results expose active fronts in the arms race between bacteria and phage.

  7. Discovery of Functional Toxin/Antitoxin Systems in Bacteria by Shotgun Cloning

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    Sberro, Hila; Leavitt, Azita; Kiro, Ruth; Koh, Eugene; Peleg, Yoav; Qimron, Udi; Sorek, Rotem

    2013-04-01

    Toxin-antitoxin (TA) modules, composed of a toxic protein and a counteracting antitoxin, play important roles in bacterial physiology. We examined the experimental insertion of 1.5 million genes from 388 microbial genomes into an Escherichia coli host using over 8.5 million random clones. This revealed hundreds of genes (toxins) that could only be cloned when the neighboring gene (antitoxin) was present on the same clone. Clustering of these genes revealed TA families widespread in bacterial genomes, some of which deviate from the classical characteristics previously described for such modules. Introduction of these genes into E. coli validated that the toxin toxicity is mitigated by the antitoxin. Infection experiments with T7 phage showed that two of the new modules can provide resistance against phage. Moreover, our experiments revealed an 'anti-defense' protein in phage T7 that neutralizes phage resistance. Our results expose active fronts in the arms race between bacteria and phage.

  8. Comprehensive comparative-genomic analysis of Type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes

    Directory of Open Access Journals (Sweden)

    Makarova Kira S

    2009-06-01

    Full Text Available Abstract Background The prokaryotic toxin-antitoxin systems (TAS, also referred to as TA loci are widespread, mobile two-gene modules that can be viewed as selfish genetic elements because they evolved mechanisms to become addictive for replicons and cells in which they reside, but also possess "normal" cellular functions in various forms of stress response and management of prokaryotic population. Several distinct TAS of type 1, where the toxin is a protein and the antitoxin is an antisense RNA, and numerous, unrelated TAS of type 2, in which both the toxin and the antitoxin are proteins, have been experimentally characterized, and it is suspected that many more remain to be identified. Results We report a comprehensive comparative-genomic analysis of Type 2 toxin-antitoxin systems in prokaryotes. Using sensitive methods for distant sequence similarity search, genome context analysis and a new approach for the identification of mobile two-component systems, we identified numerous, previously unnoticed protein families that are homologous to toxins and antitoxins of known type 2 TAS. In addition, we predict 12 new families of toxins and 13 families of antitoxins, and also, predict a TAS or TAS-like activity for several gene modules that were not previously suspected to function in that capacity. In particular, we present indications that the two-gene module that encodes a minimal nucleotidyl transferase and the accompanying HEPN protein, and is extremely abundant in many archaea and bacteria, especially, thermophiles might comprise a novel TAS. We present a survey of previously known and newly predicted TAS in 750 complete genomes of archaea and bacteria, quantitatively demonstrate the exceptional mobility of the TAS, and explore the network of toxin-antitoxin pairings that combines plasticity with selectivity. Conclusion The defining properties of the TAS, namely, the typically small size of the toxin and antitoxin genes, fast evolution, and

  9. The Antitoxin Protein of a Toxin-Antitoxin System from Xylella fastidiosa Is Secreted via Outer Membrane Vesicles

    Science.gov (United States)

    Santiago, André da Silva; Mendes, Juliano S.; dos Santos, Clelton A.; de Toledo, Marcelo A. S.; Beloti, Lilian L.; Crucello, Aline; Horta, Maria A. C.; Favaro, Marianna T. de Pinho; Munar, Duber M. M.; de Souza, Alessandra A.; Cotta, Mônica A.; de Souza, Anete P.

    2016-01-01

    The Xylella fastidiosa subsp pauca strain 9a5c is a Gram-negative, xylem-limited bacterium that is able to form a biofilm and affects citrus crops in Brazil. Some genes are considered to be involved in biofilm formation, but the specific mechanisms involved in this process remain unknown. This limited understanding of how some bacteria form biofilms is a major barrier to our comprehension of the progression of diseases caused by biofilm-producing bacteria. Several investigations have shown that the toxin-antitoxin (TA) operon is related to biofilm formation. This operon is composed of a toxin with RNAse activity and its cognate antitoxin. Previous reports have indicated that the antitoxin is able to inhibit toxin activity and modulate the expression of the operon as well as other target genes involved in oxidative stress and mobility. In this study, we characterize a toxin-antitoxin system consisting of XfMqsR and XfYgiT, respectively, from X. fastidiosa subsp. pauca strain 9a5c. These proteins display a high similarity to their homologs in X. fastidiosa strain Temecula and a predicted tridimensional structure that is similar to MqsR-YgiT from Escherichia coli. The characterization was performed using in vitro assays such as analytical ultracentrifugation (AUC), size exclusion chromatography, isothermal titration calorimetry, and Western blotting. Using a fluorometric assay to detect RNAses, we demonstrated that XfMqsR is thermostable and can degrade RNA. XfMqsR is inhibited by XfYgiT, which interacts with its own promoter. XfYgiT is known to be localized in the intracellular compartment; however, we provide strong evidence that X. fastidiosa secretes wild-type XfYgiT into the extracellular environment via outer membrane vesicles, as confirmed by Western blotting and specific immunofluorescence labeling visualized by fluorescence microscopy. Taken together, our results characterize the TA system from X. fastidiosa strain 9a5c, and we also discuss the possible

  10. The MazEF Toxin-Antitoxin System Alters the β-Lactam Susceptibility of Staphylococcus aureus.

    Directory of Open Access Journals (Sweden)

    Christopher F Schuster

    Full Text Available Toxin-antitoxin (TA systems are genetic elements of prokaryotes which encode a stable toxin and an unstable antitoxin that can counteract toxicity. TA systems residing on plasmids are often involved in episomal maintenance whereas those on chromosomes can have multiple functions. The opportunistic pathogen Staphylococcus aureus possesses at least four different families of TA systems but their physiological roles are elusive. The chromosomal mazEF system encodes the RNase toxin MazF and the antitoxin MazE. In the light of ambiguity regarding the cleavage activity, we here verify that MazF specifically targets UACAU sequences in S. aureus in vivo. In a native strain background and under non-stress conditions, cleavage was observed in the absence or presence of mazE. Transcripts of spa (staphylococcal protein A and rsbW (anti-σB factor were cut, but translational reporter fusions indicated that protein levels of the encoded products were unaffected. Despite a comparable growth rate as the wild-type, an S. aureus mazEF deletion mutant was more susceptible to β-lactam antibiotics, which suggests that further genes, putatively involved in the antibiotic stress response or cell wall synthesis or turnover, are controlled by this TA system.

  11. The MazEF Toxin-Antitoxin System Alters the β-Lactam Susceptibility of Staphylococcus aureus.

    Science.gov (United States)

    Schuster, Christopher F; Mechler, Lukas; Nolle, Nicoletta; Krismer, Bernhard; Zelder, Marc-Eric; Götz, Friedrich; Bertram, Ralph

    2015-01-01

    Toxin-antitoxin (TA) systems are genetic elements of prokaryotes which encode a stable toxin and an unstable antitoxin that can counteract toxicity. TA systems residing on plasmids are often involved in episomal maintenance whereas those on chromosomes can have multiple functions. The opportunistic pathogen Staphylococcus aureus possesses at least four different families of TA systems but their physiological roles are elusive. The chromosomal mazEF system encodes the RNase toxin MazF and the antitoxin MazE. In the light of ambiguity regarding the cleavage activity, we here verify that MazF specifically targets UACAU sequences in S. aureus in vivo. In a native strain background and under non-stress conditions, cleavage was observed in the absence or presence of mazE. Transcripts of spa (staphylococcal protein A) and rsbW (anti-σB factor) were cut, but translational reporter fusions indicated that protein levels of the encoded products were unaffected. Despite a comparable growth rate as the wild-type, an S. aureus mazEF deletion mutant was more susceptible to β-lactam antibiotics, which suggests that further genes, putatively involved in the antibiotic stress response or cell wall synthesis or turnover, are controlled by this TA system.

  12. Toward the identification of a type I toxin-antitoxin system in the plasmid DNA of dairy Lactobacillus rhamnosus.

    Science.gov (United States)

    Folli, Claudia; Levante, Alessia; Percudani, Riccardo; Amidani, Davide; Bottazzi, Stefania; Ferrari, Alberto; Rivetti, Claudio; Neviani, Erasmo; Lazzi, Camilla

    2017-09-21

    Plasmids carry genes that give bacteria beneficial traits and allow them to survive in competitive environments. In many cases, they also harbor toxin-antitoxin (TA) systems necessary for plasmid maintenance. TA systems are generally characterized by a stable "toxin", a protein or peptide capable of killing the cell upon plasmid loss and by an unstable "antitoxin", a protein or a non-coding RNA that inhibits toxin activity. Here we report data toward the identification of a RNA-regulated TA system in the plasmid DNA of L. rhamnosus isolated from cheese. The proposed TA system comprises two convergently transcribed RNAs: a toxin RNA encoding a 29 amino acid peptide named Lpt and an antitoxin non-coding RNA. Both toxin and antitoxin RNAs resulted upregulated under conditions mimicking cheese ripening. The toxicity of the Lpt peptide was demonstrated in E. coli by cloning the Lpt ORF under the control of an inducible promoter. Bioinformatics screening of the bacterial nucleotide database, shows that regions homologous to the Lpt TA locus are widely distributed in the Lactobacillus genus, particularly within the L. casei group, suggesting a relevant role of TA systems in plasmid maintenance of cheese microbiota.

  13. A Type III protein-RNA toxin-antitoxin system from Bacillus thuringiensis promotes plasmid retention during spore development.

    Science.gov (United States)

    Short, Francesca L; Monson, Rita E; Salmond, George P C

    2015-01-01

    Members of the Bacillus cereus sensu lato group of bacteria often contain multiple large plasmids, including those encoding virulence factors in B. anthracis. Bacillus species can develop into spores in response to stress. During sporulation the genomic content of the cell is heavily compressed, which could result in counterselection of extrachromosomal genomic elements, unless they have robust stabilization and segregation systems. Toxin-antitoxin (TA) systems are near-ubiquitous in prokaryotes and have multiple biological roles, including plasmid stabilization during vegetative growth. Here, we have shown that a Type III TA system, based on an RNA antitoxin and endoribonuclease toxin, from plasmid pAW63 in Bacillus thuringiensis serovar kurstaki HD-73 can dramatically promote plasmid retention in populations undergoing sporulation and germination, and we provide evidence that this occurs through the post-segregational killing of plasmid-free forespores. Our findings show how an extremely common genetic module can be used to ensure plasmid maintenance during stress-induced developmental transitions, with implications for plasmid dynamics in B. cereus s.l. bacteria.

  14. A toxin antitoxin system promotes the maintenance of the IncA/C-mobilizable Salmonella Genomic Island 1.

    Science.gov (United States)

    Huguet, Kevin T; Gonnet, Mathieu; Doublet, Benoît; Cloeckaert, Axel

    2016-08-31

    The multidrug resistance Salmonella Genomic Island 1 (SGI1) is an integrative mobilizable element identified in several enterobacterial pathogens. This chromosomal island requires a conjugative IncA/C plasmid to be excised as a circular extrachromosomal form and conjugally mobilized in trans. Preliminary observations suggest stable maintenance of SGI1 in the host chromosome but paradoxically also incompatibility between SGI1 and IncA/C plasmids. Here, using a Salmonella enterica serovar Agona clonal bacterial population as model, we demonstrate that a Toxin-Antitoxin (TA) system encoded by SGI1 plays a critical role in its stable host maintenance when an IncA/C plasmid is concomitantly present. This system, designated sgiAT for Salmonella genomic island 1 Antitoxin and Toxin respectively, thus seems to play a stabilizing role in a situation where SGI1 is susceptible to be lost through plasmid IncA/C-mediated excision. Moreover and for the first time, the incompatibility between SGI1 and IncA/C plasmids was experimentally confirmed.

  15. What Is the Link between Stringent Response, Endoribonuclease Encoding Type II Toxin-Antitoxin Systems and Persistence?

    Science.gov (United States)

    Ramisetty, Bhaskar C M; Ghosh, Dimpy; Roy Chowdhury, Maoumita; Santhosh, Ramachandran S

    2016-01-01

    Persistence is a transient and non-inheritable tolerance to antibiotics by a small fraction of a bacterial population. One of the proposed determinants of bacterial persistence is toxin-antitoxin systems (TASs) which are also implicated in a wide range of stress-related phenomena. Maisonneuve E, Castro-Camargo M, Gerdes K. 2013. Cell 154:1140-1150 reported an interesting link between ppGpp mediated stringent response, TAS, and persistence. It is proposed that accumulation of ppGpp enhances the accumulation of inorganic polyphosphate which modulates Lon protease to degrade antitoxins. The decrease in the concentration of antitoxins supposedly activated the toxin to increase in the number of persisters during antibiotic treatment. In this study, we show that inorganic polyphosphate is not required for transcriptional activation of yefM/yoeB TAS, which is an indirect indication of Lon-dependent degradation of YefM antitoxin. The Δ10 strain, an Escherichia coli MG1655 derivative in which the 10 TAS are deleted, is more sensitive to ciprofloxacin compared to wild type MG1655. Furthermore, we show that the Δ10 strain has relatively lower fitness compared to the wild type and hence, we argue that the persistence related implications based on Δ10 strain are void. We conclude that the transcriptional regulation and endoribonuclease activity of YefM/YoeB TAS is independent of ppGpp and inorganic polyphosphate. Therefore, we urge for thorough inspection and debate on the link between chromosomal endoribonuclease TAS and persistence.

  16. A novel mechanism of programmed cell death in bacteria by toxin-antitoxin systems corrupts peptidoglycan synthesis.

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    Hannes Mutschler

    2011-03-01

    Full Text Available Most genomes of bacteria contain toxin-antitoxin (TA systems. These gene systems encode a toxic protein and its cognate antitoxin. Upon antitoxin degradation, the toxin induces cell stasis or death. TA systems have been linked with numerous functions, including growth modulation, genome maintenance, and stress response. Members of the epsilon/zeta TA family are found throughout the genomes of pathogenic bacteria and were shown not only to stabilize resistance plasmids but also to promote virulence. The broad distribution of epsilon/zeta systems implies that zeta toxins utilize a ubiquitous bacteriotoxic mechanism. However, whereas all other TA families known to date poison macromolecules involved in translation or replication, the target of zeta toxins remained inscrutable. We used in vivo techniques such as microscropy and permeability assays to show that pneumococcal zeta toxin PezT impairs cell wall synthesis and triggers autolysis in Escherichia coli. Subsequently, we demonstrated in vitro that zeta toxins in general phosphorylate the ubiquitous peptidoglycan precursor uridine diphosphate-N-acetylglucosamine (UNAG and that this activity is counteracted by binding of antitoxin. After identification of the product we verified the kinase activity in vivo by analyzing metabolite extracts of cells poisoned by PezT using high pressure liquid chromatograpy (HPLC. We further show that phosphorylated UNAG inhibitis MurA, the enzyme catalyzing the initial step in bacterial peptidoglycan biosynthesis. Additionally, we provide what is to our knowledge the first crystal structure of a zeta toxin bound to its substrate. We show that zeta toxins are novel kinases that poison bacteria through global inhibition of peptidoglycan synthesis. This provides a fundamental understanding of how epsilon/zeta TA systems stabilize mobile genetic elements. Additionally, our results imply a mechanism that connects activity of zeta toxin PezT to virulence of pneumococcal

  17. What is the link between stringent response, endoribonuclease encoding Type II Toxin-Antitoxin systems and persistence?

    Directory of Open Access Journals (Sweden)

    Bhaskar Chandra Mohan Ramisetty

    2016-11-01

    Full Text Available Persistence is a transient and non-inheritable tolerance to antibiotics by a small fraction of a bacterial population. One of the proposed determinants of bacterial persistence is toxin-antitoxin systems (TAS which are also implicated in a wide range of stress-related phenomena. Maisonneuve E, Castro-Camargo M, Gerdes K. 2013. Cell 154:1140-1150 reported an interesting link between ppGpp mediated stringent response, TAS, and persistence. It is proposed that accumulation of ppGpp enhances the accumulation of inorganic polyphosphate which modulates Lon protease to degrade antitoxins. The decrease in the concentration of antitoxins supposedly activated the toxin to increase in the number of persisters during antibiotic treatment. In this study, we show that inorganic polyphosphate is not required for transcriptional activation of yefM/yoeB TAS, which is an indirect indication of Lon-dependent degradation of YefM antitoxin. The Δ10 strain, an Escherichia coli MG1655 derivative in which the ten TAS are deleted, is more sensitive to ciprofloxacin compared to wild-type MG1655. Furthermore, we show that the Δ10 strain has relatively lower fitness compared to the wild type and hence, we argue that the persistence related implications based on Δ10 strain are void. We conclude that the transcriptional regulation and endoribonuclease activity of YefM/YoeB TAS is independent of ppGpp and inorganic polyphosphate. Therefore we urge for thorough inspection and debate on the link between chromosomal endoribonuclease TAS and persistence.

  18. Characterisation of the stbD/E toxin-antitoxin system of pEP36, a plasmid of the plant pathogen Erwinia pyrifoliae.

    Science.gov (United States)

    Unterholzner, Simon J; Hailer, Barbara; Poppenberger, Brigitte; Rozhon, Wilfried

    2013-09-01

    pEP36 is a plasmid ubiquitously present in Erwinia pyrifoliae, a pathogen which causes black stem blight of Asian pear. pEP36 is highly stable in its host, even in the absence of selective pressure. The plasmid is closely related to pEA29, which is widespread in E. amylovora, the causative agent of fire blight of apple and pear trees. Here we report that pEP36 possesses a functional hybrid toxin-antitoxin module, stbD/E(pEP36), with the toxin showing homology to the RelE/ParE proteins and the antidote belonging to the Phd/YefM antitoxin family. Bacteria expressing the StbE(pEP36) toxin arrest cell growth and enter a viable but non-culturable stage. However, they maintain their typical cell length and do not show filamentation. Pulse-chase experiments revealed that StbE(pEP36) acts as a global inhibitor of protein synthesis while it does not interfere with DNA and RNA synthesis. The StbD(pEP36) antitoxin is capable of neutralising StbE(pEP36) toxicity. Additional experiments show that the stbD/E(pEP36) module can stabilise plasmids at least 20-fold. Thus the toxin-antitoxin system may contribute to the remarkable stability of pEP36.

  19. Transcriptional profiling of type II toxin-antitoxin genes of Helicobacter pylori under different environmental conditions: identification of HP0967-HP0968 system

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    MIGUEL A DE LA CRUZ

    2016-11-01

    Full Text Available Helicobacter pylori is a Gram-negative bacterium that colonizes the human gastric mucosa and is responsible for causing peptic ulcers and gastric carcinoma. The expression of virulence factors allows the persistence of H. pylori in the stomach, which results in a chronic, sometimes uncontrolled inflammatory response. Type II toxin-antitoxin systems have emerged as important virulence factors in many pathogenic bacteria. Three type II toxin-antitoxin (TA systems have previously been identified in the genome of H. pylori 26695: HP0315-HP0316, HP0892-HP0893, and HP0894-HP0895. Here we characterized a heretofore undescribed type II TA system in H. pylori, HP0967-HP0968, which is encoded by the bicistronic operon hp0968-hp0967 and belongs to the Vap family. The predicted HP0967 protein is a toxin with ribonuclease activity whereas HP0968 is an antitoxin that binds to its own regulatory region. We found that all type II TA systems were expressed in H. pylori during early stationary growth phase, and differentially expressed in the presence of urea, nickel, and iron, although the hp0968-hp0967 pair was the most affected under these environmental conditions. Transcription of hp0968-hp0967 was strongly induced in a mature H. pylori biofilm and when the bacteria interacted with AGS epithelial cells. Kanamycin and chloramphenicol considerably boosted transcription levels of all the four type II TA systems. The hp0968-hp0967 TA system was the most frequent among 317 H. pylori strains isolated from all over the world. This study is the first report on the transcription of type II TA genes in H. pylori under different environmental conditions. Our data show that the HP0967 and HP0968 proteins constitute a bona fide type II TA system in H. pylori, whose expression is regulated by environmental cues, which are relevant in the context of infection of the human gastric mucosa.

  20. Toxin-Antitoxin Battle in Bacteria

    DEFF Research Database (Denmark)

    Cataudella, Ilaria

    This PhD thesis consists of three research projects revolving around the common thread of investigation of the properties and biological functions of Toxin-Antitoxin loci. Toxin-Antitoxin (TA) loci are transcriptionally regulated via an auto-inhibition mechanism called conditional cooperativity, ...

  1. Toxin-Antitoxin Battle in Bacteria

    DEFF Research Database (Denmark)

    Cataudella, Ilaria

    This PhD thesis consists of three research projects revolving around the common thread of investigation of the properties and biological functions of Toxin-Antitoxin loci. Toxin-Antitoxin (TA) loci are transcriptionally regulated via an auto-inhibition mechanism called conditional cooperativity, ...

  2. Construction of a novel, stable, food-grade expression system by engineering the endogenous toxin-antitoxin system in Bacillus subtilis.

    Science.gov (United States)

    Yang, Sen; Kang, Zhen; Cao, Wenlong; Du, Guocheng; Chen, Jian

    2016-02-10

    Bacillus subtilis as an important workhorse that has been widely used to produce enzymes and metabolites. To broaden its applications, especially in the food and feed industry, we constructed a novel, stable, food-grade expression system by engineering its type II toxin-antitoxin system. The expression of the toxin EndoA, encoded by the chromosomal ydcE gene, was regulated by an endogenous, xylose-inducible promoter, while the ydcD gene, which encodes the unstable antitoxin EndoB, was inserted into a food-grade vector backbone, where its expression was driven by the native, constitutive promoter PylxM. By maintaining the xylose concentration above 2.0 g L(-1), this auto-regulated expression system was absolutely stable after 100 generations. Compared with traditional antibiotic-dependent expression systems, this novel expression system resulted in greater biomass and higher titers of desired products (enzymes or metabolites). Our results demonstrate that this stable, food-grade expression system is suitable for enzyme production and pathway engineering, especially for the production of food-grade enzymes and metabolites.

  3. The phage growth limitation system in Streptomyces coelicolor A(3)2 is a toxin/antitoxin system, comprising enzymes with DNA methyltransferase, protein kinase and ATPase activity.

    Science.gov (United States)

    Hoskisson, Paul A; Sumby, Paul; Smith, Margaret C M

    2015-03-01

    The phage growth limitation system of Streptomyces coelicolor A3(2) is an unusual bacteriophage defence mechanism. Progeny ϕC31 phage from an initial infection are thought to be modified such that subsequent infections are attenuated in a Pgl(+) host but normal in a Pgl(-) strain. Earlier work identified four genes required for phage resistance by Pgl. Here we demonstrate that Pgl is an elaborate and novel phage restriction system that, in part, comprises a toxin/antitoxin system where PglX, a DNA methyltransferase is toxic in the absence of a functional PglZ. In addition, the ATPase activity of PglY and a protein kinase activity in PglW are shown to be essential for phage resistance by Pgl. We conclude that on infection of a Pgl(+) cell by bacteriophage ϕC31, PglW transduces a signal, probably via phosphorylation, to other Pgl proteins resulting in the activation of the DNA methyltransferase, PglX and this leads to phage restriction.

  4. The mazEF toxin-antitoxin system as an attractive target in clinical isolates of Enterococcus faecium and Enterococcus faecalis.

    Science.gov (United States)

    Soheili, Sara; Ghafourian, Sobhan; Sekawi, Zamberi; Neela, Vasantha Kumari; Sadeghifard, Nourkhoda; Taherikalani, Morovat; Khosravi, Afra; Ramli, Ramliza; Hamat, Rukman Awang

    2015-01-01

    The toxin-antitoxin (TA) system is a regulatory system where two sets of genes encode the toxin and its corresponding antitoxin. In this study, the prevalence of TA systems in independently isolated clinical isolates of Enterococcus faecium and Enterococcus faecalis was determined, the dominant TA system was identified, different virulence genes in E. faecium and E. faecalis were surveyed, the level of expression of the virulence and TA genes in normal and stress conditions was determined, and finally their associations with the TA genes were defined. Remarkably, the analysis demonstrated higBA and mazEF in all clinical isolates, and their locations were on chromosomes and plasmids, respectively. On the other hand, a quantitative analysis of TA and virulence genes revealed that the expression level in both genes is different under normal and stress conditions. The results obtained by anti-mazF peptide nucleic acids demonstrated that the expression level of virulence genes had decreased. These findings demonstrate an association between TA systems and virulence factors. The mazEF on the plasmids and the higBA TA genes on the chromosomes of all E. faecium and E. faecalis strains were dominant. Additionally, there was a decrease in the expression of virulence genes in the presence of anti-mazF peptide nucleic acids. Therefore, it is suggested that mazEF TA systems are potent and sensitive targets in all E. faecium and E. faecalis strains.

  5. Co-evolution of quaternary organization and novel RNA tertiary interactions revealed in the crystal structure of a bacterial protein-RNA toxin-antitoxin system.

    Science.gov (United States)

    Rao, Feng; Short, Francesca L; Voss, Jarrod E; Blower, Tim R; Orme, Anastasia L; Whittaker, Tom E; Luisi, Ben F; Salmond, George P C

    2015-10-30

    Genes encoding toxin-antitoxin (TA) systems are near ubiquitous in bacterial genomes and they play key roles in important aspects of bacterial physiology, including genomic stability, formation of persister cells under antibiotic stress, and resistance to phage infection. The CptIN locus from Eubacterium rectale is a member of the recently-discovered Type III class of TA systems, defined by a protein toxin suppressed by direct interaction with a structured RNA antitoxin. Here, we present the crystal structure of the CptIN protein-RNA complex to 2.2 Å resolution. The structure reveals a new heterotetrameric quaternary organization for the Type III TA class, and the RNA antitoxin bears a novel structural feature of an extended A-twist motif within the pseudoknot fold. The retention of a conserved ribonuclease active site as well as traits normally associated with TA systems, such as plasmid maintenance, implicates a wider functional role for Type III TA systems. We present evidence for the co-variation of the Type III component pair, highlighting a distinctive evolutionary process in which an enzyme and its substrate co-evolve.

  6. Crystal Structures of Phd-Doc, HigA, and YeeU Establish Multiple Evolutionary Links between Microbial Growth-Regulating Toxin-Antitoxin Systems

    Energy Technology Data Exchange (ETDEWEB)

    Arbing, Mark A.; Handelman, Samuel K.; Kuzin, Alexandre P.; Verdon, Grégory; Wang, Chi; Su, Min; Rothenbacher, Francesca P.; Abashidze, Mariam; Liu, Mohan; Hurley, Jennifer M.; Xiao, Rong; Acton, Thomas; Inouye, Masayori; Montelione, Gaetano T.; Woychik, Nancy A.; Hunt, John F. (Rutgers); (Columbia); (RWJ-Med)

    2010-09-27

    Bacterial toxin-antitoxin (TA) systems serve a variety of physiological functions including regulation of cell growth and maintenance of foreign genetic elements. Sequence analyses suggest that TA families are linked by complex evolutionary relationships reflecting likely swapping of functional domains between different TA families. Our crystal structures of Phd-Doc from bacteriophage P1, the HigA antitoxin from Escherichia coli CFT073, and YeeU of the YeeUWV systems from E. coli K12 and Shigella flexneri confirm this inference and reveal additional, unanticipated structural relationships. The growth-regulating Doc toxin exhibits structural similarity to secreted virulence factors that are toxic for eukaryotic target cells. The Phd antitoxin possesses the same fold as both the YefM and NE2111 antitoxins that inhibit structurally unrelated toxins. YeeU, which has an antitoxin-like activity that represses toxin expression, is structurally similar to the ribosome-interacting toxins YoeB and RelE. These observations suggest extensive functional exchanges have occurred between TA systems during bacterial evolution.

  7. Characterization of the Deep-Sea Streptomyces sp. SCSIO 02999 Derived VapC/VapB Toxin-Antitoxin System in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Yunxue Guo

    2016-07-01

    Full Text Available Toxin-antitoxin (TA systems are small genetic elements that are ubiquitous in prokaryotes. Most studies on TA systems have focused on commensal and pathogenic bacteria; yet very few studies have focused on TAs in marine bacteria, especially those isolated from a deep sea environment. Here, we characterized a type II VapC/VapB TA system from the deep-sea derived Streptomyces sp. SCSIO 02999. The VapC (virulence-associated protein protein belongs to the PIN (PilT N-terminal superfamily. Overproduction of VapC strongly inhibited cell growth and resulted in a bleb-containing morphology in E. coli. The toxicity of VapC was neutralized through direct protein–protein interaction by a small protein antitoxin VapB encoded by a neighboring gene. Antitoxin VapB alone or the VapB/VapC complex negatively regulated the vapBC promoter activity. We further revealed that three conserved Asp residues in the PIN domain were essential for the toxic effect of VapC. Additionally, the VapC/VapB TA system stabilized plasmid in E. coli. Furthermore, VapC cross-activated transcription of several TA operons via a partially Lon-dependent mechanism in E. coli, and the activated toxins accumulated more preferentially than their antitoxin partners. Collectively, we identified and characterized a new deep sea TA system in the deep sea Streptomyces sp. and demonstrated that the VapC toxin in this system can cross-activate TA operons in E. coli.

  8. New toxins homologous to ParE belonging to three-component toxin-antitoxin systems in Escherichia coli O157:H7.

    Science.gov (United States)

    Hallez, Régis; Geeraerts, Damien; Sterckx, Yann; Mine, Natacha; Loris, Remy; Van Melderen, Laurence

    2010-05-01

    Type II toxin-antitoxin (TA) systems are considered as protein pairs in which a specific toxin is associated with a specific antitoxin. We have identified a novel antitoxin family (paaA) that is associated with parE toxins. The paaA-parE gene pairs form an operon with a third component (paaR) encoding a transcriptional regulator. Two paralogous paaR-paaA-parE systems are found in E. coli O157:H7. Deletions of the paaA-parE pairs in O157:H7 allowed us to show that these systems are expressed in their natural host and that PaaA antitoxins specifically counteract toxicity of their associated ParE toxin. For the paaR2-paaA2-parE2 system, PaaR2 and Paa2-ParE2 complex are able to regulate the operon expression and both are necessary to ensure complete repression. The paaR2-paaA2-parE2 system mediates ClpXP-dependent post-segregational killing. The PaaR2 regulator appears to be essential for this function, most likely by maintaining an appropriate antitoxin : toxin ratio in steady-state conditions. Ectopic overexpression of ParE2 is bactericidal and is not resuscitated by PaaA2 expression. ParE2 colocalizes with the nucleoid, while it is diffusely distributed in the cytoplasm when PaaA2 is coexpressed. This indicates that ParE2 interacts with DNA-gyrase cycling on DNA and that coexpression of PaaA2 antitoxin sequesters ParE2 away from its target by protein-protein complex formation.

  9. AvrRxo1 Is a Bifunctional Type III Secreted Effector and Toxin-Antitoxin System Component with Homologs in Diverse Environmental Contexts.

    Directory of Open Access Journals (Sweden)

    Lindsay R Triplett

    Full Text Available Toxin-antitoxin (TA systems are ubiquitous bacterial systems that may function in genome maintenance and metabolic stress management, but are also thought to play a role in virulence by helping pathogens survive stress. We previously demonstrated that the Xanthomonas oryzae pv. oryzicola protein AvrRxo1 is a type III-secreted virulence factor that has structural similarities to the zeta family of TA toxins, and is toxic to plants and bacteria in the absence of its predicted chaperone Arc1. In this work, we confirm that AvrRxo1 and its binding partner Arc1 function as a TA system when expressed in Escherichia coli. Sequences of avrRxo1 homologs were culled from published and newly generated phytopathogen genomes, revealing that avrRxo1:arc1 modules are rare or frequently inactivated in some species and highly conserved in others. Cloning and functional analysis of avrRxo1 from Acidovorax avenae, A. citrulli, Burkholderia andropogonis, Xanthomonas translucens, and Xanthomonas euvesicatoria showed that some AvrRxo1 homologs share the bacteriostatic and Rxo1-mediated cell death triggering activities of AvrRxo1 from X. oryzae. Additional distant putative homologs of avrRxo1 and arc1 were identified in genomic or metagenomic sequence of environmental bacteria with no known pathogenic role. One of these distant homologs was cloned from the filamentous soil bacterium Cystobacter fuscus. avrRxo1 from C. fuscus caused watersoaking and triggered Rxo1-dependent cell collapse in Nicotiana benthamiana, but no growth suppression in E. coli was observed. This work confirms that a type III effector can function as a TA system toxin, and illustrates the potential of microbiome data to reveal new environmental origins or reservoirs of pathogen virulence factors.

  10. Bacteriophage ΦM1 of Pectobacterium evolves to escape two bifunctional Type III toxin-antitoxin and abortive infection systems through mutations in a single viral gene.

    Science.gov (United States)

    Blower, Tim R; Chai, Ray; Przybilski, Rita; Chindhy, Shahzad; Fang, Xinzhe; Kidman, Samuel E; Tan, Hui; Luisi, Ben F; Fineran, Peter C; Salmond, George P C

    2017-02-03

    Some bacteria, when infected by their viral parasites (bacteriophages), undergo a suicidal response that also terminates productive viral replication (abortive infection; Abi). This response can be viewed as an altruistic act protecting the uninfected bacterial clonal population. Abortive infection can occur through the action of Type III protein-RNA toxin-antitoxin (TA) systems, such as ToxINPa from the phytopathogen, Pectobacterium atrosepticum Rare spontaneous mutants evolved in the generalized transducing phage, ΦM1, which escaped ToxINPa-mediated abortive infection in P. atrosepticum ΦM1 is a member of the Podoviridae and member of the "KMV-like viruses", a subset of the T7 supergroup. Genomic sequencing of ΦM1 escape mutants revealed single-base changes which clustered in a single open reading frame. The "escape" gene product, M1-23, was highly toxic to the host bacterium when over-expressed, but mutations in M1-23 that enabled an escape phenotype caused M1-23 to be less toxic. M1-23 is encoded within the DNA metabolism modular section of the phage genome, and when it was over-expressed, it co-purified with the host nucleotide excision repair protein, UvrA. While the M1-23 protein interacted with UvrA in co-immunoprecipitation assays, a UvrA mutant strain still aborted ΦM1, suggesting that the interaction is not critical for the Type III TA Abi activity. Additionally, ΦM1 escaped a heterologous Type III TA system (TenpINPl) from Photorhabdus luminescens (reconstituted in P. atrosepticum) through mutations in the same protein, M1-23. The mechanistic action of M1-23 is currently unknown but further analysis of this protein could provide insights into the mode of activation of both systems.

  11. Progress in The Study of Bacterial Toxin-antitoxin System%细菌毒素-抗毒素系统的研究进展

    Institute of Scientific and Technical Information of China (English)

    王晓蕾; 赵龙旋; 张俊杰

    2008-01-01

    毒素-抗毒素系统(toxin-antitoxin system,TA)由两个共表达的基因组成,其中一个基因编码不稳定的抗毒素蛋白(antitoxin),另一个基因编码稳定的毒素蛋白(toxin).毒素-抗毒素系统最早发现于一些低拷贝的质粒,用来维持低拷贝质粒在菌群中的稳定存在.随后的研究表明,毒素-抗毒素系统广泛存在于细菌,包括一些致病菌的染色体上.在营养缺乏等不良生长条件下,由于基因表达的抑制和蛋白酶的降解作用,不稳定的抗毒素蛋白减少,从而产生游离的毒素蛋白,导致细菌的生长抑制和死亡.毒素-抗毒素系统的生理功能目前还存在争议,有学者认为细茼染色体上的毒素-抗毒素系统可以在不良生长状况下介导细菌的死亡,即细茼程序性细胞死亡(baeterial programmedcell death).但也有证据显示,毒素-抗毒素系统的功能更偏向于应激状态下的生理调节方面,即只起应激状态下的抑菌作用而不是杀菌作用.对细菌生长调控中毒素-抗毒素系统的作用机理进行综述,并探讨毒素-抗毒素系统研究的理论和应用价值.

  12. TasA-tasB, a new putative toxin-antitoxin (TA system from Bacillus thuringiensis pGI1 plasmid is a widely distributed composite mazE-doc TA system

    Directory of Open Access Journals (Sweden)

    Mahillon Jacques

    2006-10-01

    Full Text Available Abstract Background Post-segregational killing systems are present in a large variety of microorganisms. When found on plasmids, they are described as addiction systems that act to maintain the plasmid during the partitioning of the cell. The plasmid to be maintained through the generations harbours a group of two genes, one coding for a stable toxin and the other coding for an unstable antitoxin that inhibits the effects of the toxin. If, during cell division, the plasmid is lost, the toxin and antitoxin proteins present in the cytosol cease to be newly expressed. The level of unstable antitoxin protein then rapidly decreases, leaving the toxin free to act on the cellular target, leading to cell death. Consequently, only cells harbouring the plasmid can survive. Results The pGI1 plasmid of Bacillus thuringiensis H1.1 harbours a group of two genes, one showing similarities with the Doc toxin of the phd-doc toxin-antitoxin system, potentially coding for a toxin-antitoxin system. Attempts were made to clone this putative system in the Gram-negative host Escherichia coli. The putative antitoxin tasA was easily cloned in E. coli. However, although several combinations of DNA fragment were used in the cloning strategy, only clones containing a mutation in the toxin gene could be recovered, suggesting a toxic activity of TasB. An exhaustive search was carried out in order to index genes homologous to those of the putative tasA-tasB system among microorganisms. This study revealed the presence of this system in great number and in a large variety of microorganisms, either as tasA-tasB homologues or in association with toxins (or antitoxins from other TA systems. Conclusion In this work, we showed that the pGI1 plasmid of B. thuringiensis H1.1 harbours genes resembling a toxin-antitoxin system, named tasA-tasB for thuringiensis addiction system. This system appeared to be functional but unregulated in E. coli. Bioinformatics studies showed that the tas

  13. Higher-Order Structure in Bacterial VapBC Toxin-Antitoxin Complexes

    DEFF Research Database (Denmark)

    Bendtsen, Kirstine L; Brodersen, Ditlev E

    2017-01-01

    Toxin-antitoxin systems are widespread in the bacterial kingdom, including in pathogenic species, where they allow rapid adaptation to changing environmental conditions through selective inhibition of key cellular processes, such as DNA replication or protein translation. Under normal growth...... conditions, type II toxins are inhibited through tight protein-protein interaction with a cognate antitoxin protein. This toxin-antitoxin complex associates into a higher-order macromolecular structure, typically heterotetrameric or heterooctameric, exposing two DNA binding domains on the antitoxin...... that allow auto-regulation of transcription by direct binding to promoter DNA. In this chapter, we review our current understanding of the structural characteristics of type II toxin-antitoxin complexes in bacterial cells, with a special emphasis on the staggering variety of higher-order architecture...

  14. Structure and Proposed Activity of a Member of the VapBC Family of Toxin-Antitoxin Systems: VapBC-5 from Mycobacterium tuberculosis

    Energy Technology Data Exchange (ETDEWEB)

    Miallau, L.; Faller, M.; Chiang, J.; Arbing, M.; Guo, F.; Cascio, D.; Eisenberg, D.; (UCLA)

    2009-03-02

    In prokaryotes, cognate toxin-antitoxin pairs have long been known, but no three-dimensional structure has been available for any given complex from Mycobacterium tuberculosis. Here we report the crystal structure and activity of a member of the VapBC family of complexes from M. tuberculosis. The toxin VapC-5 is a compact, 150 residues, two domain {alpha}/{beta} protein. Bent around the toxin is the VapB-5 antitoxin, a 33-residue {alpha}-helix. Assays suggest that the toxin is an Mg-enabled endoribonuclease, inhibited by the antitoxin. The lack of DNase activity is consistent with earlier suggestions that the complex represses its own operon. Furthermore, analysis of the interactions in the binding of the antitoxin to the toxin suggest that exquisite control is required to protect the bacteria cell from toxic VapC-5.

  15. Progress of the Biological Roles of Toxin-Antitoxin System in the Stress Response%毒素-抗毒素系统在应激环境下的生物学作用的研究进展

    Institute of Scientific and Technical Information of China (English)

    熊鸣; 李明; 郑丹阳; 黄伟

    2013-01-01

    毒素-抗毒素系统(toxin-antitoxin system,TAS)广泛存在于细菌染色体及质粒上,是细菌中含量丰富的小型遗传元件.TAS通常由两个紧密相连的基因组成,分别编码毒素(toxin)和抗毒素(antitoxin),稳定的毒素能够损伤宿主细胞,不稳定的抗毒素能够保护宿主细胞免于毒素的损伤作用.依据其性质和作用方式,目前已经发现三种型别的TAS.TAS具有多种生物学作用,如诱导程序性细胞死亡(programmed cell death,PCD),应激条件下介导持留菌形成(persistence),稳定基因大片段等.本文就近几年TAS在应激条件下的生物学作用的研究进展做一综述.%Toxin-antitoxin (TA) systems are small genetic modules that are widespread and abundant in bacterial chromosomes and plasmids. TA systems are usually composed of two closely linked genes that encode a stable toxin and a labile antitoxin, respectively. The toxin can harm the host cell, while the cognate antitoxin protects the host cell from the toxin's damage. So far, three types of TA system have been described based on their nature and mode of action. Several biological functions of the TA systems have been proposed, such as inducing programmed cell death (PCD), mediating arrest under stress conditions (persistence), promoting stability of large genomic fragments, etc. This review summarizes recent findings on the biological roles of TA systems under stress conditions.

  16. Higher-Order Structure in Bacterial VapBC Toxin-Antitoxin Complexes.

    Science.gov (United States)

    Bendtsen, Kirstine L; Brodersen, Ditlev E

    2017-01-01

    Toxin-antitoxin systems are widespread in the bacterial kingdom, including in pathogenic species, where they allow rapid adaptation to changing environmental conditions through selective inhibition of key cellular processes, such as DNA replication or protein translation. Under normal growth conditions, type II toxins are inhibited through tight protein-protein interaction with a cognate antitoxin protein. This toxin-antitoxin complex associates into a higher-order macromolecular structure, typically heterotetrameric or heterooctameric, exposing two DNA binding domains on the antitoxin that allow auto-regulation of transcription by direct binding to promoter DNA. In this chapter, we review our current understanding of the structural characteristics of type II toxin-antitoxin complexes in bacterial cells, with a special emphasis on the staggering variety of higher-order architecture observed among members of the VapBC family. This structural variety is a result of poor conservation at the primary sequence level and likely to have significant and functional implications on the way toxin-antitoxin expression is regulated.

  17. The proteolytic activation of the relNEs (ssr1114/slr0664) toxin-antitoxin system by both proteases Lons and ClpP2s/Xs of Synechocystis sp. PCC 6803.

    Science.gov (United States)

    Ning, Degang; Ye, Sen; Liu, Biao; Chang, Jianing

    2011-11-01

    The proteolytic regulation of toxin-antitoxin (TA) systems has been well studied in Escherichia coli but remains unclear in other bacteria. A chromosomal gene pair ssr1114/slr0664, named relNEs, of Synechocystis sp. PCC 6803 forms a TA system belonging to rel family. Here, we used E. coli strain BL21 (DE3) as a host to characterize the proteolytic regulation of relNEs. The proteases of this strain could not degrade the antitoxin RelN, and the ectopic production of the ATP-dependant protease Lons or ClpP2s/Xs of Synechocystis sp. PCC6803 did not affect E. coli growth. Either Lons or ClpP2s/Xs was able to degrade RelN resulting in growth arrest of E. coli due to the activation of RelEs's toxicity, and the presence of RelEs could protect RelN to a certain extent against Lons and ClpP2s/Xs. Our observations suggest that both Lons and ClpP2s/Xs are responsible for RelN proteolysis in the native host under certain conditions. RelN is the first protein substrate identified for cyanobacterial ATP-dependent proteases.

  18. Toxins-antitoxins: diversity, evolution and function.

    Science.gov (United States)

    Hayes, Finbarr; Van Melderen, Laurence

    2011-10-01

    Genes for toxin-antitoxin (TA) complexes are widespread in prokaryote genomes, and species frequently possess tens of plasmid and chromosomal TA loci. The complexes are categorized into three types based on genetic organization and mode of action. The toxins universally are proteins directed against specific intracellular targets, whereas the antitoxins are either proteins or small RNAs that neutralize the toxin or inhibit toxin synthesis. Within the three types of complex, there has been extensive evolutionary shuffling of toxin and antitoxin genes leading to considerable diversity in TA combinations. The intracellular targets of the protein toxins similarly are varied. Numerous toxins, many of which are sequence-specific endoribonucleases, dampen protein synthesis levels in response to a range of stress and nutritional stimuli. Key resources are conserved as a result ensuring the survival of individual cells and therefore the bacterial population. The toxin effects generally are transient and reversible permitting a set of dynamic, tunable responses that reflect environmental conditions. Moreover, by harboring multiple toxins that intercede in protein synthesis in response to different physiological cues, bacteria potentially sense an assortment of metabolic perturbations that are channeled through different TA complexes. Other toxins interfere with the action of topoisomersases, cell wall assembly, or cytoskeletal structures. TAs also play important roles in bacterial persistence, biofilm formation and multidrug tolerance, and have considerable potential both as new components of the genetic toolbox and as targets for novel antibacterial drugs.

  19. Advances in Biological Function of Toxin-Antitoxin Molecular Systems%毒性分子-抗毒性分子系统的生物学作用研究进展

    Institute of Scientific and Technical Information of China (English)

    李国利; 胡福泉

    2015-01-01

    毒性分子-抗毒性分子系统( toxin-antitoxin systems,TA systems)被发现广泛存在于细菌染色体、质粒以及古细菌基因组中。TA系统是由2个基因组成的操纵子,这2个基因分别编码稳定的毒性分子和不稳定的抗毒性分子。毒性分子总是蛋白质,抗毒性分子可能是蛋白质或RNA。因此,根据抗毒性分子的性质和作用方式的不同可将TA系统家族分为5种类型。Ⅰ型和Ⅲ型的抗毒性分子是RNA,能抑制毒性分子的合成或者与其隔离;II、IV和V型的抗毒性分子是蛋白质,能隔离、平衡毒性分子作用或抑制其合成。TA系统具有多种生物学功能。目前研究表明,TA系统可能在细菌应激应答、程序化细胞死亡、多重耐药的形成、防止DNA入侵、稳定大基因组片段等方面有重要的作用。%Toxin-antitoxin systems( TA systems)extensively exist in bacterial chromosomes and plasmids as well as in archaic genomes. TA systems is an operon consisting of two genes,they are respectively toxin molecule of stably encoded and anti-toxin molecule of unstably encoded. Toxin molecule is always protein,while antitoxin molecule may be protein or RNA. Therefore,currently TA systems family can be divided into five different types. Antitoxin molecule of type I and type III is RNA,it can inhibit the synthesis of toxin molecule or isolate toxin molecule. Antitoxin mole-cule of type II,IV,and V is protein,it can isolate,balance the role of toxin molecule or inhibit its synthesis. TA systems possess multiple biological functions. Recent studies suggested that TA systems might play important role and have involved in the cell stress response,programmed cell death,the form of multidrug resistance,prevention from DNA invasion,as well as stabilization of large genomic fragments and other aspects.

  20. The Influence of the Toxin/Antitoxin mazEF on Growth and Survival of Listeria monocytogenes under Stress

    DEFF Research Database (Denmark)

    Curtis, Thomas; Takeuchi, Ippei; Gram, Lone

    2017-01-01

    A major factor in the resilience of Listeria monocytogenes is the alternative sigma factor B (σB). Type II Toxin/Antitoxin (TA) systems are also known to have a role in the bacterial stress response upon activation via the ClpP or Lon proteases. Directly upstream of the σB operon in L...

  1. Emerging Roles of Toxin-Antitoxin Modules in Bacterial Pathogenesis

    Directory of Open Access Journals (Sweden)

    Barbara Kędzierska

    2016-06-01

    Full Text Available Toxin-antitoxin (TA cassettes are encoded widely by bacteria. The modules typically comprise a protein toxin and protein or RNA antitoxin that sequesters the toxin factor. Toxin activation in response to environmental cues or other stresses promotes a dampening of metabolism, most notably protein translation, which permits survival until conditions improve. Emerging evidence also implicates TAs in bacterial pathogenicity. Bacterial persistence involves entry into a transient semi-dormant state in which cells survive unfavorable conditions including killing by antibiotics, which is a significant clinical problem. TA complexes play a fundamental role in inducing persistence by downregulating cellular metabolism. Bacterial biofilms are important in numerous chronic inflammatory and infectious diseases and cause serious therapeutic problems due to their multidrug tolerance and resistance to host immune system actions. Multiple TAs influence biofilm formation through a network of interactions with other factors that mediate biofilm production and maintenance. Moreover, in view of their emerging contributions to bacterial virulence, TAs are potential targets for novel prophylactic and therapeutic approaches that are required urgently in an era of expanding antibiotic resistance. This review summarizes the emerging evidence that implicates TAs in the virulence profiles of a diverse range of key bacterial pathogens that trigger serious human disease.

  2. Structural and thermodynamic characterization of the Escherichia coli RelBE toxin-antitoxin system: indication for a functional role of differential stability

    DEFF Research Database (Denmark)

    Cherny, Izhack; Overgaard, Martin; Borch, Jonas

    2007-01-01

    on the folding and stability of the protein pair in solution. Here we structurally and thermodynamically characterize the RelBE system components from E. coli in solution, both separately and in their complexed state. The RelB antitoxin, an alpha-helical protein according to circular dichroism and infrared......B is responsible for RelB-RelE interaction, being protease sensitive in its free state, while it becomes protected from proteolysis when complexed with RelE. Overall, our findings support the notion that RelB lacks a well-organized hydrophobic core in solution whereas RelE is a well-folded protein. Furthermore...

  3. Structural studies of the toxin-antitoxin proteins RelE and RelB from E. coli

    DEFF Research Database (Denmark)

    Andersen, Kasper Røjkjær; Overgaard, Martin; Gerdes, Kenn;

    the special tRNA-mRNA mimic, tmRNA [1]. Questions to be addressed Many questions remain to be answered in the bacterial toxin-antitoxin system. The crystal structure of RelBE from Pyrococcus horikoshii OT3 was previously solved at 2.3Å [2]. This structure shows the molecule in an inactive state, but OT3......The bacterial toxin-antitoxin system The relBE operon in E. coli encodes two small proteins: A toxin, RelE (12 kDa) and an antitoxin, RelB (9 kDa). RelE is activated under nutritional stress and is able to inhibit protein synthesis by cleaving the mRNA in the ribosomal A-site. This stress response...... serves to down-regulate metabolism in the cell when growth conditions are limited. RelB is expressed in excess over RelE during balanced growth, and inhibits the toxicity of RelE by forming an extremely stable toxin-antitoxin complex. The activation of RelE is induced when the labile RelB protein...

  4. 高致病性2型猪链球菌毒素-抗毒素系统SezAT的鉴定与活性研究%Identification and activity assay of the SezAT toxin-antitoxin system of highly pathogenic Streptococcus suis serotype 2

    Institute of Scientific and Technical Information of China (English)

    王敏; 李明; 钟秋; 赵岩; 饶贤才; 黎庶; 谭银玲; 胡福泉

    2012-01-01

    [目的]对我国高致病性2型猪链球菌05ZYH33基因组的89K毒力岛序列进行生物信息学分析,发现存在一对与化脓链球菌Epsilon-zeta(ε-ζ)同源的Ⅱ型毒素-抗毒素系统(Toxin-antitoxin system,TA)-SezAT,推测该系统具有稳定89K毒力岛使其不易丢失的作用.验证SezAT为有活性的TA系统.[方法]对SezAT进行了生物信息学分析;RT-PCR验证SezAT共转录特性;在大肠杆菌中选择性地诱导表达毒素蛋白SezT和抗毒素蛋白SezA;最后通过同源重组技术敲除SezAT系统.[结果]sezAT由同一操纵子控制,SezT可抑制细菌生长,SezA可中和SezT的毒性作用,同源重组成功获得sezT敲除突变株.[结论]证实SezAT为一对有活性的毒素-抗毒素(TA)系统,为进一步研究SezAT可能发挥稳定89K毒力岛的功能,同时获得89K毒力岛缺失突变株并深入认识89K在我国高致病性SS2中的作用奠定了基础.%[Objective] Bioinformatics analysis revealed that the 89K pathogenicity island(PAI) of highly pathogenic Streptococcus suis serotype 2 (SS2) in China encodes a putative type II toxin-antitoxin (TA) system named SezAT, which is homologous to the epsilon-zeta system from S. Pyogenes. SezAT is presumed to be requisite for the stability of the 89K PAI in SS2. To confirm the SezAT system is a functional TA system. [Methods] The sequence characteristics of SezAT were subjected to further bioinformatics analysis. RT-PCR was performed to analyze the transcriptions of the sezAT locus and the flanking genes. The SezT toxin and SezA antitoxin proteins were selectively overexpressed in Escherichia coli. Deletion mutagenesis was carried out to obtain a SezAT-deficient mutant. [Results] Bioinformatics analysis and RT-PCR results suggest that sezAT are in the same operon. Overexpression of SezT led to severe growth inhibition of the host bacteria, while this toxicity was counteracted by the expression of SezA. Finally, the toxin-encoding gene sezT was successfully

  5. THE NATURE OF THE TOXIN-ANTITOXIN FLOCCULATION PHENOMENON.

    Science.gov (United States)

    Bronfenbrenner, J J; Reichert, P

    1926-09-30

    1. Animals immunized with the formalinized filtrates of young toxic cultures of B. botulinus produce an antitoxic serum poor in precipitins. 2. Animals immunized with the formalinized filtrates of old and partly autolyzed toxic cultures produce an antitoxic serum containing precipitins. 3. Animals immunized with toxin-free autolyzed bacteria produce a serum free from antitoxin but rich in specific precipitins. 4. Animals immunized with the filtrates of an atoxic variant produce a serum free from antitoxin but rich in precipitins for the homologous toxin. 5. Animals immunized with the washed bacteria of the atoxic variant produce a serum that contains no antitoxin, but is rich in precipitins for the homologous toxin. 6. Removal of the precipitins by flocculation with a non-toxic antigen does not materially reduce the antitoxic value of a serum. 7. Removal of the proteins of the antigen by add coagulation removes the specific precipitable substance. 8. All the sera that contain precipitins produce the specific flocculus when combined with homologous toxins, anatoxins, or with the filtrates of the atoxic variant. The flocculation is restricted within the type. The amount of the precipitate and the width of the zone vary approximately with the estimated amount of bacterial protein in the antigen that is used for the immunization of animals. We conclude, therefore, that the toxin-antitoxin flocculation is a specific bacterial precipitation phenomenon.

  6. Characterization of a novel toxin-antitoxin module, VapBC, encoded by Leptospira interrogans chromosome

    Institute of Scientific and Technical Information of China (English)

    Yi Xuan ZHANG; Xiao Kui GUO; Chuan WU; Bo BI; Shuang Xi REN; Chun Fu WU; Guo Ping ZHAO

    2004-01-01

    Comparative genomic analysis of the coding sequences (CDSs) of Leptospira interrogans revealed a pair of closely linked genes homologous to the vapBC loci of many other bacteria with respect to both deduced amino acid sequences and operon organizations. Expression of single vapC gene in Escherichia coli resulted in inhibition of bacterial growth,whereas co-expression of vapBC restored the growth effectively. This phenotype is typical for three other characterized toxin-antitoxin systems of bacteria, i.e., mazEF[1], relBE[2] and chpIK[3]. The VapC proteins of bacteria and a thermophilic archeae, Solfolobus tokodaii, form a structurally distinguished group of toxin different from the other known toxins of bacteria. Phylogenetic analysis of both toxins and antitoxins of all categories indicated that although toxins were evolved from divergent sources and may or may not follow their speciation paths (as indicated by their 16s RNA sequences), co-evolution with their antitoxins was obvious.

  7. Crystallization of the HigBA2 toxin-antitoxin complex from Vibrio cholerae

    DEFF Research Database (Denmark)

    Hadǽi, San; Garcia-Pino, Abel; Martinez-Rodriguez, Sergio

    2013-01-01

    The genome of Vibrio cholerae encodes two higBA toxin-antitoxin (TA) modules that are activated by amino-acid starvation. Here, the TA complex of the second module, higBA2, as well as the C-terminal domain of the corresponding HigA2 antitoxin, have been purified and crystallized. The HigBA2 complex...

  8. Mutagenesis and functional characterization of the RNA and protein components of the toxIN abortive infection and toxin-antitoxin locus of Erwinia.

    Science.gov (United States)

    Blower, T R; Fineran, P C; Johnson, M J; Toth, I K; Humphreys, D P; Salmond, G P C

    2009-10-01

    Bacteria are constantly challenged by bacteriophage (phage) infection and have developed multiple adaptive resistance mechanisms. These mechanisms include the abortive infection systems, which promote "altruistic suicide" of an infected cell, protecting the clonal population. A cryptic plasmid of Erwinia carotovora subsp. atroseptica, pECA1039, has been shown to encode an abortive infection system. This highly effective system is active across multiple genera of gram-negative bacteria and against a spectrum of phages. Designated ToxIN, this two-component abortive infection system acts as a toxin-antitoxin module. ToxIN is the first member of a new type III class of protein-RNA toxin-antitoxin modules, of which there are multiple homologues cross-genera. We characterized in more detail the abortive infection phenotype of ToxIN using a suite of Erwinia phages and performed mutagenesis of the ToxI and ToxN components. We determined the minimal ToxI RNA sequence in the native operon that is both necessary and sufficient for abortive infection and to counteract the toxicity of ToxN. Furthermore, site-directed mutagenesis of ToxN revealed key conserved amino acids in this defining member of the new group of toxic proteins. The mechanism of phage activation of the ToxIN system was investigated and was shown to have no effect on the levels of the ToxN protein. Finally, evidence of negative autoregulation of the toxIN operon, a common feature of toxin-antitoxin systems, is presented. This work on the components of the ToxIN system suggests that there is very tight toxin regulation prior to suicide activation by incoming phage.

  9. An efficient method for the purification of proteins from four distinct toxin-antitoxin modules.

    Science.gov (United States)

    Sterckx, Yann G-J; De Gieter, Steven; Zorzini, Valentina; Hadži, San; Haesaerts, Sarah; Loris, Remy; Garcia-Pino, Abel

    2015-04-01

    Toxin-antitoxin (TA) modules are stress response elements that are ubiquitous in the genomes of bacteria and archaea. Production and subsequent purification of individual TA proteins is anything but straightforward as over-expression of the toxin gene is lethal to bacterial and eukaryotic cells and over-production of the antitoxin leads to its proteolytic degradation because of its inherently unstructured nature. Here we describe an effective production and purification strategy centered on an on-column denaturant-induced dissociation of the toxin-antitoxin complex. The success of the method is demonstrated by its application on four different TA families, encoding proteins with distinct activities and folds. A series of biophysical and in vitro activity tests show that the purified proteins are of high quality and suitable for structural studies.

  10. 结核分枝杆菌毒素-抗毒素伴侣系统基因多态性初步研究%Polymorphisms of toxin-antitoxin-chaperone system of Mycobacterium tuberculosis complex in China

    Institute of Scientific and Technical Information of China (English)

    肖彤洋; 赵丽丽; 刘海灿; 李马超; 赵秀芹; 万康林

    2016-01-01

    目的 研究结核分枝杆菌毒素-抗毒素伴侣(TAC)系统中higA、higB和Rv1957在结核分枝杆菌及其不同亚型菌株中的基因多态性,并探讨其生理意义.方法 选取183株结核分枝杆菌临床菌株,经间隔区寡核苷酸方法进行基因分型,同时分析TAC系统基因higA、higB和Rv1957的PCR扩增及序列,利用I-Mutant 2.0软件预测非同义突变对蛋白结构和功能的影响.结果 183株中138株(75.41%)属北京家族,45株(24.59%)属非北京家族.共149株菌(81.42%)的TAC系统发生突变,包括2种同义突变和6种非同义突变:同义突变发生于higA基因,仅见于北京家族菌株;3个基因均可见非同义突变,其中2种非同义突变仅见于非北京家族菌株,其余4种突变仅见于北京家族菌株.6种非同义突变中有4种突变可能影响蛋白的功能.位于higA基因的CAC121CAT突变位点在单耐链霉素和单耐利福平菌株中的突变频率高于敏感株,且差异有统计学意义(P<0.05).结论 结核分枝杆菌中的TAC系统具有一定的基因多态性,其中北京家族呈现更高的多态性水平,可能更有利于适应不同的宿主环境.%Objective To investigate the single nucleotide polymorphism (SNP) of toxinantitoxin-chaperone (TAC) system of Mycobacterium (M.) tuberculosis with different genotypes and its biological significance.Methods A total of 183 clinical M.tuberculosis isolates were collected for spoligotyping.The sequences of higA,higB and Rv1957 were obtained by using PCR and DNA sequencing.The sequences were compared for possible mutations.Functional consequences of nonsynonymous SNPs were predicted by using I-Mutant 2.0 servers.Results Among the 183 M.tuberculosis isolates,138(75.41%) belonged to the Beijing family,while 45(24.59%) belonged to the non-Beijing family.A total of 149(81.42%) isolates showed polymorphisms in the TAC system.We discovered 6 nonsynonymous SNPs and 2 synonymous SNPs.All the synonymous mutations

  11. A vapBC-type toxin-antitoxin module of Sinorhizobium meliloti influences symbiotic efficiency and nodule senescence of Medicago sativa.

    Science.gov (United States)

    Lipuma, Justine; Cinege, Gyöngyi; Bodogai, Monica; Oláh, Boglárka; Kiers, Aurélie; Endre, Gabriella; Dupont, Laurence; Dusha, Ilona

    2014-12-01

    The symbiotic nitrogen-fixing soil bacterium Sinorhizobium meliloti carries a large number of toxin-antitoxin (TA) modules both on the chromosome and megaplasmids. One of them, the vapBC-5 module that belongs to the type II systems was characterized here. It encodes an active toxin vapC-5, and was shown to be controlled negatively by the complex of its own proteins. Different mutants of the vapBC-5 genes exhibited diverse effects on symbiotic efficiency during interaction with the host plant Medicago sativa. The absence of the entire vapBC-5 region had no influence on nodule formation and nitrogen fixation properties. The strain carrying an insertion in the antitoxin gene showed a reduced nitrogen fixation capacity resulting in a lower plant yield. In contrast, when the toxin gene was mutated, the strain developed more efficient symbiosis with the host plant. The nitrogen fixing root nodules had a delayed senescent phenotype and contained elevated level of plant-derived molecules characteristic of later steps of nodule development. The longer bacteroid viability and abundance of active nitrogen fixing zone resulted in increased production of plant material. These data indicate that modification of the toxin/antitoxin production may influence bacteroid metabolism and may have an impact on the adaptation to changing environmental conditions.

  12. Rapid Curtailing of the Stringent Response by Toxin-Antitoxin Encoded mRNases

    DEFF Research Database (Denmark)

    Tian, Chengzhe; Roghanian, Mohammad; Jørgensen, Mikkel Girke

    2016-01-01

    Escherichia coli regulates its metabolism to adapt to changes in the environment, in particular to stressful downshifts in nutrient quality. Such shifts elicit the so-called stringent response coordinated by the alarmone guanosine tetra- and pentaphosphate [(p)ppGpp]. At sudden amino-acid (aa...... %. IMPORTANCE: The early stringent response elicited by amino-acid starvation is controlled by a sharp increase of the cellular (p)ppGpp level. Toxin-antitoxin encoded mRNases are activated by (p)ppGpp through enhanced degradation of antitoxins. The present work shows that this activation happens at a very...

  13. Expression of the toxin-antitoxin genes yefM(Lrh), yoeB(Lrh) in human Lactobacillus rhamnosus isolates.

    Science.gov (United States)

    Krügel, Hans; Klimina, Ksenia M; Mrotzek, Grit; Tretyakov, Alexander; Schöfl, Gerhard; Saluz, Hans-Peter; Brantl, Sabine; Poluektova, Elena U; Danilenko, Valery N

    2015-08-01

    Lactobacilli are important microorganisms in various activities, for example, diary products, meat ripening, bread and pickles, but, moreover, are associated directly with human skin and cavities (e.g., mouth, gut, or vagina). Some of them are used as probiotics. Therefore, the molecular biological investigation of these bacteria is important. Earlier we described several toxin antitoxin systems (type II) in lactobacilli. Here, we describe the structure and transcriptional regulation of genes, encoding TA system YefM-YoeB(Lrh) in three strains of Lactobacillus rhamnosus comparing stationary and exponential growth phases, the influence of stress factors and mRNA stability. The same TA system is responding to physiological and stress conditions differently in related strains. Using primer extension and RLM-RACE methods we determined three transcription start sites of RNAs in the operon. The promoter region of the operon is preceded by a conserved BOX element occurring at multiple positions in the genomes of L. rhamnosus strains. Downstream of and partially overlapping with the 3' end of the yoeB(Lrh) toxin gene, a divergently transcribed unexpected RNA was detected. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. (p)ppGpp controls bacterial persistence by stochastic induction of toxin-antitoxin activity.

    Science.gov (United States)

    Maisonneuve, Etienne; Castro-Camargo, Manuela; Gerdes, Kenn

    2013-08-29

    Persistence refers to the phenomenon in which isogenic populations of antibiotic-sensitive bacteria produce rare cells that transiently become multidrug tolerant. Whether slow growth in a rare subset of cells underlies the persistence phenotype has not be examined in wild-type bacteria. Here, we show that an exponentially growing population of wild-type Escherichia coli cells produces rare cells that stochastically switch into slow growth, that the slow-growing cells are multidrug tolerant, and that they are able to resuscitate. The persistence phenotype depends hierarchically on the signaling nucleotide (p)ppGpp, Lon protease, inorganic polyphosphate, and toxin-antitoxins. We show that the level of (p)ppGpp varies stochastically in a population of exponentially growing cells and that the high (p)ppGpp level in rare cells induces slow growth and persistence. (p)ppGpp triggers slow growth by activating toxin-antitoxin loci through a regulatory cascade depending on inorganic polyphosphate and Lon protease.

  15. Remarkable Functional Convergence: Alarmone ppGpp Mediates Persistence by Activating Type I and II Toxin-Antitoxins.

    Science.gov (United States)

    Gerdes, Kenn; Maisonneuve, Etienne

    2015-07-01

    In this issue of Molecular Cell, Verstraeten et al. (2015) demonstrate that the conserved GTPase Obg and the second messenger ppGpp mediate persistence by activation of a type I toxin-antitoxin module (hokB/sokB) in E. coli.

  16. Identification and characterization of chromosomal relBE toxin-antitoxin locus in Streptomyces cattleya DSM46488.

    Science.gov (United States)

    Li, Peng; Tai, Cui; Deng, Zixin; Gan, Jianhua; Oggioni, Marco R; Ou, Hong-Yu

    2016-08-18

    The relBE family of Type II toxin-antitoxin (TA) systems have been widely reported in bacteria but none in Streptomyces. With the conserved domain searches for TA pairs in the sequenced Streptomyces genomes, we identified two putative relBE loci, relBE1sca and relBE2sca, on the chromosome of Streptomyces cattleya DSM 46488. Overexpression of the S. cattleya toxin RelE2sca caused severe growth inhibition of E. coli and S. lividans, but RelE1sca had no toxic effect. The toxicity of RelE2sca could be abolished by the co-expression of its cognate RelB2sca antitoxin. Moreover, the RelBE2sca complex, or the antitoxin RelB2sca alone, specifically interacted with the relBE2sca operon and repressed its transcription. The relBE2sca operon transcription was induced under osmotic stress, along with the ClpP proteinase genes. The subsequent in vivo analysis showed that the antitoxin was degraded by ClpP. Interestingly, the E. coli antitoxin RelBeco was able to alleviate the toxicity of S. cattleya RelE2sca while the mutant RelB2sca(N61V&M68L) but not the wild type could alleviate the toxicity of E. coli RelEeco as well. The experimental demonstration of the relBEsca locus might be helpful to investigate the key roles of type II TA systems in Streptomyces physiology and environmental stress responses.

  17. A toxin-antitoxin module in Bacillus subtilis can both mitigate and amplify effects of lethal stress.

    Directory of Open Access Journals (Sweden)

    Xiangli Wu

    Full Text Available BACKGROUND: Bacterial type-2 (protein-protein toxin-antitoxin (TA modules are two-gene operons that are thought to participate in the response to stress. Previous work with Escherichia coli has led to a debate in which some investigators conclude that the modules protect from stress, while others argue that they amplify lethal stress and lead to programmed cell death. To avoid ambiguity arising from the presence of multiple TA modules in E. coli, the effect of the sole type-2 toxin-antitoxin module of Bacillus subtilis was examined for several types of lethal stress. METHODOLOGY/PRINCIPAL FINDINGS: Genetic knockout of the toxin gene, ndoA (ydcE, conferred protection to lethal stressors that included kanamycin, moxifloxacin, hydrogen peroxide, and UV irradiation. However, at low doses of UV irradiation the ndoA deficiency increased lethality. Indeed, gradually increasing UV dose with the ndoA mutant revealed a crossover response--from the mutant being more sensitive than wild-type cells to being less sensitive. For high temperature and nutrient starvation, the toxin deficiency rendered cells hypersensitive. The ndoA deficiency also reduced sporulation frequency, indicating a role for toxin-antitoxin modules in this developmental process. In the case of lethal antimicrobial treatment, deletion of the toxin eliminated a surge in hydrogen peroxide accumulation observed in wild-type cells. CONCLUSIONS: A single toxin-antitoxin module can mediate two opposing effects of stress, one that lowers lethality and another that raises it. Protective effects are thought to arise from toxin-mediated inhibition of translation based on published work. The enhanced, stress-mediated killing probably involves toxin-dependent accumulation of reactive oxygen species, since a deficiency in the NdoA toxin suppressed peroxide accumulation following antimicrobial treatment. The type and perhaps the level of stress appear to be important for determining whether this toxin

  18. Crystallization of two operator complexes from the Vibrio cholerae HigBA2 toxin-antitoxin module

    DEFF Research Database (Denmark)

    Hadzi, San; Garcia-Pino, Abel; Gerdes, Kenn

    2015-01-01

    The HigA2 antitoxin and the HigBA2 toxin-antitoxin complex from Vibrio cholerae were crystallized in complex with their operator box. Screening of 22 different DNA duplexes led to two crystal forms of HigA2 complexes and one crystal form of a HigBA2 complex. Crystals of HigA2 in complex with a 17...

  19. Regulation of the vapBC-1 toxin-antitoxin locus in nontypeable Haemophilus influenzae.

    Directory of Open Access Journals (Sweden)

    Susan D Cline

    Full Text Available Nontypeable Haemophilus influenzae (NTHi are human-adapted commensal bacteria that can cause a number of chronic mucosal infections, including otitis media and bronchitis. One way for these organisms to survive antibiotic therapy and cause recurrent disease is to stop replicating, as most antimicrobials target essential biosynthetic pathways. Toxin-antitoxin (TA gene pairs have been shown to facilitate entry into a reversible bacteriostatic state. Characteristically, these operons encode a protein toxin and an antitoxin that associate following translation to form a nontoxic complex, which then binds to and regulates the cognate TA promoter. Under stressful conditions, the labile antitoxin is degraded and the complex disintegrates, freeing the stable toxin to facilitate growth arrest. How these events affected the regulation of the TA locus, as well as how the transcription of the operon was subsequently returned to its normal state upon resumption of growth, was not fully understood. Here we show that expression of the NTHi vapBC-1 TA locus is repressed by a complex of VapB-1 and VapC-1 under conditions favorable for growth, and activated by the global transactivator Factor for Inversion Stimulation (Fis upon nutrient upshift from stationary phase. Further, we demonstrate for the first time that the VapC-1 toxin alone can bind to its cognate TA locus control region and that the presence of VapB-1 directs the binding of the VapBC-1 complex in the transcriptional regulation of vapBC-1.

  20. One cannot rule them all: Are bacterial toxins-antitoxins druggable?

    Science.gov (United States)

    Chan, Wai Ting; Balsa, Dolors; Espinosa, Manuel

    2015-07-01

    Type II (proteic) toxin-antitoxin (TA) operons are widely spread in bacteria and archaea. They are organized as operons in which, usually, the antitoxin gene precedes the cognate toxin gene. The antitoxin generally acts as a transcriptional self-repressor, whereas the toxin acts as a co-repressor, both proteins constituting a harmless complex. When bacteria encounter a stressful environment, TAs are triggered. The antitoxin protein is unstable and will be degraded by host proteases, releasing the free toxin to halt essential processes. The result is a cessation of cell growth or even death. Because of their ubiquity and the essential processes targeted, TAs have been proposed as good candidates for development of novel antimicrobials. We discuss here the possible druggability of TAs as antivirals and antibacterials, with focus on the potentials and the challenges that their use may find in the 'real' world. We present strategies to develop TAs as antibacterials in view of novel technologies, such as the use of very small molecules (fragments) as inhibitors of protein-protein interactions. Appropriate fragments could disrupt the T:A interfaces leading to the release of the targeted TA pair. Possible ways of delivery and formulation of Tas are also discussed. © FEMS 2015.

  1. Regulating Toxin-Antitoxin Expression: Controlled Detonation of Intracellular Molecular Timebombs

    Directory of Open Access Journals (Sweden)

    Finbarr Hayes

    2014-01-01

    Full Text Available Genes for toxin-antitoxin (TA complexes are widely disseminated in bacteria, including in pathogenic and antibiotic resistant species. The toxins are liberated from association with the cognate antitoxins by certain physiological triggers to impair vital cellular functions. TAs also are implicated in antibiotic persistence, biofilm formation, and bacteriophage resistance. Among the ever increasing number of TA modules that have been identified, the most numerous are complexes in which both toxin and antitoxin are proteins. Transcriptional autoregulation of the operons encoding these complexes is key to ensuring balanced TA production and to prevent inadvertent toxin release. Control typically is exerted by binding of the antitoxin to regulatory sequences upstream of the operons. The toxin protein commonly works as a transcriptional corepressor that remodels and stabilizes the antitoxin. However, there are notable exceptions to this paradigm. Moreover, it is becoming clear that TA complexes often form one strand in an interconnected web of stress responses suggesting that their transcriptional regulation may prove to be more intricate than currently understood. Furthermore, interference with TA gene transcriptional autoregulation holds considerable promise as a novel antibacterial strategy: artificial release of the toxin factor using designer drugs is a potential approach to induce bacterial suicide from within.

  2. RnlB Antitoxin of the Escherichia coli RnlA-RnlB Toxin-Antitoxin Module Requires RNase HI for Inhibition of RnlA Toxin Activity.

    Science.gov (United States)

    Naka, Kenta; Qi, Dan; Yonesaki, Tetsuro; Otsuka, Yuichi

    2017-01-11

    The Escherichia coli RnlA-RnlB toxin-antitoxin system is related to the anti-phage mechanism. Under normal growth conditions, an RnlA toxin with endoribonuclease activity is inhibited by binding of its cognate RnlB antitoxin. After bacteriophage T4 infection, RnlA is activated by the disappearance of RnlB, resulting in the rapid degradation of T4 mRNAs and consequently no T4 propagation when T4 dmd encoding a phage antitoxin against RnlA is defective. Intriguingly, E. coli RNase HI, which plays a key role in DNA replication, is required for the activation of RnlA and stimulates the RNA cleavage activity of RnlA. Here, we report an additional role of RNase HI in the regulation of RnlA-RnlB system. Both RNase HI and RnlB are associated with NRD (one of three domains of RnlA). The interaction between RnlB and NRD depends on RNase HI. Exogenous expression of RnlA in wild-type cells has no effect on cell growth because of endogenous RnlB and this inhibition of RnlA toxicity requires RNase HI and NRD. These results suggest that RNase HI recruits RnlB to RnlA through NRD for inhibiting RnlA toxicity and thus plays two contrary roles in the regulation of RnlA-RnlB system.

  3. Neutralization of Bacterial YoeBSpn Toxicity and Enhanced Plant Growth in Arabidopsis thaliana via Co-Expression of the Toxin-Antitoxin Genes

    Directory of Open Access Journals (Sweden)

    Fauziah Abu Bakar

    2016-04-01

    Full Text Available Bacterial toxin-antitoxin (TA systems have various cellular functions, including as part of the general stress response. The genome of the Gram-positive human pathogen Streptococcus pneumoniae harbors several putative TA systems, including yefM-yoeBSpn, which is one of four systems that had been demonstrated to be biologically functional. Overexpression of the yoeBSpn toxin gene resulted in cell stasis and eventually cell death in its native host, as well as in Escherichia coli. Our previous work showed that induced expression of a yoeBSpn toxin-Green Fluorescent Protein (GFP fusion gene apparently triggered apoptosis and was lethal in the model plant, Arabidopsis thaliana. In this study, we investigated the effects of co-expression of the yefMSpn antitoxin and yoeBSpn toxin-GFP fusion in transgenic A. thaliana. When co-expressed in Arabidopsis, the YefMSpn antitoxin was found to neutralize the toxicity of YoeBSpn-GFP. Interestingly, the inducible expression of both yefMSpn antitoxin and yoeBSpn toxin-GFP fusion in transgenic hybrid Arabidopsis resulted in larger rosette leaves and taller plants with a higher number of inflorescence stems and increased silique production. To our knowledge, this is the first demonstration of a prokaryotic antitoxin neutralizing its cognate toxin in plant cells.

  4. Role of vapBC toxin-antitoxin loci in the thermal stress response of Sulfolobus solfataricus.

    Science.gov (United States)

    Cooper, Charlotte R; Daugherty, Amanda J; Tachdjian, Sabrina; Blum, Paul H; Kelly, Robert M

    2009-02-01

    TA (toxin-antitoxin) loci are ubiquitous in prokaryotic micro-organisms, including archaea, yet their physiological function is largely unknown. For example, preliminary reports have suggested that TA loci are microbial stress-response elements, although it was recently shown that knocking out all known chromosomally located TA loci in Escherichia coli did not have an impact on survival under certain types of stress. The hyperthermophilic crenarchaeon Sulfolobus solfataricus encodes at least 26 vapBC (where vap is virulence-associated protein) family TA loci in its genome. VapCs are PIN (PilT N-terminus) domain proteins with putative ribonuclease activity, while VapBs are proteolytically labile proteins, which purportedly function to silence VapCs when associated as a cognate pair. Global transcriptional analysis of S. solfataricus heat-shock-response dynamics (temperature shift from 80 to 90 degrees C) revealed that several vapBC genes were triggered by the thermal shift, suggesting a role in heat-shock-response. Indeed, knocking out a specific vapBC locus in S. solfataricus substantially changed the transcriptome and, in one case, rendered the crenarchaeon heat-shock-labile. These findings indicate that more work needs to be done to determine the role of VapBCs in S. solfataricus and other thermophilic archaea, especially with respect to post-transcriptional regulation.

  5. The ToxAvapA toxin-antitoxin locus contributes to the survival of nontypeable Haemophilus influenzae during infection.

    Science.gov (United States)

    Ren, Dabin; Kordis, Alexis A; Sonenshine, Daniel E; Daines, Dayle A

    2014-01-01

    Nontypeable Haemophilus influenzae (NTHi) is an opportunistic pathogen that is a common cause of acute and recurrent mucosal infections. One uncharacterized NTHi toxin-antitoxin (TA) module, NTHI1912-1913, is a host inhibition of growth (higBA) homologue. We hypothesized that this locus, which we designated toxAvapA, contributed to NTHi survival during infection. We deleted toxAvapA and determined that growth of the mutant in defined media was not different from the parent strain. We tested the mutant for persistence during long-term in vitro co-culture with primary human respiratory tissues, which revealed that the ΔtoxAvapA mutant was attenuated for survival. We then performed challenge studies using the chinchilla model of otitis media and determined that mutant survival was also reduced in vivo. Following purification, the toxin exhibited ribonuclease activity on RNA in vitro, while the antitoxin did not. A microarray comparison of the transcriptome revealed that the tryptophan biosynthetic regulon was significantly repressed in the mutant compared to the parent strain. HPLC studies of conditioned medium confirmed that there was no significant difference in the concentration of tryptophan remaining in the supernatant, indicating that the uptake of tryptophan by the mutant was not affected. We conclude that the role of the NTHi toxAvapA TA module in persistence following stress is multifactorial and includes effects on essential metabolic pathways.

  6. The ToxAvapA toxin-antitoxin locus contributes to the survival of nontypeable Haemophilus influenzae during infection.

    Directory of Open Access Journals (Sweden)

    Dabin Ren

    Full Text Available Nontypeable Haemophilus influenzae (NTHi is an opportunistic pathogen that is a common cause of acute and recurrent mucosal infections. One uncharacterized NTHi toxin-antitoxin (TA module, NTHI1912-1913, is a host inhibition of growth (higBA homologue. We hypothesized that this locus, which we designated toxAvapA, contributed to NTHi survival during infection. We deleted toxAvapA and determined that growth of the mutant in defined media was not different from the parent strain. We tested the mutant for persistence during long-term in vitro co-culture with primary human respiratory tissues, which revealed that the ΔtoxAvapA mutant was attenuated for survival. We then performed challenge studies using the chinchilla model of otitis media and determined that mutant survival was also reduced in vivo. Following purification, the toxin exhibited ribonuclease activity on RNA in vitro, while the antitoxin did not. A microarray comparison of the transcriptome revealed that the tryptophan biosynthetic regulon was significantly repressed in the mutant compared to the parent strain. HPLC studies of conditioned medium confirmed that there was no significant difference in the concentration of tryptophan remaining in the supernatant, indicating that the uptake of tryptophan by the mutant was not affected. We conclude that the role of the NTHi toxAvapA TA module in persistence following stress is multifactorial and includes effects on essential metabolic pathways.

  7. 结核分枝杆菌毒素-抗毒素系统 maz EF6缺失突变株的构建及其表型的初步探讨%Construction and characterization of toxin-antitoxin system mazEF6 deletion in Mycobacterium tuberculosis

    Institute of Scientific and Technical Information of China (English)

    申爱平; 曹帅丽; 邢建新; 袁俐

    2015-01-01

    To study the toxin‐antitoxin system mazEF6 of Mycobacterium tuberculosis (M . tuberculosis) , deletion mutants were constructed and subjected to phenotype analysis .First ,the flanking (homology arms) of mazEF6 gene from H37Rv and kanamycin resistance gene ( kan gene ) from plasmid PUC‐19K were amplified by polymerase chain reaction (PCR) respectively .Second ,fusion PCR was used for the hybrid splicing of mazEF6 homology arms and kan gene ,and the desired fusion fragment was obtained .Then the fragment was cloned into pMD‐19T (simple) vector to form a suicide plasmid (pMD‐19T‐ΔmazEF6‐kan) , and the suicide plasmid was transformed into Escherichia coli (E . coli) DH5α.At last ,the constructed plasmid was transformed into H37Rv by electroporation .Single colonies of M . tuberculosis were screened on L‐J medium with kanamycin , the genomic DNA of positive strains were extracted , and the targeted fragments were amplified by PCR and sequenced .The genetic stability and other phenotypes of the H 37RvΔmazEF6 deletion mutant were studied .The results showed that the deletion mutant strains did not present reverse mutant within 15 generations . Compared with the wild‐type strains , H37Rv ΔmazEF6 deletion mutant strains grew more slowly and the bacterial cell was relatively shorter .This study demonstrated that it is practical to obtain M . tuberculosis deletion mutant by fusion PCR technology ,and the survival ability of M . tuberculosis without toxin‐antitoxin mazEF6 gene is decreased .%为构建结核分枝杆菌毒素‐抗毒素系统 m azEF6缺失突变株,并对其表型进行初步探讨,首先用聚合酶链反应(PCR)分别从H37Rv标准株和PUC‐19K质粒扩增出 mazEF6基因的同源臂及卡那霉素抗性基因kan ;然后应用融合PCR技术将 mazEF6基因的同源臂与 kan基因进行杂交拼接,获得目的融合片段,将该融合片段克隆于pMD‐19T(simple)载体形成自杀质粒pMD‐19T‐ΔmazEF6

  8. Conditional Cooperativity in Toxin-Antitoxin Regulation Prevents Random Toxin Activation and Promotes Fast Translational Recovery

    DEFF Research Database (Denmark)

    Cataudella, Ilaria; Trusina, Ala; Sneppen, Kim;

    2012-01-01

    Many toxin–antitoxin (TA) loci are known to strongly repress their own transcription. This auto-inhibition is often called ‘conditional cooperativity’ as it relies on cooperative binding of TA complexes to operator DNA that occurs only when toxins are in a proper stoichiometric relationship...... system, relBE of Escherichia coli. We show that the model with the in vivo and in vitro established parameters reproduces experimentally observed response to nutritional stress. We further demonstrate that conditional cooperativity stabilizes the level of antitoxin in rapidly growing cells...

  9. Toxin-antitoxin loci as stress-response-elements: ChpAK/MazF and ChpBK cleave translated RNAs and are counteracted by tmRNA

    DEFF Research Database (Denmark)

    Christensen, S.K.; Pedersen, K.; Hansen, Flemming G.

    2003-01-01

    Prokaryotic chromosomes encode toxin-antitoxin loci, often in multiple copies. In most cases, the function of these genes is not known. The chpA (mazEF) locus of Escherichia coli has been described as a cell killing module that induces bacterial apoptosis during nutritional stress. However, we...... found recently that ChpAK (MazF) does not confer cell killing but rather, induces a bacteriostatic condition from which the cells could be resuscitated. Results presented here yield a mechanistic explanation for the detrimental effect on cell growth exerted by ChpAK and the homologous ChpBK protein of E....... coli. We show that both proteins inhibit translation by inducing cleavage of translated mRNAs. Consistently, the inhibitory effect of the proteins was counteracted by tmRNA. Amino acid starvation induced strong transcription of chpA that depended on Lon protease but not on ppGpp. Simultaneously, Chp...

  10. The crystal structure of the Rv0301-Rv0300 VapBC-3 toxin-antitoxin complex from M. tuberculosis reveals a Mg2+ ion in the active site and a putative RNA-binding site

    Energy Technology Data Exchange (ETDEWEB)

    Min, Andrew B; Miallau, Linda; Sawaya, Michael R; Habel, Jeff; Cascio, Duilio; Eisenberg, David [UCLA; (UCB)

    2013-01-10

    VapBC pairs account for 45 out of 88 identified toxin-antitoxin (TA) pairs in the Mycobacterium tuberculosis (Mtb) H37Rv genome. A working model suggests that under times of stress, antitoxin molecules are degraded, releasing the toxins to slow the metabolism of the cell, which in the case of VapC toxins is via their RNase activity. Otherwise the TA pairs remain bound to their promoters, autoinhibiting transcription. The crystal structure of Rv0301-Rv0300, an Mtb VapBC TA complex determined at 1.49 Å resolution, suggests a mechanism for these three functions: RNase activity, its inhibition by antitoxin, and its ability to bind promoter DNA. The Rv0301 toxin consists of a core of five parallel beta strands flanked by alpha helices. Three proximal aspartates coordinate a Mg2+ ion forming the putative RNase active site. The Rv0300 antitoxin monomer is extended in structure, consisting of an N-terminal beta strand followed by four helices. The last two helices wrap around the toxin and terminate near the putative RNase active site, but with different conformations. In one conformation, the C-terminal arginine interferes with Mg2+ ion coordination, suggesting a mechanism by which the antitoxin can inhibit toxin activity. At the N-terminus of the antitoxin, two pairs of Ribbon-Helix-Helix (RHH) motifs are related by crystallographic twofold symmetry. The resulting hetero-octameric complex is similar to the FitAB system, but the two RHH motifs are about 30 Å closer together in the Rv0301-Rv0300 complex, suggesting either a different span of the DNA recognition sequence or a conformational change.

  11. Functional validation of putative toxin-antitoxin genes from the Gram-positive pathogen Streptococcus pneumoniae: phd-doc is the fourth bona-fide operon

    Directory of Open Access Journals (Sweden)

    Wai Ting eChan

    2014-12-01

    Full Text Available Bacterial toxin-antitoxin (TAs loci usually consist of two genes organized as an operon, where their products are bound together and inert under normal conditions. However, under stressful circumstances the antitoxin, which is more labile, will be degraded more rapidly, thereby unleashing its cognate toxin to act on the cell. This, in turn, causes cell stasis or cell death, depending on the type of TAs and/or time of toxin exposure. Previously based on in silico analyses, we proposed that Streptococcus pneumoniae, a pathogenic Gram-positive bacterium, may harbor between four to ten putative TA loci depending on the strains. Here we have chosen the pneumococcal strain Hungary19A-6 which contains all possible ten TA loci. In addition to the three well-characterized operons, namely relBE2, yefM-yoeB, and pezAT, we show here the functionality of a fourth operon that encodes the pneumococcal equivalent of the phd-doc TA. Transcriptional fusions with gene encoding Green Fluorescent Protein showed that the promoter was slightly repressed by the Phd antitoxin, and exhibited almost background values when both Phd-Doc were expressed together. These findings demonstrate that phd-doc shows the negative self-regulatory features typical for an authentic TA. Further, we also show that the previously proposed TAs XreA-Ant and Bro-XreB, although they exhibit a genetic organization resembling those of typical TAs, did not appear to confer a functional behavior corresponding to bona fide TAs. In addition, we have also discovered new interesting bioinformatics results for the known pneumococcal TAs RelBE2 and PezAT. A global analysis of the four identified toxins-antitoxins in the pneumococcal genomes (PezAT, RelBE2, YefM-YoeB, and Phd-Doc showed that RelBE2 and Phd-Doc are the most conserved ones. Further, there was good correlation among TA types, clonal complexes and sequence types in the 48 pneumococcal strains analyzed.

  12. The Bacillus cereus spoIIS programmed cell death system

    Directory of Open Access Journals (Sweden)

    Jana eMelnicakova

    2015-08-01

    Full Text Available Programmed cell death in bacteria is generally associated with two¬ component toxin antitoxin systems. The SpoIIS toxin-antitoxin system, consisting of a membrane bound SpoIISA toxin and a small, cytosolic antitoxin SpoIISB, was originally identified in Bacillus subtilis. In this work we describe the Bacillus cereus SpoIIS system which is a three-component system, harbouring an additional gene spoIISC. Its protein product serves as an antitoxin, and similarly as SpoIISB, is able to bind SpoIISA and abolish its toxic effect. Our results indicate that SpoIISC seems to be present not only in B. cereus but also in other Bacilli containing a SpoIIS toxin antitoxin system. In addition, we show that B. cereus SpoIISA can form higher oligomers and we discuss the possible role of this multimerization for the protein’s toxic function.

  13. Analysis of the Bacillus cereus SpoIIS antitoxin-toxin system reveals its three-component nature.

    Science.gov (United States)

    Melničáková, Jana; Bečárová, Zuzana; Makroczyová, Jana; Barák, Imrich

    2015-01-01

    Programmed cell death in bacteria is generally associated with two-component toxin-antitoxin systems. The SpoIIS toxin-antitoxin system, consisting of a membrane-bound SpoIISA toxin and a small, cytosolic antitoxin SpoIISB, was originally identified in Bacillus subtilis. In this work we describe the Bacillus cereus SpoIIS system which is a three-component system, harboring an additional gene spoIISC. Its protein product serves as an antitoxin, and similarly as SpoIISB, is able to bind SpoIISA and abolish its toxic effect. Our results indicate that SpoIISC seems to be present not only in B. cereus but also in other Bacilli containing a SpoIIS toxin-antitoxin system. In addition, we show that B. cereus SpoIISA can form higher oligomers and we discuss the possible role of this multimerization for the protein's toxic function.

  14. Cell growth inhibition upon deletion of four toxin-antitoxin loci from the megaplasmids of Sinorhizobium meliloti.

    Science.gov (United States)

    Milunovic, Branislava; diCenzo, George C; Morton, Richard A; Finan, Turlough M

    2014-02-01

    Toxin and antitoxin (TA) gene pairs are addiction systems that are present in many microbial genomes. Sinorhizobium meliloti is an N2-fixing bacterial symbiont of alfalfa and other leguminous plants, and its genome consists of three large replicons, a circular chromosome (3.7 Mb) and the megaplasmids pSymA (1.4 Mb) and pSymB (1.7 Mb). S. meliloti carries 211 predicted type II TA genes, each encoding a toxin or an antitoxin. We constructed defined deletion strains that collectively removed the entire pSymA and pSymB megaplasmids except for their oriV regions. Of approximately 100 TA genes on pSymA and pSymB, we identified four whose loss was associated with cell death or stasis unless copies of the genes were supplied in trans. Orthologs of three of these loci have been characterized in other organisms (relB/E [sma0471/sma0473], Fic [DOC] [sma2105], and VapC [PIN] [orf2230/sma2231]), and this report contains the first experimental proof that RES/Xre (smb21127/smb21128) loci can function as a TA system. Transcriptome sequencing (RNA-seq) analysis did not reveal transcriptional differences between the TA systems to account for why deletion of the four "active" systems resulted in cell toxicity. These data suggest that severe cell growth phenotypes result from the loss of a few TA systems and that loss of most TA systems may result in more subtle phenotypes. These four TA systems do not appear to play a direct role in the S. meliloti-alfalfa symbiosis, as strains lacking these TA systems had a symbiotic N2 fixation phenotype that was indistinguishable from the wild type.

  15. The HigB/HigA Toxin/Antitoxin System of Pseudomonas aeruginosa Influences the Virulence Factors Pyochelin, Pyocyanin, and Biofilm Formation

    Science.gov (United States)

    2016-08-24

    Wood PA14 (Lee et al. 2006) and cloning into pCA24N at the NotI and PstI restriction sites placed higB under the control of T5 -lac promoter. The higB...model for programmed bacterial cell death. Proc. Natl. Acad. Sci. USA 93:6059– 6063 . Ankenbauer, R. G., and H. N. Quan. 1994. Fpta, the Fe(Iii

  16. Protein (Cyanobacteria): 134500 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available toxic translational repressor of toxin-antitoxin stability system Cylindrospermum stagnale PCC 7417 MCVHSLPSAVNSCLLQKIKSVIEEVENAVSLGEINNVKKLKADGDYYRIRVGDYRIGIAVSGDVVIFMRILHRREVYRYFR ...

  17. Progress in research on toxins-antitoxins system in bacterial programmed cell death%细菌的细胞程序性死亡中毒素-抗毒素系统的研究进展

    Institute of Scientific and Technical Information of China (English)

    季建军; 邱景富; 杨瑞馥

    2006-01-01

    与哺乳动物细胞相同,细菌也存在着细胞程序性死亡.本文对细菌中存在的细胞程序性死亡现象、引发细菌造成细胞程序性死亡的毒素-抗毒素系统的组成、分类、意义以及影响细胞程序性死亡的因素进行了介绍.

  18. The Molecular Evolution of Type Ⅱ Toxin-antitoxin(TA)System-MazEF in Bifidobacterial Genomes%双歧杆菌Ⅱ型毒素-抗毒素系统-MazEF的分子进化分析

    Institute of Scientific and Technical Information of China (English)

    韦艳霞; 刘佃滨; 郑纪伟; 尤红娟; 张鹏; 李阳; 汤仁仙

    2014-01-01

    Objective:To perform molecular evolution analysis of MazEF in genomes of Bifidobacterium. Method:The Protein sequences of MazF in bifidobacterial genomes were obtained by employing the PSI-BLAST search from NCBI. The Protein sequences of MazF encoded by other bacteria were obtained from non-redundant protein database of NCBI. All of the 16 S rRNA sequences used in this study were obtained from non-redundant nucleotide database of NCBI. Clustal χ² and MEGA4 were used to analyze molecular evolution of MazF. Result:The total number of MazF in bifidobacterial genomes were searched of 26 The molecular evolution analysis showed that MazF in bifidobacterial genomes had less conservation;the co-evolution of MazF with the 16 S RNA was only observed in individual species and most homologous analysis results of MazF were not in concordance with 16 S rRNA. Conclusion:MazEF was integrated in bifidobacterial chromosomes through horizontal transfer,which was a part of the non-core genome.%目的:对双歧杆菌属编码的Ⅱ类毒素-抗毒素(TA)系统MazEF进行分子进化分析。方法:利用PSI-BLAST在NCBI中搜索获得双歧杆菌编码的MazF分子序列,在NCBI蛋白数据库、核酸数据库分别下载其他菌属基因组编码的MazF蛋白序列和本研究所涉及菌属的16 S rRNA序列,应用Clustal X2和MEGA4软件对MazF做分子进化分析。结果:共搜索到双歧杆菌株染色体编码毒素蛋白MazF 26个。分子进化分析显示:整个双歧杆菌属的MazF保守性不好;MazF与16 S rRNA的共进化仅在个别菌种中发现,大部分MazF的聚类结果与相应菌种16 S rRNA的聚类结果不同。结论:双歧杆菌中的TA系统MazEF可能是通过基因的水平转移整合入基因组中,属于菌株非核心基因组部分。

  19. Viral evasion of a bacterial suicide system by RNA-based molecular mimicry enables infectious altruism.

    Science.gov (United States)

    Blower, Tim R; Evans, Terry J; Przybilski, Rita; Fineran, Peter C; Salmond, George P C

    2012-01-01

    Abortive infection, during which an infected bacterial cell commits altruistic suicide to destroy the replicating bacteriophage and protect the clonal population, can be mediated by toxin-antitoxin systems such as the Type III protein-RNA toxin-antitoxin system, ToxIN. A flagellum-dependent bacteriophage of the Myoviridae, ΦTE, evolved rare mutants that "escaped" ToxIN-mediated abortive infection within Pectobacterium atrosepticum. Wild-type ΦTE encoded a short sequence similar to the repetitive nucleotide sequence of the RNA antitoxin, ToxI, from ToxIN. The ΦTE escape mutants had expanded the number of these "pseudo-ToxI" genetic repeats and, in one case, an escape phage had "hijacked" ToxI from the plasmid-borne toxIN locus, through recombination. Expression of the pseudo-ToxI repeats during ΦTE infection allowed the phage to replicate, unaffected by ToxIN, through RNA-based molecular mimicry. This is the first example of a non-coding RNA encoded by a phage that evolves by selective expansion and recombination to enable viral suppression of a defensive bacterial suicide system. Furthermore, the ΦTE escape phages had evolved enhanced capacity to transduce replicons expressing ToxIN, demonstrating virus-mediated horizontal transfer of genetic altruism.

  20. Viral evasion of a bacterial suicide system by RNA-based molecular mimicry enables infectious altruism.

    Directory of Open Access Journals (Sweden)

    Tim R Blower

    Full Text Available Abortive infection, during which an infected bacterial cell commits altruistic suicide to destroy the replicating bacteriophage and protect the clonal population, can be mediated by toxin-antitoxin systems such as the Type III protein-RNA toxin-antitoxin system, ToxIN. A flagellum-dependent bacteriophage of the Myoviridae, ΦTE, evolved rare mutants that "escaped" ToxIN-mediated abortive infection within Pectobacterium atrosepticum. Wild-type ΦTE encoded a short sequence similar to the repetitive nucleotide sequence of the RNA antitoxin, ToxI, from ToxIN. The ΦTE escape mutants had expanded the number of these "pseudo-ToxI" genetic repeats and, in one case, an escape phage had "hijacked" ToxI from the plasmid-borne toxIN locus, through recombination. Expression of the pseudo-ToxI repeats during ΦTE infection allowed the phage to replicate, unaffected by ToxIN, through RNA-based molecular mimicry. This is the first example of a non-coding RNA encoded by a phage that evolves by selective expansion and recombination to enable viral suppression of a defensive bacterial suicide system. Furthermore, the ΦTE escape phages had evolved enhanced capacity to transduce replicons expressing ToxIN, demonstrating virus-mediated horizontal transfer of genetic altruism.

  1. Two programmed cell death systems in Escherichia coli: an apoptotic-like death is inhibited by the mazEF-mediated death pathway.

    Directory of Open Access Journals (Sweden)

    Ariel Erental

    Full Text Available In eukaryotes, the classical form of programmed cell death (PCD is apoptosis, which has as its specific characteristics DNA fragmentation and membrane depolarization. In Escherichia coli a different PCD system has been reported. It is mediated by the toxin-antitoxin system module mazEF. The E. coli mazEF module is one of the most thoroughly studied toxin-antitoxin systems. mazF encodes a stable toxin, MazF, and mazE encodes a labile antitoxin, MazE, which prevents the lethal effect of MazF. mazEF-mediated cell death is a population phenomenon requiring the quorum-sensing pentapeptide NNWNN designated Extracellular Death Factor (EDF. mazEF is triggered by several stressful conditions, including severe damage to the DNA. Here, using confocal microscopy and FACS analysis, we show that under conditions of severe DNA damage, the triggered mazEF-mediated cell death pathway leads to the inhibition of a second cell death pathway. The latter is an apoptotic-like death (ALD; ALD is mediated by recA and lexA. The mazEF-mediated pathway reduces recA mRNA levels. Based on these results, we offer a molecular model for the maintenance of an altruistic characteristic in cell populations. In our model, the ALD pathway is inhibited by the altruistic EDF-mazEF-mediated death pathway.

  2. Bacillus globigii cell size is influenced by variants of the quorum sensing peptide extracellular death factor

    NARCIS (Netherlands)

    Sijbrandij, T.; Kaman, W.E.; Ligtenberg, A.J.M.; Nazmi, K.; Veerman, E.C.I.; Bikker, F.J.

    2014-01-01

    Toxin-antitoxin modules are necessary for the mode of action of several antibiotics. One of the most studied toxin-antitoxin modules is the quorum sensing - dependent MazEF system in Escherichia coli. The quorum sensing factor in this system is called the extracellular death factor (EDF), a linear p

  3. Bacillus globigii cell size is influenced by variants of the quorum sensing peptide extracellular death factor

    NARCIS (Netherlands)

    T. Sijbrandij (T.); W.E. Kaman (Wendy); A.J.M. Ligtenberg (A. J M); K. Nazmi (Kamran); E.C.I. Veerman (Enno); F.J. Bikker (Floris)

    2014-01-01

    textabstractToxin-antitoxin modules are necessary for the mode of action of several antibiotics. One of the most studied toxin-antitoxin modules is the quorum sensing - dependent MazEF system in Escherichia coli. The quorum sensing factor in this system is called the extracellular death factor (EDF)

  4. A New Selectable Marker System for Genetic Studies of Bacteria: Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Parsons, D; Tolmasky, M; Chain, P; Segelke, B W

    2011-03-18

    Genetic manipulations in bacteria currently rely on the introduction of antibiotic resistance genes into a bacterial strain; for those organisms that will be used for commercial or industrial applications, the genetic cassette encoding the antibiotic resistance is sometimes removed after selection. it is clear that if alternative technologies could obviate the need to introduce antibiotic resistance into bacteria, they would most certainly become a standard tool in molecular micriobiology for commercial, industrial as well as research applications. Here, they present the development of a novel genetic engineering technology based on toxin-antitoxin systems to modify bacterial genomes without the use of antibiotic resistance in the mutagenesis process. The primary goal is to develop antibiotic-free selection for genetically altered select agent pathogens. They are adapting the toxinc-antitoxin system to enable gene replacement in select agent pathogens since the NIH restrictions introducing antibiotic resistance into select agent pathogens have hindered research with select agent pathogens.

  5. 毒素蛋白基因mazF在基因修饰系统中的应用进展%Application Progress ofmazF Gene in Genetic Modification System

    Institute of Scientific and Technical Information of China (English)

    石杨; 董会娜; 张大伟

    2014-01-01

    毒素-抗毒素系统(Toxin-antitoxin system,TA系统)存在于大部分细菌中。mazEF是大肠杆菌中一种毒素-抗毒素系统。毒素基因mazF编码的MazF毒素蛋白可以特异性地剪切自由mRNA的ACA序列,从而抑制蛋白合成、引起细胞生长停滞;近些年,许多学者利用mazF基因作为反向筛选标记对不同种微生物建立了无标记或无痕的基因修饰系统,并实现了不同菌株的基因组修饰。主要综述了大肠杆菌mazF基因作为反向筛选基因的应用原理及其在不同种类微生物的基因修饰系统中的应用进展,然后对mazF基因及其他毒素基因在基因修饰系统中的应用进行了展望。%Toxin-antitoxin system(TA)exists in most of the genetic material of bacteria.mazEF is a kind of toxin-antitoxin system in E. coli. MazF encoded bymazF is an mRNA interferase that specifically cleaves free mRNAs at ACA sequences, resulting in inhibited protein synthesis and cell growth arrest. Recently, some scholars have usedmazF as a counter-selection marker in genetic modification systems, and achieved modifications of the genome in various strains. In this article, the research advances of E. coli mazF used as counter-selection marker in bacterial genetic modification were reviewed, followed by application of other toxin gene. Finally, perspective of the possible new pathways for developing new genetic modification methods were addressed.

  6. ccdAB system and the encoding toxin protein-CcdB%ccdAB系统及其编码的毒素蛋白CcdB

    Institute of Scientific and Technical Information of China (English)

    贾卉; 井申荣

    2009-01-01

    ccdAB系统(control of cell division or death system)是目前已知的一种毒素-抗毒素系统(toxin-antitoxin system,TA系统),存在于致病性大肠杆菌F质粒及染色体骨架上,由ccdA和ccdB两个基因组成.质粒上的ccdAB系统编码一种毒素蛋白CcdB,在缺乏抗毒素的情况下,CcdB使细胞内促旋酶中毒,从而干扰DNA的合成,杀伤宿主细胞.本文对ccdAB系统的结构和功能,以及所编码CcdB的作用机制进行了综述.

  7. Identification of mazEF Toxin – Antitoxin system and biofilm formation in clinical isolates of MRSA isolated from Eastern India

    Directory of Open Access Journals (Sweden)

    Sonia Jain

    2016-01-01

    Full Text Available Introduction: Interest on Toxin-Antitoxin (TA systems has increased dramatically over recent years. It is ubiquitously present in many bacterial genomes including pathogens like MRSA. Several cellular functions of TA systems are proposed like programmed cell death, persister cell formation, biofilm formation etc. However, their exact role in cell physiology remains unclear. Due to the biofilm development the rate of morbidity and mortality of chronic MRSA infections are increasing day by day. Objectives: The aim of the study is to find any association between biofilm formation and mazEF toxin-antitoxin systems in clinical isolates of MRSA, isolated from tertiary care hospital, Kolkata. Materials and Methods: MRSA isolates were detected for biofilm formation by tube method and simultaneously the presence of mazEF TA gene in these biofilm forming isolates were evaluated. Results: It was found that 52.47 % MRSA isolates were potent biofilm producers by Tube method. The results indicated that 55.26 % of the biofilm forming isolates possessed mazEF gene. And 44% of the biofilm forming isolates did not possessed mazEF gene. Conclusions: The analysis recommended that TA genes are prevalent in clinical isolates of MRSA strains but no significant difference is found in the presence of mazEF TA system in the biofilm producer and non-biofilm producer isolates. Further to come into any conclusion reverse transcription studies are needed to be done in order to find out the exact amount of mazEF expression in all MRSA isolates.

  8. PCR-based plasmid typing in Enterococcus faecium strains reveals widely distributed pRE25-, pRUM-, pIP501-and pHT beta-related replicons associated with glycopeptide resistance and stabilizing toxin-antitoxin systems

    DEFF Research Database (Denmark)

    Rosvoll, T.C.S.; Pedersen, T.; Sletvold, H.;

    2010-01-01

    A PCR-based typing scheme was applied to identify plasmids in an epidemiologically and geographically diverse strain collection of Enterococcus faecium (n=93). Replicon types of pRE25 (n=56), pRUM (n=41), pIP501 (n=17) and pHT beta (n=14) were observed in 83% of the strains, while pS86, pCF10, p......RUM replicons (74%) than non-CC17 strains (2.2% and 35%, respectively). A prevalent genetic linkage between the pRUM-replicon type and axe-txe was demonstrated by cohybridization analyses. The vanA resistance determinant was associated with all four replicon types, but we also confirmed the genetic linkage...... of vanA to unknown transferable replicons. PCR-based replicon typing, linked to the detection of other important plasmid-encoded traits, seems to be a feasible tool for tracing disseminating resistance plasmids stably maintained in various environments....

  9. The natural history of ADP-ribosyltransferases and the ADP-ribosylation system.

    Science.gov (United States)

    Aravind, L; Zhang, Dapeng; de Souza, Robson F; Anand, Swadha; Iyer, Lakshminarayan M

    2015-01-01

    Catalysis of NAD(+)-dependent ADP-ribosylation of proteins, nucleic acids, or small molecules has evolved in at least three structurally unrelated superfamilies of enzymes, namely ADP-ribosyltransferase (ART), the Sirtuins, and probably TM1506. Of these, the ART superfamily is the most diverse in terms of structure, active site residues, and targets that they modify. The primary diversification of the ART superfamily occurred in the context of diverse bacterial conflict systems, wherein ARTs play both offensive and defensive roles. These include toxin-antitoxin systems, virus-host interactions, intraspecific antagonism (polymorphic toxins), symbiont/parasite effectors/toxins, resistance to antibiotics, and repair of RNAs cleaved in conflicts. ARTs evolving in these systems have been repeatedly acquired by lateral transfer throughout eukaryotic evolution, starting from the PARP family, which was acquired prior to the last eukaryotic common ancestor. They were incorporated into eukaryotic regulatory/epigenetic control systems (e.g., PARP family and NEURL4), and also used as defensive (e.g., pierisin and CARP-1 families) or immunity-related proteins (e.g., Gig2-like ARTs). The ADP-ribosylation system also includes other domains, such as the Macro, ADP-ribosyl glycohydrolase, NADAR, and ADP-ribosyl cyclase, which appear to have initially diversified in bacterial conflict-related systems. Unlike ARTs, sirtuins appear to have a much smaller presence in conflict-related systems.

  10. The role of DNA restriction-modification systems in the biology of Bacillus anthracis

    Directory of Open Access Journals (Sweden)

    Ramakrishnan eSitaraman

    2016-01-01

    Full Text Available Restriction-modification (R-M systems are widespread among prokaryotes and, depending on their type, may be viewed as selfish genetic elements that persist as toxin-antitoxin modules or as cellular defense systems against phage infection. Studies in the last decade have made it amply clear that these two options do not exhaust the list of possible biological roles for R-M systems. Their presence in a cell may also have a bearing on other processes such as horizontal gene transfer and gene regulation. From genome sequencing and experimental data, we know that Bacillus anthracis encodes at least three methylation-dependent (typeIV restriction endonucleases, and an orphan DNA methyltransferase. In this article, we first present an outline of our current knowledge of R-M systems in Bacillus anthracis. Based on available DNA sequence data, and on our current understanding of the functions of similar genes in other systems, we conclude with hypotheses on the possible roles of the three restriction endonucleases and the orphan DNA methyltransferase.

  11. Modeling sRNA-Regulated Plasmid Maintenance

    Science.gov (United States)

    Klumpp, Stefan

    2017-01-01

    We study a theoretical model for the toxin-antitoxin (hok/sok) mechanism for plasmid maintenance in bacteria. Toxin-antitoxin systems enforce the maintenance of a plasmid through post-segregational killing of cells that have lost the plasmid. Key to their function is the tight regulation of expression of a protein toxin by an sRNA antitoxin. Here, we focus on the nonlinear nature of the regulatory circuit dynamics of the toxin-antitoxin mechanism. The mechanism relies on a transient increase in protein concentration rather than on the steady state of the genetic circuit. Through a systematic analysis of the parameter dependence of this transient increase, we confirm some known design features of this system and identify new ones: for an efficient toxin-antitoxin mechanism, the synthesis rate of the toxin’s mRNA template should be lower that of the sRNA antitoxin, the mRNA template should be more stable than the sRNA antitoxin, and the mRNA-sRNA complex should be more stable than the sRNA antitoxin. Moreover, a short half-life of the protein toxin is also beneficial to the function of the toxin-antitoxin system. In addition, we study a therapeutic scenario in which a competitor mRNA is introduced to sequester the sRNA antitoxin, causing the toxic protein to be expressed. PMID:28085919

  12. Bacterial Programmed Cell Death Mediated by mazEF System Under Stressful Conditions%mazEF系统介导胁迫诱导细菌细胞程序性死亡

    Institute of Scientific and Technical Information of China (English)

    庄强; 宁德刚

    2009-01-01

    mazEF是细菌染色体上的"毒素-抗毒素系统"基因(Toxin-antitoxin system,TA系统),可介导胁迫诱导细菌细胞程序性死亡.本文介绍了mazEF系统的遗传结构特征、生理生化功能、环境胁迫激活mazEF系统介导的细菌细胞程序性死亡的机制,参与细胞死亡过程中的细胞信号和细胞因子的调控,以及关于mazEF系统介导的细菌细胞程序性死亡理论的争论,提出了进一步丰富和完善细菌细胞程序性死亡理论亟待解决的问题.

  13. Persistence of Vancomycin Resistance in Multiple Clones of Enterococcus faecium Isolated from Danish Broilers 15 Years after the Ban of Avoparcin

    DEFF Research Database (Denmark)

    Bortolaia, Valeria; Mander, Manuela; Jensen, Lars Bogø

    2015-01-01

    associated with a transferable nontypeable plasmid lineage occurring in multiple E. faecium clones. Coselection of sequence type 842 by tetracycline use only partly explained the persistence of vancomycin resistance in the absence of detectable plasmid coresistance and toxin-antitoxin systems....

  14. Modeling sRNA-regulated Plasmid Maintenance

    CERN Document Server

    Gong, Chen Chris

    2016-01-01

    We study a theoretical model for the toxin-antitoxin (hok/sok) mechanism for plasmid maintenance in bacteria. Toxin-antitoxin systems enforce the maintenance of a plasmid through post-segregational killing of cells that have lost the plasmid. Key to their function is the tight regulation of expression of a protein toxin by an sRNA antitoxin. Here, we focus on the nonlinear nature of the regulatory circuit dynamics of the toxin-antitoxin mechanism. The mechanism relies on a transient increase in protein concentration rather than on the steady state of the genetic circuit. Through a systematic analysis of the parameter dependence of this transient increase, we confirm some known design features of this system and identify new ones: for an efficient toxin-antitoxin mechanism, the synthesis rate of the toxin's mRNA template should be lower that of the sRNA antitoxin, the mRNA template should be more stable than the sRNA antitoxin, and the mRNA-sRNA complex should be more stable than the sRNA antitoxin. Moreover, ...

  15. Structural studies of the toxin-antitoxin proteins RelE and RelB from E. coli

    DEFF Research Database (Denmark)

    Andersen, Kasper Røjkjær; Overgaard, Martin; Gerdes, Kenn

    these questions by solving the structure of both RelB and RelE alone. Biochemical evidences show that both RelB and RelBE complex auto-regulate their own promoter, but how is this performed? In order to address this from a structural point of view we are currently trying to form and crystallize a complex between...... that RelE changes conformation upon release of RelB. We wish to answer these questions by solving the structure of both RelB and RelE alone. Biochemical evidences show that both RelB and RelBE complex auto-regulate their own promoter, but how is this performed? In order to address this from a structural...... was previously solved at 2.3Å [2]. This structure shows the molecule in an inactive state, but how do these proteins look when they are separate? It is likely that RelE changes conformation upon release of RelB. We wish to answer these questions by solving the structure of both RelB and RelE alone. Biochemical...

  16. Toxin-antitoxin loci as stress-response-elements: ChpAK/MazF and ChpBK cleave translated RNAs and are counteracted by tmRNA

    DEFF Research Database (Denmark)

    Christensen, S.K.; Pedersen, K.; Hansen, Flemming G.;

    2003-01-01

    . coli. We show that both proteins inhibit translation by inducing cleavage of translated mRNAs. Consistently, the inhibitory effect of the proteins was counteracted by tmRNA. Amino acid starvation induced strong transcription of chpA that depended on Lon protease but not on ppGpp. Simultaneously, Chp...

  17. AAU-Specific RNA Cleavage Mediated by MazF Toxin Endoribonuclease Conserved in Nitrosomonas europaea

    Directory of Open Access Journals (Sweden)

    Tatsuki Miyamoto

    2016-06-01

    Full Text Available Nitrosomonas europaea carries numerous toxin-antitoxin systems. However, despite the abundant representation in its chromosome, studies have not surveyed the underlying molecular functions in detail, and their biological roles remain enigmatic. In the present study, we found that a chromosomally-encoded MazF family member, predicted at the locus NE1181, is a functional toxin endoribonuclease, and constitutes a toxin-antitoxin system, together with its cognate antitoxin, MazE. Massive parallel sequencing provided strong evidence that this toxin endoribonuclease exhibits RNA cleavage activity, primarily against the AAU triplet. This sequence-specificity was supported by the results of fluorometric assays. Our results indicate that N. europaea alters the translation profile and regulates its growth using the MazF family of endoribonuclease under certain stressful conditions.

  18. Toxin MqsR Cleaves Single-Stranded mRNA with Various 5 Ends

    Science.gov (United States)

    2016-08-24

    al. 2014), and TA sys- tems are ubiquitous in prokaryotes (Goeders and Van Melderen 2014). For example, the Escherichia coli genome contains at...With Various 5′ Ends ATP levels through membrane damage (Wang et al. 2012, 2013; Cheng et al. 2014). Therefore, the results here demonstrate that...Benedik, and T. K. Wood. 2014. Toxin GhoT of the GhoT/GhoS toxin/antitoxin system damages the cell membrane to reduce adenosine triphosphate and

  19. mazEF-mediated programmed cell death in bacteria: "what is this?".

    Science.gov (United States)

    Ramisetty, Bhaskar Chandra Mohan; Natarajan, Bhargavi; Santhosh, Ramachandran Sarojini

    2015-02-01

    Toxin-antitoxin (TA) systems consist of a bicistronic operon, encoding a toxin and an antitoxin. They are widely distributed in the prokaryotic kingdom, often in multiple numbers. TAs are implicated in contradicting phenomena of persistence and programmed cell death (PCD) in bacteria. mazEF TA system, one of the widely distributed type II toxin-antitoxin systems, is particularly implicated in PCD of Escherichia coli. Nutrient starvation, antibiotic stress, heat shock, DNA damage and other kinds of stresses are shown to elicit mazEF-mediated-PCD. ppGpp and extracellular death factor play a central role in regulating mazEF-mediated PCD. The activation of mazEF system is achieved through inhibition of transcription or translation of mazEF loci. Upon activation, MazF cleaves RNA in a ribosome-independent fashion and subsequent processes result in cell death. It is hypothesized that PCD aids in perseverance of the population during stress; the surviving minority of the cells can scavenge the nutrients released by the dead cells, a kind of "nutritional-altruism." Issues regarding the strains, reproducibility of experimental results and ecological plausibility necessitate speculation. We review the molecular mechanisms of the activation of mazEF TA system, the consequences leading to cell death and the pros and cons of the altruism hypothesis from an ecological perspective.

  20. Selectivity and self-assembly in the control of a bacterial toxin by an antitoxic noncoding RNA pseudoknot.

    Science.gov (United States)

    Short, Francesca L; Pei, Xue Y; Blower, Tim R; Ong, Shue-Li; Fineran, Peter C; Luisi, Ben F; Salmond, George P C

    2013-01-15

    Bacterial small RNAs perform numerous regulatory roles, including acting as antitoxic components in toxin-antitoxin systems. In type III toxin-antitoxin systems, small processed RNAs directly antagonize their toxin protein partners, and in the systems characterized the toxin and antitoxin components together form a trimeric assembly. In the present study, we sought to define how the RNA antitoxin, ToxI, inhibits its potentially lethal protein partner, ToxN. We show through cross-inhibition experiments with the ToxIN systems from Pectobacterium atrosepticum (ToxIN(Pa)) and Bacillus thuringiensis (ToxIN(Bt)) that ToxI RNAs are highly selective enzyme inhibitors. Both systems have an "addictive" plasmid maintenance phenotype. We demonstrate that ToxI(Pa) can inhibit ToxN(Pa) in vitro both in its processed form and as a repetitive precursor RNA, and this inhibition is linked to the self-assembly of the trimeric complex. Inhibition and self-assembly are both mediated entirely by the ToxI(Pa) RNA, with no requirement for cellular factors or exogenous energy. Finally, we explain the origins of ToxI antitoxin selectivity through our crystal structure of the ToxIN(Bt) complex. Our results show how a processed RNA pseudoknot can inhibit a deleterious protein with exquisite molecular specificity and how these self-contained and addictive RNA-protein pairs can confer different adaptive benefits in their bacterial hosts.

  1. A Conserved Mode of Protein Recognition and Binding in a ParD−ParE Toxin−Antitoxin Complex

    Energy Technology Data Exchange (ETDEWEB)

    Dalton, Kevin M.; Crosson, Sean (UC)

    2010-05-06

    Toxin-antitoxin (TA) systems form a ubiquitous class of prokaryotic proteins with functional roles in plasmid inheritance, environmental stress response, and cell development. ParDE family TA systems are broadly conserved on plasmids and bacterial chromosomes and have been well characterized as genetic elements that promote stable plasmid inheritance. We present a crystal structure of a chromosomally encoded ParD-ParE complex from Caulobacter crescentus at 2.6 {angstrom} resolution. This TA system forms an {alpha}{sub 2}{beta}{sub 2} heterotetramer in the crystal and in solution. The toxin-antitoxin binding interface reveals extensive polar and hydrophobic contacts of ParD antitoxin helices with a conserved recognition and binding groove on the ParE toxin. A cross-species comparison of this complex structure with related toxin structures identified an antitoxin recognition and binding subdomain that is conserved between distantly related members of the RelE/ParE toxin superfamily despite a low level of overall primary sequence identity. We further demonstrate that ParD antitoxin is dimeric, stably folded, and largely helical when not bound to ParE toxin. Thus, the paradigmatic model in which antitoxin undergoes a disorder-to-order transition upon toxin binding does not apply to this chromosomal ParD-ParE TA system.

  2. Expression, Purification, and Functional Analysis of Novel RelE Operon from X. nematophila

    Directory of Open Access Journals (Sweden)

    Jitendra Singh Rathore

    2014-01-01

    Full Text Available Bacterial toxin-antitoxin (TA complexes induce programmed cell death and also function to relieve cell from stress by various response mechanisms. Escherichia coli RelB-RelE TA complex consists of a RelE toxin functionally counteracted by RelB antitoxin. In the present study, a novel homolog of RelE toxin designated as Xn-relE toxin from Xenorhabdus nematophila possessing its own antitoxin designated as Xn-relEAT has been identified. Expression and purification of recombinant proteins under native conditions with GST and Ni-NTA chromatography prove the existence of novel TA module. The expression of recombinant Xn-relE under tightly regulated ara promoter in E. coli Top 10 cells confirms its toxic nature in endogenous toxicity assay. The neutralization activity in endogenous toxicity assay by Xn-relEAT antitoxin confirms its antidote nature when studying the whole TA operon under ara regulated promoter. This study promotes newly discovered TA module to be regarded as important as other proteins of type II toxin-antitoxin system.

  3. Síntese, caracterização e estudos de interação de um análogo da antitoxina CcdA empregando fluorescência no estado estacionário Synthesis, characterization and interaction studies of an analog of CcdA antitoxin by steady state fluorescence

    Directory of Open Access Journals (Sweden)

    Camila Aparecida Cotrim

    2010-01-01

    Full Text Available Toxin-antitoxin (TA systems contribute to plasmid stability by a mechanism called post-segregational killing. The ccd was the first TA system to be discovered with CcdB being the toxin and CcdA the antitoxin. CcdA, an 8.3 kDa protein, interacts with CcdB (11.7 kDa, preventing the cytotoxic activity of CcdB on the DNA gyrase. As an approach to understanding this interaction, CcdA41, a polypeptide derived from CcdA, was synthesized by solid-phase methodology and its interaction with CcdB was analyzed by steady state fluorescence. CcdA41 formed a stable complex with CcdBET2, a peptide based on CcdB, the more recently described bacterial topoisomerase inhibitor.

  4. Toxin inhibition in C. crescentus VapBC1 is mediated by a flexible pseudo-palindromic protein motif and modulated by DNA binding

    DEFF Research Database (Denmark)

    Bendtsen, Kirstine L; Xu, Kehan; Luckmann, Majbritt

    2017-01-01

    for binding and inactivation of the VapC1 toxin dimer. Sequence analysis of 4127 orthologous VapB sequences reveals that such palindromic protein sequences are widespread and unique to bacterial and archaeal VapB antitoxins suggesting a general principle governing regulation of VapBC TA systems. Finally......Expression of bacterial type II toxin-antitoxin (TA) systems is regulated at the transcriptional level through direct binding of the antitoxin to pseudo-palindromic sequences on operator DNA. In this context, the toxin functions as a co-repressor by stimulating DNA binding through direct...... architectural rearrangement of conserved TA interactions in which C-terminal extended structures of the antitoxin VapB1 swap positions to interlock the complex in the DNA-bound state. We further show that a pseudo-palindromic protein sequence in the antitoxin is responsible for this interaction and required...

  5. Genotyping, evolution and epidemiological findings of Rickettsia species.

    Science.gov (United States)

    Merhej, Vicky; Angelakis, Emmanouil; Socolovschi, Cristina; Raoult, Didier

    2014-07-01

    Rickettsiae are obligate intracellular bacteria that can cause mild to life-threatening diseases, including epidemic typhus, one of the oldest pernicious diseases of mankind. Clinical awareness of rickettsial diseases and molecular diagnosis have shown that rickettsioses should be viewed as new emerging and reemerging diseases. Rickettsia has been shown to be a large genus with a worldwide distribution, a very diverse host range, including hosts that have no relationship with vertebrate. Genomic studies have demonstrated genome reduction due to gene loss associated with increased pathogenicity and horizontal DNA acquisition according to a sympatric mode of evolution in hosts that contain several organisms. This article presents a review of genotyping techniques and examines the principle of genotype determination in terms of taxonomic strategies and detection methods. This article summarizes the epidemiological and pathological features of Rickettsia and discusses the genomic findings that help the understanding of the evolution of pathogenicity including the deleterious mutations of repair systems and the toxin-antitoxin systems.

  6. Genomics and genetics of Sulfolobus islandicus LAL14/1, a model hyperthermophilic archaeon

    DEFF Research Database (Denmark)

    Jaubert, Carole; Danioux, Chloë; Oberto, Jacques;

    2013-01-01

    have developed a genetic system for S. islandicus LAL14/1 and created ¿pyrEF and ¿CRISPR_1 mutants using double cross-over and pop-in/pop-out approaches, respectively. Thus, LAL14/1 is a promising model to study virus-host interactions and the CRISPR/Cas defence mechanism in Archaea....... common core genome of approximately 2 Mb and a long hyperplastic region containing most of the strain-specific genes. In LAL14/1, the latter region is enriched in insertion sequences, CRISPR (clustered regularly interspaced short palindromic repeats), glycosyl transferase genes, toxin-antitoxin genes...... and MITE (miniature inverted-repeat transposable elements). The tRNA genes of LAL14/1 are preferential targets for the integration of mobile elements but clusters of atypical genes (CAG) are also integrated elsewhere in the genome. LAL14/1 carries five CRISPR loci with 10 per cent of spacers matching...

  7. Comprehensive mapping of the Helicobacter pylori NikR regulon provides new insights in bacterial nickel responses

    Science.gov (United States)

    Vannini, Andrea; Pinatel, Eva; Costantini, Paolo Emidio; Pelliciari, Simone; Roncarati, Davide; Puccio, Simone; De Bellis, Gianluca; Peano, Clelia; Danielli, Alberto

    2017-01-01

    Nickel homeostasis is important for pathogenic and ureolytic bacteria, which use this metal ion as enzymatic cofactor. For example, in the human pathogen Helicobacter pylori an optimal balance between nickel uptake and incorporation in metallo-enzymes is fundamental for colonization of the host. Nickel is also used as cofactor to modulate DNA binding of the NikR regulator, which controls transcription of genes involved in nickel trafficking or infection in many bacteria. Accordingly, there is much interest in a systematic characterization of NikR regulation. Herein we use H. pylori as a model to integrate RNA-seq and ChIP-seq data demonstrating that NikR not only regulates metal-ion transporters but also virulence factors, non-coding RNAs, as well as toxin-antitoxin systems in response to nickel stimulation. Altogether, results provide new insights into the pathobiology of H. pylori and contribute to understand the responses to nickel in other bacteria. PMID:28393877

  8. Proteomic insight into the primycin fermentation process of Saccharomonospora azurea.

    Science.gov (United States)

    Valasek, Andrea; Kiss, Írisz Éva; Fodor, István; Kovács, Márk; Urbán, Péter; Jámbor, Éva; Fekete, Csaba; Kerepesi, Ildikó

    2016-12-01

    Saccharomonospora azurea SZMC 14600 is a member of the family Pseudonocardiaceae exclusively used for industrial scale production of primycin a large 36-membered non-polyene macrolide lactone antibiotic belonging to the polyketide class of natural products. Even though maximum antibiotic yield has been achieved by empirically optimized two-step fermentation process, little is known about the molecular components and mechanisms underlying the efficient antibiotic production. In order to identify differentially expressed proteins (DEPs) between the pre- and main-fermentation stages of primycin, comparative 2D-PAGE experiments were performed. In total, 98 DEP spots were reproducibly detected, out of which four spots were excised from gels, and identified through MALDI-TOF/TOF mass spectrometry. Peptide mass fingerprint analysis revealed peptide matches to HicB antitoxin for the HicAB toxin-antitoxin system (EHK86651), to a nucleoside diphosphate kinase regulator ((Ndk; EHK81899) and two other proteins with unknown function (EHK88946 and EHK86777).

  9. [The molecular physiological and genetic mechanisms underlying the superb efficacy of quinolones].

    Science.gov (United States)

    Long, Quan-xin; He, Ying; Xie, Jian-ping

    2012-08-01

    The fluoroquinolones are the most widely used broad-spectrum antibiotics, accounting for 18% of global antibacterial market share. They can kill bacteria rapidly with variety of derivatives available. Different quinolones vary significantly in rate and spectrum of killing, oxygen requirement for metabolism and reliance upon protein synthesis. Further understanding the sophisticated mechanisms of action of this important antibiotic family based on the molecular genetic response of bacteria can facilitate the discovery of better quinolone derivatives. Factors such as SOS response, bacterial toxin-antitoxin system, programmed death, chromosome fragmentation and reactive oxygen have been implicated in the action to some extent. "Two steps characteristic" of quinolones killing is also emphasized, which might inspire future better quinolones modification.

  10. High Persister Mutants in Mycobacterium tuberculosis.

    Directory of Open Access Journals (Sweden)

    Heather L Torrey

    Full Text Available Mycobacterium tuberculosis forms drug-tolerant persister cells that are the probable cause of its recalcitrance to antibiotic therapy. While genetically identical to the rest of the population, persisters are dormant, which protects them from killing by bactericidal antibiotics. The mechanism of persister formation in M. tuberculosis is not well understood. In this study, we selected for high persister (hip mutants and characterized them by whole genome sequencing and transcriptome analysis. In parallel, we identified and characterized clinical isolates that naturally produce high levels of persisters. We compared the hip mutants obtained in vitro with clinical isolates to identify candidate persister genes. Genes involved in lipid biosynthesis, carbon metabolism, toxin-antitoxin systems, and transcriptional regulators were among those identified. We also found that clinical hip isolates exhibited greater ex vivo survival than the low persister isolates. Our data suggest that M. tuberculosis persister formation involves multiple pathways, and hip mutants may contribute to the recalcitrance of the infection.

  11. Characterization and comparative overview of complete sequences of the first plasmids of Pandoraea across clinical and non-clinical strains

    Directory of Open Access Journals (Sweden)

    Delicia Yong

    2016-10-01

    Full Text Available To date, information on plasmid analysis in Pandoraea spp. is scarce. To address the gap of knowledge on this, the complete sequences of eight plasmids from Pandoraea spp. namely Pandoraea faecigallinarum DSM 23572 (pPF72-1, pPF72-2, Pandoraea oxalativorans DSM 23570 (pPO70-1, pPO70-2, pPO70-3, pPO70-4, Pandoraea vervacti NS15 (pPV15 and Pandoraea apista DSM 16535 (pPA35 were studied for the first time in this study. The information on plasmid sequences in Pandoraea spp. is useful because these plasmid sequences did not match to any known plasmid sequence deposited in public databases. Replication genes were not identified in some plasmids, a situation that has led to the possibility of host interaction involvement. Some plasmids were also void of par genes and intriguingly, repA gene was also not discovered in these plasmids. This further leads to the hypothesis of host-plasmid interaction. Plasmid stabilization/stability protein-encoding genes were observed in some plasmids but were not established for participating in plasmid segregation. Toxin-antitoxin systems MazEF, VapBC, RelBE, YgiT-MqsR, HigBA and ParDE were identified across the plasmids and their presence would improve plasmid maintenance. Conjugation genes were identified portraying the conjugation ability amongst Pandoraea plasmids. Additionally, we found a shared region amongst some of the plasmids that consists of conjugation genes. The identification of genes involved in replication, segregation, toxin-antitoxin systems and conjugation, would aid the design of drugs to prevent the survival or transmission of plasmids carrying pathogenic properties. Additionally, genes conferring virulence and antibiotic resistance were identified among the plasmids. The observed features in the plasmids shed light on the Pandoraea spp. as opportunistic pathogens.

  12. Analysis of a novel 8.9kb cryptic plasmid from Bacteroides uniformis, its long-term stability and spread within human microbiota.

    Science.gov (United States)

    Shkoporov, Andrei N; Khokhlova, Ekaterina V; Kulagina, Elena V; Smeianov, Vladimir V; Kuchmiy, Anna A; Kafarskaya, Lyudmila I; Efimov, Boris A

    2013-03-01

    The analysis of plasmid content in dominant Bacteroidales order intestinal strains isolated from the same child at a 5 year interval identified a 8.9 kb plasmid in Bacteroides uniformis BUN24 strain isolated at age 6 and indistinguishably sized plasmids in the isolates of B. uniformis, B. vulgatus, B. intesinalis, and Parabacteroides distasonis at age 11. We sequenced a B. uniformis BUN24 plasmid, designated pBUN24, and using molecular surveys of diverse species we established that this 8944bp molecule (G+C content 43.5%) represents a novel family of small cryptic Bacteroidales plasmids. The replication region of pBUN24 was experimentally localized to a 1707-bp fragment that includes a putative repA gene, coding for a protein of Rep_3 superfamily of replication proteins of theta-type plasmids preceded by a putative iteron-containing origin of replication. The other open reading frames (ORFs) identified in pBUN24 sequence include a putative tad-ata-type toxin-antitoxin and mobA-mobB mobilization modules, as well as seven additional cryptic ORFs. The interaction of Tad and Ada components demonstrated by a pull-down assay and the toxicity of Tad in Escherichia coli host suggests the functionality of the plasmid addiction module. Re-sequencing of plasmids in two Bacteroides strains isolated at the age of 11 showed 100% nucleotide identity to pBUN24. This data supports the notion that this plasmid is transmissible to other Bacteroidales strains in the natural ecosystem. The possible roles of toxin-antitoxin system and other proteins encoded by pBUN24 in providing an apparent ecological advantage to the plasmid-harbouring strains of a bacterial symbiont in the human gut deserve further investigation. Copyright © 2012 Elsevier Inc. All rights reserved.

  13. The Chromosomal Toxin Gene yafQ Is a Determinant of Multidrug Tolerance for Escherichia coli Growing in a Biofilm▿

    Science.gov (United States)

    Harrison, Joe J.; Wade, William D.; Akierman, Sarah; Vacchi-Suzzi, Caterina; Stremick, Carol A.; Turner, Raymond J.; Ceri, Howard

    2009-01-01

    Escherichia coli is refractory to elevated doses of antibiotics when it is growing in a biofilm, and this is potentially due to high numbers of multidrug-tolerant persister cells in the surface-adherent population. Previously, the chromosomal toxin-antitoxin loci hipBA and relBE have been linked to the frequency at which persister cells occur in E. coli populations. In the present study, we focused on the dinJ-yafQ-encoded toxin-antitoxin system and hypothesized that deletion of the toxin gene yafQ might influence cell survival in antibiotic-exposed biofilms. By using confocal laser scanning microscopy and viable cell counting, it was determined that a ΔyafQ mutant produced biofilms with a structure and a cell density equivalent to those of the parental strain. In-depth susceptibility testing identified that relative to wild-type E. coli, the ΔyafQ strain had up to a ∼2,400-fold decrease in cell survival after the biofilms were exposed to bactericidal concentrations of cefazolin or tobramycin. Corresponding to these data, controlled overexpression of yafQ from a high-copy-number plasmid resulted in up to a ∼10,000-fold increase in the number of biofilm cells surviving exposure to these bactericidal drugs. In contrast, neither the inactivation nor the overexpression of yafQ affected the tolerance of biofilms to doxycycline or rifampin (rifampicin). Furthermore, deletion of yafQ did not affect the tolerance of stationary-phase planktonic cells to any of the antibacterials tested. These results suggest that yafQ mediates the tolerance of E. coli biofilms to multiple but specific antibiotics; moreover, our data imply that this cellular pathway for persistence is likely different from that of multidrug-tolerant cells in stationary-phase planktonic cell cultures. PMID:19307375

  14. The chromosomal toxin gene yafQ is a determinant of multidrug tolerance for Escherichia coli growing in a biofilm.

    Science.gov (United States)

    Harrison, Joe J; Wade, William D; Akierman, Sarah; Vacchi-Suzzi, Caterina; Stremick, Carol A; Turner, Raymond J; Ceri, Howard

    2009-06-01

    Escherichia coli is refractory to elevated doses of antibiotics when it is growing in a biofilm, and this is potentially due to high numbers of multidrug-tolerant persister cells in the surface-adherent population. Previously, the chromosomal toxin-antitoxin loci hipBA and relBE have been linked to the frequency at which persister cells occur in E. coli populations. In the present study, we focused on the dinJ-yafQ-encoded toxin-antitoxin system and hypothesized that deletion of the toxin gene yafQ might influence cell survival in antibiotic-exposed biofilms. By using confocal laser scanning microscopy and viable cell counting, it was determined that a Delta yafQ mutant produced biofilms with a structure and a cell density equivalent to those of the parental strain. In-depth susceptibility testing identified that relative to wild-type E. coli, the Delta yafQ strain had up to a approximately 2,400-fold decrease in cell survival after the biofilms were exposed to bactericidal concentrations of cefazolin or tobramycin. Corresponding to these data, controlled overexpression of yafQ from a high-copy-number plasmid resulted in up to a approximately 10,000-fold increase in the number of biofilm cells surviving exposure to these bactericidal drugs. In contrast, neither the inactivation nor the overexpression of yafQ affected the tolerance of biofilms to doxycycline or rifampin (rifampicin). Furthermore, deletion of yafQ did not affect the tolerance of stationary-phase planktonic cells to any of the antibacterials tested. These results suggest that yafQ mediates the tolerance of E. coli biofilms to multiple but specific antibiotics; moreover, our data imply that this cellular pathway for persistence is likely different from that of multidrug-tolerant cells in stationary-phase planktonic cell cultures.

  15. Molecular mechanisms of bacterial persistence and phenotypic antibiotic resistance%细菌持留与抗生素表型耐药机制

    Institute of Scientific and Technical Information of China (English)

    崔鹏; 许涛; 张文宏; 张颖

    2016-01-01

    Bacterial persistence refers to a state of reduced metabolic activity that endows a subpopulation of isogenic bacteria with multidrug tolerance. Persisters are phenotypic variants but not mutants. Since its discovery in 1944, bacterial persistence has not received enough attention until recently when its implications in persistent infections and biofilm infections become apparent. Much research has been done in recent years to investigate the mechanisms underlying bacterial persistence and phenotypic antibiotic resistance. The mechanisms of bacterial persistence are complex and the following pathways are involved in persister formation: toxin-antitoxin systems, reduced metabolism, energy production, protein and nucleic acid synthesis, DNA repair and protection, protein degradation, transporters/efflux systems, and transcriptional regulators etc. Although persistence mechanisms are conserved in terms of the gene function and pathways involved among different bacterial species, they may vary in gene homology and relative importance of a given pathway. For example, Escherichia coli toxin-antitoxin systems play an important role in persister formation, while Staphylococcus aureus persister formation does not appear to use toxin-antitoxin systems. Here we provide an update on recent progress in persistence mechanisms using E. coli and S. aureus as models, as well as discuss approaches in the treatment of persistent bacterial infections.%持留菌是细菌群体中一小部分具有表型耐药的细菌。自1944年被发现后,近几十年来因其在慢性持续性感染和生物膜感染中的重要作用而得到越来越多的重视。已有的研究结果表明,细菌持留的机理复杂,涉及的相关信号通路有毒素-抗毒素系统、细胞能量代谢及蛋白核酸合成等生理状态的降低、DNA保护修复系统、蛋白酶系统、反式翻译、外排泵系统等。虽然不同细菌的持留机理有一定的相似性和保守性,但

  16. systems

    Directory of Open Access Journals (Sweden)

    Alexander Leonessa

    2000-01-01

    Full Text Available A nonlinear robust control-system design framework predicated on a hierarchical switching controller architecture parameterized over a set of moving nominal system equilibria is developed. Specifically, using equilibria-dependent Lyapunov functions, a hierarchical nonlinear robust control strategy is developed that robustly stabilizes a given nonlinear system over a prescribed range of system uncertainty by robustly stabilizing a collection of nonlinear controlled uncertain subsystems. The robust switching nonlinear controller architecture is designed based on a generalized (lower semicontinuous Lyapunov function obtained by minimizing a potential function over a given switching set induced by the parameterized nominal system equilibria. The proposed framework robustly stabilizes a compact positively invariant set of a given nonlinear uncertain dynamical system with structured parametric uncertainty. Finally, the efficacy of the proposed approach is demonstrated on a jet engine propulsion control problem with uncertain pressure-flow map data.

  17. Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome

    Directory of Open Access Journals (Sweden)

    Marchesi Julian R

    2010-01-01

    Full Text Available Abstract Background Little is known regarding the pool of mobile genetic elements associated with the human gut microbiome. In this study we employed the culture independent TRACA system to isolate novel plasmids from the human gut microbiota, and a comparative metagenomic analysis to investigate the distribution and relative abundance of functions encoded by these plasmids in the human gut microbiome. Results Novel plasmids were acquired from the human gut microbiome, and homologous nucleotide sequences with high identity (>90% to two plasmids (pTRACA10 and pTRACA22 were identified in the multiple human gut microbiomes analysed here. However, no homologous nucleotide sequences to these plasmids were identified in the murine gut or environmental metagenomes. Functions encoded by the plasmids pTRACA10 and pTRACA22 were found to be more prevalent in the human gut microbiome when compared to microbial communities from other environments. Among the most prevalent functions identified was a putative RelBE toxin-antitoxin (TA addiction module, and subsequent analysis revealed that this was most closely related to putative TA modules from gut associated bacteria belonging to the Firmicutes. A broad phylogenetic distribution of RelE toxin genes was observed in gut associated bacterial species (Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria, but no RelE homologues were identified in gut associated archaeal species. We also provide indirect evidence for the horizontal transfer of these genes between bacterial species belonging to disparate phylogenetic divisions, namely Gram negative Proteobacteria and Gram positive species from the Firmicutes division. Conclusions The application of a culture independent system to capture novel plasmids from the human gut mobile metagenome, coupled with subsequent comparative metagenomic analysis, highlighted the unexpected prevalence of plasmid encoded functions in the gut microbial ecosystem. In

  18. systems

    Directory of Open Access Journals (Sweden)

    Patrick L. Brockett

    1978-01-01

    Full Text Available Suppose S={{Xnj,   j=1,2,…,kn}} is an infinitesimal system of random variables whose centered sums converge in law to a (necessarily infinitely divisible distribution with Levy representation determined by the triple (γ,σ2,M. If {Yj,   j=1,2,…} are independent indentically distributed random variables independent of S, then the system S′={{YjXnj,j=1,2,…,kn}} is obtained by randomizing the scale parameters in S according to the distribution of Y1. We give sufficient conditions on the distribution of Y in terms of an index of convergence of S, to insure that centered sums from S′ be convergent. If such sums converge to a distribution determined by (γ′,(σ′2,Λ, then the exact relationship between (γ,σ2,M and (γ′,(σ′2,Λ is established. Also investigated is when limit distributions from S and S′ are of the same type, and conditions insuring products of random variables belong to the domain of attraction of a stable law.

  19. Genomics of Clostridium tetani.

    Science.gov (United States)

    Brüggemann, Holger; Brzuszkiewicz, Elzbieta; Chapeton-Montes, Diana; Plourde, Lucile; Speck, Denis; Popoff, Michel R

    2015-05-01

    Genomic information about Clostridium tetani, the causative agent of the tetanus disease, is scarce. The genome of strain E88, a strain used in vaccine production, was sequenced about 10 years ago. One additional genome (strain 12124569) has recently been released. Here we report three new genomes of C. tetani and describe major differences among all five C. tetani genomes. They all harbor tetanus-toxin-encoding plasmids that contain highly conserved genes for TeNT (tetanus toxin), TetR (transcriptional regulator of TeNT) and ColT (collagenase), but substantially differ in other plasmid regions. The chromosomes share a large core genome that contains about 85% of all genes of a given chromosome. The non-core chromosome comprises mainly prophage-like genomic regions and genes encoding environmental interaction and defense functions (e.g. surface proteins, restriction-modification systems, toxin-antitoxin systems, CRISPR/Cas systems) and other fitness functions (e.g. transport systems, metabolic activities). This new genome information will help to assess the level of genome plasticity of the species C. tetani and provide the basis for detailed comparative studies.

  20. system

    Science.gov (United States)

    Garcilazo, H.; Valcarce, A.; Vijande, J.

    2017-07-01

    Using local central Yukawa-type Malfliet-Tjon interactions reproducing the low-energy parameters and phase shifts of the nn system, and the latest updates of the nΛ and ΛΛ Nijmegen ESC08c potentials, we study the possible existence of a bound state. Our results indicate that the is unbound, being just above threshold. We discuss the role played by the 1 S 0 nn repulsive term of the Yukawa-type Malfliet-Tjon interaction. Supported by COFAA-IPN (México), Ministerio de Economía, Industria y Competitividad and EU FEDER (FPA2013-47443, FPA2015-69714-REDT, FPA2016-77177), Junta de Castilla y León (SA041U16) and Generalitat Valenciana PrometeoII/2014/066

  1. SYSTEM

    Directory of Open Access Journals (Sweden)

    K. Swarnalatha

    2013-01-01

    Full Text Available Risk analysis of urban aquatic systems due to heavy metals turns significant due to their peculiar properties viz. persis tence, non-degradab ility, toxicity, and accumulation. Akkulam Veli (AV, an urba n tropical lake in south India is subjected to various environmental stresses due to multiple waste discharge, sand mining, developmental activities, tour ism related activitie s etc. Hence, a comprehensive approach is adopted for risk assessment using modified degree of contamination factor, toxicity units based on numerical sediment quality guidelines (SQGs, and potentialecological risk indices. The study revealed the presence of toxic metals such as Cr, C d, Pb and As and the lake is rated under ‘low ecological risk’ category.

  2. Toxin YafQ increases persister cell formation by reducing indole signalling.

    Science.gov (United States)

    Hu, Ying; Kwan, Brian W; Osbourne, Devon O; Benedik, Michael J; Wood, Thomas K

    2015-04-01

    Persister cells survive antibiotic and other environmental stresses by slowing metabolism. Since toxins of toxin/antitoxin (TA) systems have been postulated to be responsible for persister cell formation, we investigated the influence of toxin YafQ of the YafQ/DinJ Escherichia coli TA system on persister cell formation. Under stress, YafQ alters metabolism by cleaving transcripts with in-frame 5'-AAA-G/A-3' sites. Production of YafQ increased persister cell formation with multiple antibiotics, and by investigating changes in protein expression, we found that YafQ reduced tryptophanase levels (TnaA mRNA has 16 putative YafQ cleavage sites). Consistently, TnaA mRNA levels were also reduced by YafQ. Tryptophanase is activated in the stationary phase by the stationary-phase sigma factor RpoS, which was also reduced dramatically upon production of YafQ. Tryptophanase converts tryptophan into indole, and as expected, indole levels were reduced by the production of YafQ. Corroborating the effect of YafQ on persistence, addition of indole reduced persistence. Furthermore, persistence increased upon deleting tnaA, and persistence decreased upon adding tryptophan to the medium to increase indole levels. Also, YafQ production had a much smaller effect on persistence in a strain unable to produce indole. Therefore, YafQ increases persistence by reducing indole, and TA systems are related to cell signalling.

  3. New insights into the mechanisms of acetic acid resistance in Acetobacter pasteurianus using iTRAQ-dependent quantitative proteomic analysis.

    Science.gov (United States)

    Xia, Kai; Zang, Ning; Zhang, Junmei; Zhang, Hong; Li, Yudong; Liu, Ye; Feng, Wei; Liang, Xinle

    2016-12-05

    Acetobacter pasteurianus is the main starter in rice vinegar manufacturing due to its remarkable abilities to resist and produce acetic acid. Although several mechanisms of acetic acid resistance have been proposed and only a few effector proteins have been identified, a comprehensive depiction of the biological processes involved in acetic acid resistance is needed. In this study, iTRAQ-based quantitative proteomic analysis was adopted to investigate the whole proteome of different acidic titers (3.6, 7.1 and 9.3%, w/v) of Acetobacter pasteurianus Ab3 during the vinegar fermentation process. Consequently, 1386 proteins, including 318 differentially expressed proteins (pacetic acid stress, where >150 proteins were differentially expressed. Specifically, proteins involved in amino acid metabolic processes and fatty acid biosynthesis were differentially expressed, which may contribute to the acetic acid resistance of Acetobacter. Transcription factors, two component systems and toxin-antitoxin systems were implicated in the modulatory network at multiple levels. In addition, the identification of proteins involved in redox homeostasis, protein metabolism, and the cell envelope suggested that the whole cellular system is mobilized in response to acid stress. These findings provide a differential proteomic profile of acetic acid resistance in Acetobacter pasteurianus and have potential application to highly acidic rice vinegar manufacturing. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Comparative Genomics of Acetobacterpasteurianus Ab3, an Acetic Acid Producing Strain Isolated from Chinese Traditional Rice Vinegar Meiguichu.

    Science.gov (United States)

    Xia, Kai; Li, Yudong; Sun, Jing; Liang, Xinle

    2016-01-01

    Acetobacter pasteurianus, an acetic acid resistant bacterium belonging to alpha-proteobacteria, has been widely used to produce vinegar in the food industry. To understand the mechanism of its high tolerance to acetic acid and robust ability of oxidizing ethanol to acetic acid (> 12%, w/v), we described the 3.1 Mb complete genome sequence (including 0.28 M plasmid sequence) with a G+C content of 52.4% of A. pasteurianus Ab3, which was isolated from the traditional Chinese rice vinegar (Meiguichu) fermentation process. Automatic annotation of the complete genome revealed 2,786 protein-coding genes and 73 RNA genes. The comparative genome analysis among A. pasteurianus strains revealed that A. pasteurianus Ab3 possesses many unique genes potentially involved in acetic acid resistance mechanisms. In particular, two-component systems or toxin-antitoxin systems may be the signal pathway and modulatory network in A. pasteurianus to cope with acid stress. In addition, the large numbers of unique transport systems may also be related to its acid resistance capacity and cell fitness. Our results provide new clues to understanding the underlying mechanisms of acetic acid resistance in Acetobacter species and guiding industrial strain breeding for vinegar fermentation processes.

  5. Molecular characterization of a 21.4 kilobase antibiotic resistance plasmid from an α-hemolytic Escherichia coli O108:H- human clinical isolate.

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    Fay E Dawes

    Full Text Available This study characterizes the 21.4 kilobase plasmid pECTm80 isolated from Escherichia coli strain 80, an α hemolytic human clinical diarrhoeal isolate (serotype O108:H-. DNA sequence analysis of pECTm80 revealed it belonged to incompatibility group X1, and contained plasmid partition and toxin-antitoxin systems, an R6K-like triple origin (ori replication system, genes required for replication regulation, insertion sequences IS1R, ISEc37 and a truncated transposase gene (Tn3-like ΔtnpA of the Tn3 family, and carried a class 2 integron. The class 2 integron of pECTm80 contains an intact cassette array dfrA1-sat2, encoding resistance to trimethoprim and streptothricin, and an aadA1 gene cassette truncated by the insertion of IS1R. The complex plasmid replication system includes α, β and γ origins of replication. Pairwise BLASTn comparison of pECTm80 with plasmid pE001 reveals a conserved plasmid backbone suggestive of a common ancestral lineage. Plasmid pECTm80 is of potential clinical importance, as it carries multiple genes to ensure its stable maintenance through successive bacterial cell divisions and multiple antibiotic resistance genes.

  6. Escherichia coli Quorum-Sensing EDF, A Peptide Generated by Novel Multiple Distinct Mechanisms and Regulated by trans-Translation

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    Sathish Kumar

    2016-01-01

    Full Text Available Eshcerichia coli mazEF is a stress-induced toxin-antitoxin module mediating cell death and requiring a quorum-sensing (QS extracellular death factor (EDF, the pentapeptide NNWNN. Here we uncovered several distinct molecular mechanisms involved in its generation from the zwf mRNA encoding glucose-6-phosphate dehydrogenase. In particular, we show that, under stress conditions, the endoribonuclease MazF cleaves specific ACA sites, thereby generating a leaderless zwf mRNA which is truncated 30 codons after the EDF-encoding region. Since the nascent ribosome peptide exit tunnel can accommodate up to 40 amino acids, this arrangement allows the localization of the EDF residues inside the tunnel when the ribosome is stalled at the truncation site. Moreover, ribosome stalling activates the trans-translation system, which provides a means for the involvement of ClpPX in EDF generation. Furthermore, the trans-translation is described as a regulatory system that attenuated the generation of EDF, leading to low levels of EDF in the single cell. Therefore, the threshold EDF molecule concentration required is achieved only by the whole population, as expected for QS.

  7. Physiologic Stresses Reveal a Salmonella Persister State and TA Family Toxins Modulate Tolerance to These Stresses.

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    Eugenia Silva-Herzog

    Full Text Available Bacterial persister cells are considered a basis for chronic infections and relapse caused by bacterial pathogens. Persisters are phenotypic variants characterized by low metabolic activity and slow or no replication. This low metabolic state increases pathogen tolerance to antibiotics and host immune defenses that target actively growing cells. In this study we demonstrate that within a population of Salmonella enterica serotype Typhimurium, a small percentage of bacteria are reversibly tolerant to specific stressors that mimic the macrophage host environment. Numerous studies show that Toxin-Antitoxin (TA systems contribute to persister states, based on toxin inhibition of bacterial metabolism or growth. To identify toxins that may promote a persister state in response to host-associated stressors, we analyzed the six TA loci specific to S. enterica serotypes that cause systemic infection in mammals, including five RelBE family members and one VapBC member. Deletion of TA loci increased or decreased tolerance depending on the stress conditions. Similarly, exogenous expression of toxins had mixed effects on bacterial survival in response to stress. In macrophages, S. Typhimurium induced expression of three of the toxins examined. These observations indicate that distinct toxin family members have protective capabilities for specific stressors but also suggest that TA loci have both positive and negative effects on tolerance.

  8. Physiologic Stresses Reveal a Salmonella Persister State and TA Family Toxins Modulate Tolerance to These Stresses.

    Science.gov (United States)

    Silva-Herzog, Eugenia; McDonald, Erin M; Crooks, Amy L; Detweiler, Corrella S

    2015-01-01

    Bacterial persister cells are considered a basis for chronic infections and relapse caused by bacterial pathogens. Persisters are phenotypic variants characterized by low metabolic activity and slow or no replication. This low metabolic state increases pathogen tolerance to antibiotics and host immune defenses that target actively growing cells. In this study we demonstrate that within a population of Salmonella enterica serotype Typhimurium, a small percentage of bacteria are reversibly tolerant to specific stressors that mimic the macrophage host environment. Numerous studies show that Toxin-Antitoxin (TA) systems contribute to persister states, based on toxin inhibition of bacterial metabolism or growth. To identify toxins that may promote a persister state in response to host-associated stressors, we analyzed the six TA loci specific to S. enterica serotypes that cause systemic infection in mammals, including five RelBE family members and one VapBC member. Deletion of TA loci increased or decreased tolerance depending on the stress conditions. Similarly, exogenous expression of toxins had mixed effects on bacterial survival in response to stress. In macrophages, S. Typhimurium induced expression of three of the toxins examined. These observations indicate that distinct toxin family members have protective capabilities for specific stressors but also suggest that TA loci have both positive and negative effects on tolerance.

  9. Effect of clpP and clpC deletion on persister cell number in Staphylococcus aureus.

    Science.gov (United States)

    Springer, Matthew T; Singh, Vineet K; Cheung, Ambrose L; Donegan, Niles P; Chamberlain, Neal R

    2016-08-01

    Staphylococcus aureus is responsible for a wide variety of infections that include superficial skin and soft tissue infections, septicaemia, central nervous system infections, endocarditis, osteomyelitis and pneumonia. Others have demonstrated the importance of toxin-antitoxin (TA) modules in the formation of persisters and the role of the Clp proteolytic system in the regulation of these TA modules. This study was conducted to determine the effect of clpP and clpC deletion on S. aureus persister cell numbers following antibiotic treatment. Deletion of clpP resulted in a significant decrease in persister cells following treatment with oxacillin and erythromycin but not with levofloxacin and daptomycin. Deletion of clpC resulted in a decrease in persister cells following treatment with oxacillin. These differences were dependent on the antibiotic class and the CFU ml-1 in which the cells were treated. Persister revival assays for all the bacterial strains in these studies demonstrated a significant delay in resumption of growth characteristic of persister cells, indicating that the surviving organisms in this study were not likely due to spontaneous antibiotic resistance. Based on our results, ClpP and possibly ClpC play a role in persister cell formation or maintenance, and this effect is dependent on antibiotic class and the CFU ml-1 or the growth phase of the cells.

  10. Novel Escherichia coli RF1 mutants with decreased translation termination activity and increased sensitivity to the cytotoxic effect of the bacterial toxins Kid and RelE.

    Science.gov (United States)

    Diago-Navarro, Elizabeth; Mora, Liliana; Buckingham, Richard H; Díaz-Orejas, Ramón; Lemonnier, Marc

    2009-01-01

    Novel mutations in prfA, the gene for the polypeptide release factor RF1 of Escherichia coli, were isolated using a positive genetic screen based on the parD (kis, kid) toxin-antitoxin system. This original approach allowed the direct selection of mutants with altered translational termination efficiency at UAG codons. The isolated prfA mutants displayed a approximately 10-fold decrease in UAG termination efficiency with no significant changes in RF1 stability in vivo. All three mutations, G121S, G301S and R303H, were situated close to the nonsense codon recognition site in RF1:ribosome complexes. The prfA mutants displayed increased sensitivity to the RelE toxin encoded by the relBE system of E. coli, thus providing in vivo support for the functional interaction between RF1 and RelE. The prfA mutants also showed increased sensitivity to the Kid toxin. Since this toxin can cleave RNA in a ribosome-independent manner, this result was not anticipated and provided first evidence for the involvement of RF1 in the pathway of Kid toxicity. The sensitivity of the prfA mutants to RelE and Kid was restored to normal levels upon overproduction of the wild-type RF1 protein. We discuss these results and their utility for the design of novel antibacterial strategies in the light of the recently reported structure of ribosome-bound RF1.

  11. Differential Rickettsial Transcription in Bloodfeeding and Non-Bloodfeeding Arthropod Hosts

    Science.gov (United States)

    Verhoeve, Victoria I.; Jirakanwisal, Krit; Utsuki, Tadanobu; Macaluso, Kevin R.

    2016-01-01

    Crucial factors influencing the epidemiology of Rickettsia felis rickettsiosis include pathogenesis and transmission. Detection of R. felis DNA in a number of arthropod species has been reported, with characterized isolates, R. felis strain LSU and strain LSU-Lb, generated from the cat flea, Ctenocephalides felis, and the non-hematophagous booklouse, Liposcelis bostrychophila, respectively. While it is realized that strain influence on host biology varies, the rickettsial response to these distinct host environments remained undefined. To identify a panel of potential rickettsial transmission determinants in the cat flea, the transcriptional profile for these two strains of R. felis were compared in their arthropod hosts using RNAseq. Rickettsial genes with increased transcription in the flea as compared to the booklouse were identified. Genes previously associated with bacterial virulence including LPS biosynthesis, Type IV secretion system, ABC transporters, and a toxin-antitoxin system were selected for further study. Transcription of putative virulence-associated genes was determined in a flea infection bioassay for both strains of R. felis. A host-dependent transcriptional profile during bloodfeeding, specifically, an increased expression of selected transcripts in newly infected cat fleas and flea feces was detected when compared to arthropod cell culture and incubation in vertebrate blood. Together, these studies have identified novel, host-dependent rickettsial factors that likely contribute to successful horizontal transmission by bloodfeeding arthropods. PMID:27662479

  12. Orphan Toxin OrtT (YdcX of Escherichia coli Reduces Growth during the Stringent Response

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    Sabina Islam

    2015-01-01

    Full Text Available Toxin/antitoxin (TA systems are nearly universal in prokaryotes; toxins are paired with antitoxins which inactivate them until the toxins are utilized. Here we explore whether toxins may function alone; i.e., whether a toxin which lacks a corresponding antitoxin (orphan toxin is physiologically relevant. By focusing on a homologous protein of the membrane-damaging toxin GhoT of the Escherichia coli GhoT/GhoS type V TA system, we found that YdcX (renamed OrtT for orphan toxin related to tetrahydrofolate is toxic but is not part of TA pair. OrtT is not inactivated by neighboring YdcY (which is demonstrated to be a protein, nor is it inactivated by antitoxin GhoS. Also, OrtT is not inactivated by small RNA upstream or downstream of ortT. Moreover, screening a genomic library did not identify an antitoxin partner for OrtT. OrtT is a protein and its toxicity stems from membrane damage as evidenced by transmission electron microscopy and cell lysis. Furthermore, OrtT reduces cell growth and metabolism in the presence of both antimicrobials trimethoprim and sulfamethoxazole; these antimicrobials induce the stringent response by inhibiting tetrahydrofolate synthesis. Therefore, we demonstrate that OrtT acts as an independent toxin to reduce growth during stress related to amino acid and DNA synthesis.

  13. The ClpXP protease is responsible for the degradation of the Epsilon antidote to the Zeta toxin of the streptococcal pSM19035 plasmid.

    Science.gov (United States)

    Brzozowska, Iwona; Zielenkiewicz, Urszula

    2014-03-14

    Most bacterial genomes contain different types of toxin-antitoxin (TA) systems. The ω-ε-ζ proteinaceous type II TA cassette from the streptococcal pSM19035 plasmid is a member of the ε/ζ family, which is commonly found in multiresistance plasmids and chromosomes of various human pathogens. Regulation of type II TA systems relies on the proteolysis of antitoxin proteins. Under normal conditions, the Epsilon antidote neutralizes the Zeta toxin through the formation of a tight complex. In this study, we show, using both in vivo and in vitro analyses, that the ClpXP protease is responsible for Epsilon antitoxin degradation. Using in vivo studies, we examined the stability of the plasmids with active or inactive ω-ε-ζ TA cassettes in B. subtilis mutants that were defective for different proteases. Using in vitro assays, the degradation of purified His6-Epsilon by the His6-LonBs, ClpPBs, and ClpXBs proteases from B. subtilis was analyzed. Additionally, we showed that purified Zeta toxin protects the Epsilon protein from rapid ClpXP-catalyzed degradation.

  14. Ethanol-induced stress response of Staphylococcus aureus.

    Science.gov (United States)

    Pando, Jasmine M; Pfeltz, Richard F; Cuaron, Jesus A; Nagarajan, Vijayaraj; Mishra, Mukti N; Torres, Nathanial J; Elasri, Mohamed O; Wilkinson, Brian J; Gustafson, John E

    2017-09-01

    Transcriptional profiles of 2 unrelated clinical methicillin-resistant Staphylococcus aureus (MRSA) isolates were analyzed following 10% (v/v) ethanol challenge (15 min), which arrested growth but did not reduce viability. Ethanol-induced stress (EIS) resulted in differential gene expression of 1091 genes, 600 common to both strains, of which 291 were upregulated. With the exception of the downregulation of genes involved with osmotic stress functions, EIS resulted in the upregulation of genes that contribute to stress response networks, notably those altered by oxidative stress, protein quality control in general, and heat shock in particular. In addition, genes involved with transcription, translation, and nucleotide biosynthesis were downregulated. relP, which encodes a small alarmone synthetase (RelP), was highly upregulated in both MRSA strains following ethanol challenge, and relP inactivation experiments indicated that this gene contributed to EIS growth arrest. A number of persistence-associated genes were also upregulated during EIS, including those that encode toxin-antitoxin systems. Overall, transcriptional profiling indicated that the MRSA investigated responded to EIS by entering a state of dormancy and by altering the expression of elements from cross protective stress response systems in an effort to protect preexisting proteins.

  15. Characterization of the Lactobacillus plantarum plasmid pCD033 and generation of the plasmid free strain L. plantarum 3NSH.

    Science.gov (United States)

    Heiss, Silvia; Grabherr, Reingard; Heinl, Stefan

    2015-09-01

    Lactobacillus plantarum CD033, a strain isolated from grass silage in Austria, harbors a 7.9 kb plasmid designated pCD033. Sequence analysis identified 14 open reading frames and 8 of these were supposed to be putative coding sequences. Gene annotation revealed no putative essential genes being plasmid encoded, but a plasmid addiction system based on a PemI/PemK-like toxin-antitoxin system, able to stabilize plasmid maintenance. Absence of a replication initiation protein, a double strand origin as well as a single strand origin on plasmid pCD033 suggests replication via a new type of theta mechanism, whereby plasmid replication is potentially initiated and regulated by non-coding RNA. Detailed examination of segregational stability of plasmid vectors consisting of pCD033-fragments, combined with a selection marker, resulted in definition of a stably maintained minimal replicon. A gene encoding a RepB/OrfX-like protein was found to be not essential for plasmid replication. Alignment of the amino acid sequence of this protein with related proteins unveiled a highly conserved amino acid motif (LLDQQQ). L. plantarum CD033 was cured of pCD033 resulting in the novel plasmid free strain L. plantarum 3NSH. Plasmid curing demonstrated that no essential features are provided by pCD033 under laboratory conditions.

  16. A novel membrane-bound toxin for cell division, CptA (YgfX), inhibits polymerization of cytoskeleton proteins, FtsZ and MreB, in Escherichia coli.

    Science.gov (United States)

    Masuda, Hisako; Tan, Qian; Awano, Naoki; Yamaguchi, Yoshihiro; Inouye, Masayori

    2012-03-01

    Nearly all free-living bacteria carry toxin-antitoxin (TA) systems on their genomes, through which cell growth and death are regulated. Toxins target a variety of essential cellular functions, including DNA replication, translation, and cell division. Here, we identified a novel toxin, YgfX, on the Escherichia coli genome. The toxin, consisting of 135 residues, is composed of the N-terminal membrane domain, which encompasses two transmembrane segments, and the C-terminal cytoplasmic domain. Upon YgfX expression, the cells were initially elongated and then the middle portion of the cells became inflated to form a lemon shape. YgfX was found to interact with MreB and FtsZ, two essential cytoskeletal proteins in E. coli. The cytoplasmic domain [YgfX(C)] was found to be responsible for the YgfX toxicity, as purified YgfX(C) was found to block the polymerization of FtsZ and MreB in vitro. YgfY, located immediately upstream of YgfX, was shown to be the cognate antitoxin; notably, YgfX is the first membrane-associating toxin in bacterial TA systems. We propose to rename the toxin and the antitoxin as CptA and CptB (for Cytoskeleton Polymerization inhibiting Toxin), respectively.

  17. Dual Toxic-Peptide-Coding Staphylococcus aureus RNA under Antisense Regulation Targets Host Cells and Bacterial Rivals Unequally

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    Marie-Laure Pinel-Marie

    2014-04-01

    Full Text Available Produced from the pathogenicity islands of Staphylococcus aureus clinical isolates, stable SprG1 RNA encodes two peptides from a single internal reading frame. These two peptides accumulate at the membrane, and inducing their expression triggers S. aureus death. Replacement of the two initiation codons by termination signals reverses this toxicity. During growth, cis-antisense RNA SprF1 is expressed, preventing mortality by reducing SprG1 RNA and peptide levels. The peptides are secreted extracellularly, where they lyse human host erythrocytes, a process performed more efficiently by the longer peptide. The two peptides also inactivate Gram-negative and -positive bacteria, with the shorter peptide more effective against S. aureus rivals. Two peptides are secreted from an individual RNA containing two functional initiation codons. Thus, we present an unconventional type I toxin-antitoxin system expressed from a human pathogen producing two hemolytic and antibacterial peptides from a dual-coding RNA, negatively regulated by a dual-acting antisense RNA.

  18. Comparative Genomics of Carriage and Disease Isolates of Streptococcus pneumoniae Serotype 22F Reveals Lineage-Specific Divergence and Niche Adaptation.

    Science.gov (United States)

    Cleary, David W; Devine, Vanessa T; Jefferies, Johanna M C; Webb, Jeremy S; Bentley, Stephen D; Gladstone, Rebecca A; Faust, Saul N; Clarke, Stuart C

    2016-04-21

    Streptococcus pneumoniae is a major cause of meningitis, sepsis, and pneumonia worldwide. Pneumococcal conjugate vaccines have been part of the United Kingdom's childhood immunization program since 2006 and have significantly reduced the incidence of disease due to vaccine efficacy in reducing carriage in the population. Here we isolated two clones of 22F (an emerging serotype of clinical concern, multilocus sequence types 433 and 698) and conducted comparative genomic analysis on four isolates, paired by Sequence Type (ST) with one of each pair being derived from carriage and the other disease (sepsis). The most compelling observation was of nonsynonymous mutations in pgdA, encoding peptidoglycan N-acetylglucosamine deacetylase A, which was found in the carriage isolates of both ST433 and 698. Deacetylation of pneumococcal peptidoglycan is known to enable resistance to lysozyme upon invasion. Althought no other clear genotypic signatures related to disease or carriage could be determined, additional intriguing comparisons between the two STs were possible. These include the presence of an intact prophage, in addition to numerous additional phage insertions, within the carriage isolate of ST433. Contrasting gene repertoires related to virulence and colonization, including bacteriocins, lantibiotics, and toxin--antitoxin systems, were also observed.

  19. Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new Thermococcus plasmids.

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    Mart Krupovic

    Full Text Available Mobilome of hyperthermophilic archaea dwelling in deep-sea hydrothermal vents is poorly characterized. To gain insight into genetic diversity and dynamics of mobile genetic elements in these environments we have sequenced five new plasmids from different Thermococcus strains that have been isolated from geographically remote hydrothermal vents. The plasmids were ascribed to two subfamilies, pTN2-like and pEXT9a-like. Gene content and phylogenetic analyses illuminated a robust connection between pTN2-like plasmids and Pyrococcus abyssi virus 1 (PAV1, with roughly half of the viral genome being composed of genes that have homologues in plasmids. Unexpectedly, pEXT9a-like plasmids were found to be closely related to the previously sequenced plasmid pMETVU01 from Methanocaldococcus vulcanius M7. Our data suggests that the latter observation is most compatible with an unprecedented horizontal transfer of a pEXT9a-like plasmid from Thermococcales to Methanococcales. Gene content analysis revealed that thermococcal plasmids encode Hfq-like proteins and toxin-antitoxin (TA systems of two different families, VapBC and RelBE. Notably, although abundant in archaeal genomes, to our knowledge, TA and hfq-like genes have not been previously found in archaeal plasmids or viruses. Finally, the plasmids described here might prove to be useful in developing new genetic tools for hyperthermophiles.

  20. The Mechanisms of Virulence Regulation by Small Noncoding RNAs in Low GC Gram-Positive Pathogens

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    Stephanie Pitman

    2015-12-01

    Full Text Available The discovery of small noncoding regulatory RNAs (sRNAs in bacteria has grown tremendously recently, giving new insights into gene regulation. The implementation of computational analysis and RNA sequencing has provided new tools to discover and analyze potential sRNAs. Small regulatory RNAs that act by base-pairing to target mRNAs have been found to be ubiquitous and are the most abundant class of post-transcriptional regulators in bacteria. The majority of sRNA studies has been limited to E. coli and other gram-negative bacteria. However, examples of sRNAs in gram-positive bacteria are still plentiful although the detailed gene regulation mechanisms behind them are not as well understood. Strict virulence control is critical for a pathogen’s survival and many sRNAs have been found to be involved in that process. This review outlines the targets and currently known mechanisms of trans-acting sRNAs involved in virulence regulation in various gram-positive pathogens. In addition, their shared characteristics such as CU interaction motifs, the role of Hfq, and involvement in two-component regulators, riboswitches, quorum sensing, or toxin/antitoxin systems are described.

  1. Toxic shock syndrome toxin-1, not α-toxin, mediated Bundaberg fatalities.

    Science.gov (United States)

    Mueller, Elizabeth A; Merriman, Joseph A; Schlievert, Patrick M

    2015-12-01

    The 1928 Bundaberg disaster is one of the greatest vaccine tragedies in history. Of 21 children immunized with a diphtheria toxin-antitoxin preparation contaminated with Staphylococcus aureus, 18 developed life-threatening disease and 12 died within 48  h. Historically, the deaths have been attributed to α-toxin, a secreted cytotoxin produced by most S. aureus strains, yet the ability of the Bundaberg contaminant microbe to produce the toxin has never been verified. For the first time, the ability of the original strain to produce α-toxin and other virulence factors is investigated. The study investigates the genetic and regulatory loci mediating α-toxin expression by PCR and assesses production of the cytotoxin in vitro using an erythrocyte haemolysis assay. This analysis is extended to other secreted virulence factors produced by the strain, and their sufficiency to cause lethality in New Zealand white rabbits is determined. Although the strain possesses a wild-type allele for α-toxin, it must have a defective regulatory system, which is responsible for the strain's minimal α-toxin production. The strain encodes and produces staphylococcal superantigens, including toxic shock syndrome toxin-1 (TSST-1), which is sufficient to cause lethality in patients. The findings cast doubt on the belief that α-toxin is the major virulence factor responsible for the Bundaberg fatalities and point to the superantigen TSST-1 as the cause of the disaster.

  2. The SecB-like chaperone Rv1957 from Mycobacterium tuberculosis: crystallization and X-ray crystallographic analysis.

    Science.gov (United States)

    Lu, Zuokun; Wang, Han; Yu, TingTing

    2016-06-01

    Protein export is important in all bacteria, and bacteria have evolved specialized export machineries to fulfil this task. In Mycobacterium tuberculosis, the causative agent of tuberculosis, the general secretion pathway (Sec pathway) is conserved and is essential in performing the export of proteins. The bacterial Sec pathway post-translationally exports unfolded proteins out of the cytoplasm, and the core of the Sec pathway is composed of a heterotrimeric membrane-embedded channel, SecYEG, and two cytosolic components, SecA and SecB. SecB functions by stabilizing unfolded proteins, maintaining them in an export-competent state. Although SecB is mainly found in Proteobacteria, a SecB-like protein, Rv1957, that controls a stress-response toxin-antitoxin system, is found in M. tuberculosis. Rv1957 can also functionally replace the Escherichia coli SecB chaperone both in vivo and in vitro. In this work, the production, crystallization and X-ray crystallographic analysis of Rv1957 are reported. Notably, diffraction-quality crystals were obtained only at high concentrations of dimethyl sulfoxide, i.e. about 12%(v/v). The crystals of Rv1957 belonged to space group P212121, with unit-cell parameters a = 64.5, b = 92.0, c = 115.4 Å.

  3. Three dimensional structure of the MqsR:MqsA complex: a novel TA pair comprised of a toxin homologous to RelE and an antitoxin with unique properties.

    Directory of Open Access Journals (Sweden)

    Breann L Brown

    2009-12-01

    Full Text Available One mechanism by which bacteria survive environmental stress is through the formation of bacterial persisters, a sub-population of genetically identical quiescent cells that exhibit multidrug tolerance and are highly enriched in bacterial toxins. Recently, the Escherichia coli gene mqsR (b3022 was identified as the gene most highly upregulated in persisters. Here, we report multiple individual and complex three-dimensional structures of MqsR and its antitoxin MqsA (B3021, which reveal that MqsR:MqsA form a novel toxin:antitoxin (TA pair. MqsR adopts an alpha/beta fold that is homologous with the RelE/YoeB family of bacterial ribonuclease toxins. MqsA is an elongated dimer that neutralizes MqsR toxicity. As expected for a TA pair, MqsA binds its own promoter. Unexpectedly, it also binds the promoters of genes important for E. coli physiology (e.g., mcbR, spy. Unlike canonical antitoxins, MqsA is also structured throughout its entire sequence, binds zinc and coordinates DNA via its C- and not N-terminal domain. These studies reveal that TA systems, especially the antitoxins, are significantly more diverse than previously recognized and provide new insights into the role of toxins in maintaining the persister state.

  4. The role of bacteriocins as selfish genetic elements.

    Science.gov (United States)

    Inglis, R Fredrik; Bayramoglu, Bihter; Gillor, Osnat; Ackermann, Martin

    2013-06-23

    Bacteria produce a wide arsenal of toxic compounds in order to kill competing species. Bacteriocins, protein-based toxins produced by nearly all bacteria, have generally been considered a ubiquitous anti-competitor strategy, used to kill competing bacterial strains. Some of these bacteriocins are encoded on plasmids, which also code for closely linked immunity compounds (thereby rendering toxin producing cells immune to their own toxin). However, the production of bacteriocins can also be interpreted as a means to promote plasmid stability by preferentially selecting for cells carrying the plasmid. If, for example, a cell were to lose the plasmid, it would no longer produce the immunity compound and would be killed by its bacteriocin-producing clone mates. In this respect, bacteriocins can be regarded as similar to previously described toxin-antitoxin systems that are able promote the stable transmission of plasmids to daughter cells. In order to test this prediction, we carried out an experimental evolution study using the bacterium Escherichia coli, finding that bacteriocins can indeed select for the stable maintenance of plasmids. This suggests that bacteriocins can act primarily as selfish genetic elements promoting their own transmission in the population, which may help explain their unique ecology and evolution.

  5. HicA of Escherichia coli defines a novel family of translation-independent mRNA interferases in bacteria and archaea

    DEFF Research Database (Denmark)

    Jørgensen, Mikkel G; Pandey, Deo P; Jaskolska, Milena

    2009-01-01

    Toxin-antitoxin (TA) loci are common in free-living bacteria and archaea. TA loci encode a stable toxin that is neutralized by a metabolically unstable antitoxin. The antitoxin can be either a protein or an antisense RNA. So far, six different TA gene families, in which the antitoxins are proteins......, have been identified. Recently, Makarova et al. (K. S. Makarova, N. V. Grishin, and E. V. Koonin, Bioinformatics 22:2581-2584, 2006) suggested that the hicAB loci constitute a novel TA gene family. Using the hicAB locus of Escherichia coli K-12 as a model system, we present evidence that supports...... this inference: expression of the small HicA protein (58 amino acids [aa]) induced cleavage in three model mRNAs and tmRNA. Concomitantly, the global rate of translation was severely reduced. Using tmRNA as a substrate, we show that HicA-induced cleavage does not require the target RNA to be translated...

  6. Multitasking SecB chaperones in bacteria

    Directory of Open Access Journals (Sweden)

    Ambre eSala

    2014-12-01

    Full Text Available Protein export in bacteria is facilitated by the canonical SecB chaperone, which binds to unfolded precursor proteins, maintains them in a translocation competent state and specifically cooperates with the translocase motor SecA to ensure their proper targeting to the Sec translocon at the cytoplasmic membrane. Besides its key contribution to the Sec pathway, SecB chaperone tasking is critical for the secretion of the Sec-independent heme-binding protein HasA and actively contributes to the cellular network of chaperones that control general proteostasis in Escherichia coli, as judged by the significant interplay found between SecB and the Trigger Factor, DnaK and GroEL chaperones. Although SecB is mainly a proteobacterial chaperone associated with the presence of an outer membrane and outer membrane proteins, secB-like genes are also found in Gram-positive bacteria as well as in certain phages and plasmids, thus suggesting alternative functions. In addition, a SecB-like protein is also present in the major human pathogen M. tuberculosis where it specifically controls a stress-responsive toxin-antitoxin (TA system. This review focuses on such very diverse chaperone functions of SecB, both in E. coli and in other unrelated bacteria.

  7. Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new Thermococcus plasmids.

    Science.gov (United States)

    Krupovic, Mart; Gonnet, Mathieu; Hania, Wajdi Ben; Forterre, Patrick; Erauso, Gaël

    2013-01-01

    Mobilome of hyperthermophilic archaea dwelling in deep-sea hydrothermal vents is poorly characterized. To gain insight into genetic diversity and dynamics of mobile genetic elements in these environments we have sequenced five new plasmids from different Thermococcus strains that have been isolated from geographically remote hydrothermal vents. The plasmids were ascribed to two subfamilies, pTN2-like and pEXT9a-like. Gene content and phylogenetic analyses illuminated a robust connection between pTN2-like plasmids and Pyrococcus abyssi virus 1 (PAV1), with roughly half of the viral genome being composed of genes that have homologues in plasmids. Unexpectedly, pEXT9a-like plasmids were found to be closely related to the previously sequenced plasmid pMETVU01 from Methanocaldococcus vulcanius M7. Our data suggests that the latter observation is most compatible with an unprecedented horizontal transfer of a pEXT9a-like plasmid from Thermococcales to Methanococcales. Gene content analysis revealed that thermococcal plasmids encode Hfq-like proteins and toxin-antitoxin (TA) systems of two different families, VapBC and RelBE. Notably, although abundant in archaeal genomes, to our knowledge, TA and hfq-like genes have not been previously found in archaeal plasmids or viruses. Finally, the plasmids described here might prove to be useful in developing new genetic tools for hyperthermophiles.

  8. Mechanisms of post-transcriptional gene regulation in bacterial biofilms

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    Viveka eVadyvaloo

    2014-03-01

    Full Text Available Abstract Biofilms are characterized by a dense multicellular community of microorganisms that can be formed by the attachment of bacteria to an inert surface and to each other. The development of biofilm involves the initial attachment of planktonic bacteria to a surface, followed by replication, cell-to-cell adhesion to form microcolonies, maturation and detachment. Mature biofilms are embedded in a self-produced extracellular polymeric matrix composed primarily of bacterial-derived exopolysaccharides, specialized proteins, adhesins and occasionally DNA. Because the synthesis and assembly of biofilm matrix components is an exceptionally complex process, the transition between its different phases requires the coordinate expression and simultaneous regulation of many genes by complex genetic networks involving all levels of gene regulation. The finely controlled intracellular level of the chemical second messenger molecule, cyclic-di-GMP is central to the post-transcriptional mechanisms governing the switch between the motile planktonic lifestyle and the sessile biofilm forming state in many bacteria. Several other post-transcriptional regulatory mechanisms are known to dictate biofilm development and assembly and these include RNA-binding proteins, small non-coding RNAs, toxin-antitoxin systems, riboswitches and RNases. Post-transcriptional regulation is therefore a powerful molecular mechanism employed by bacteria to rapidly adjust to the changing environment and to fine tune gene expression to the developmental needs of the cell. In this review, we discuss post-transcriptional mechanisms that influence the biofilm developmental cycle in a variety of pathogenic bacteria.

  9. Starvation, together with the SOS response, mediates high biofilm-specific tolerance to the fluoroquinolone ofloxacin.

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    Steve P Bernier

    Full Text Available High levels of antibiotic tolerance are a hallmark of bacterial biofilms. In contrast to well-characterized inherited antibiotic resistance, molecular mechanisms leading to reversible and transient antibiotic tolerance displayed by biofilm bacteria are still poorly understood. The physiological heterogeneity of biofilms influences the formation of transient specialized subpopulations that may be more tolerant to antibiotics. In this study, we used random transposon mutagenesis to identify biofilm-specific tolerant mutants normally exhibited by subpopulations located in specialized niches of heterogeneous biofilms. Using Escherichia coli as a model organism, we demonstrated, through identification of amino acid auxotroph mutants, that starved biofilms exhibited significantly greater tolerance towards fluoroquinolone ofloxacin than their planktonic counterparts. We demonstrated that the biofilm-associated tolerance to ofloxacin was fully dependent on a functional SOS response upon starvation to both amino acids and carbon source and partially dependent on the stringent response upon leucine starvation. However, the biofilm-specific ofloxacin increased tolerance did not involve any of the SOS-induced toxin-antitoxin systems previously associated with formation of highly tolerant persisters. We further demonstrated that ofloxacin tolerance was induced as a function of biofilm age, which was dependent on the SOS response. Our results therefore show that the SOS stress response induced in heterogeneous and nutrient-deprived biofilm microenvironments is a molecular mechanism leading to biofilm-specific high tolerance to the fluoroquinolone ofloxacin.

  10. Metabolic aspects of bacterial persisters

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    Marcel ePrax

    2014-10-01

    Full Text Available Persister cells form a multi-drug tolerant subpopulation within an isogenic culture of bacteria that are genetically susceptible to antibiotics. Studies with different Gram negative and Gram positive bacteria have identified a large number of genes associated with the persister state. In contrast, the revelation of persister metabolism has only been addressed recently. We here summarize metabolic aspects of persisters, which includes an overview about the bifunctional role of selected carbohydrates as both triggers for the exit from the drug tolerant state and metabolites which persisters feed on. Also alarmones as indicators for starvation have been shown to influence persister levels via different signaling cascades involving the activation of toxin-antitoxin systems and other regulatory factors. Finally, recent data obtained by 13C-isotopologue profiling demonstrated an active amino acid anabolism in Staphylococcus aureus cultures challenged with high drug concentrations. Understanding the metabolism of persister cells poses challenges but also paves the way for the development of anti-persister compounds.

  11. Persistence Increases in the Absence of the Alarmone Guanosine Tetraphosphate by Reducing Cell Growth.

    Science.gov (United States)

    Chowdhury, Nityananda; Kwan, Brian W; Wood, Thomas K

    2016-02-03

    Most bacterial cells are stressed, and as a result, some become tolerant to antibiotics by entering a dormant state known as persistence. The key intracellular metabolite that has been linked to this persister state is guanosine tetraphosphate (ppGpp), the alarmone that was first linked to nutrient stress. In Escherichia coli, ppGpp redirects protein production during nutrient stress by interacting with RNA polymerase directly and by inhibiting several proteins. Consistently, increased levels of ppGpp lead to increased persistence; but, the mechanism by which elevated ppGpp translates into persistence has not been determined. Hence, we explored persistence in the absence of ppGpp so that the underlying mechanism of persister cell formation could be explored. We found that persister cells still form, although at lower levels, in the absence of ppGpp. Additionally, the toxin/antitoxin systems that we investigated (MqsR, MazF, GhoT, and YafQ) remain able to increase persistence dramatically in the absence of ppGpp. By overproducing each E. coli protein from the 4287 plasmid vectors of the ASKA library and selecting for increased persistence in the absence of ppGpp (via a relA spoT mutant), we identified five new proteins, YihS, PntA, YqjE, FocA, and Zur, that increase persistence simply by reducing cell growth.

  12. Dynamic metabolic adjustments and genome plasticity are implicated in the heat shock response of the extremely thermoacidophilic archaeon Sulfolobus solfataricus.

    Science.gov (United States)

    Tachdjian, Sabrina; Kelly, Robert M

    2006-06-01

    Approximately one-third of the open reading frames encoded in the Sulfolobus solfataricus genome were differentially expressed within 5 min following an 80 to 90 degrees C temperature shift at pH 4.0. This included many toxin-antitoxin loci and insertion elements, implicating a connection between genome plasticity and metabolic regulation in the early stages of stress response.

  13. Stochastic induction of persister cells by HipA through (p)ppGpp-mediated activation of mRNA endonucleases

    DEFF Research Database (Denmark)

    Germain-Maisonneuve, Elsa; Roghanian, Mohammad; Gerdes, Kenn

    2015-01-01

    The model organism Escherichia coli codes for at least 11 type II toxin-antitoxin (TA) modules, all implicated in bacterial persistence (multidrug tolerance). Ten of these encode messenger RNA endonucleases (mRNases) inhibiting translation by catalytic degradation of mRNA, and the 11th module, hi...

  14. Translation affects YoeB and MazF messenger RNA interferase activities by different mechanisms

    DEFF Research Database (Denmark)

    Christensen-Dalsgaard, Mikkel; Gerdes, Kenn

    2008-01-01

    Prokaryotic toxin-antitoxin loci encode mRNA cleaving enzymes that inhibit translation. Two types are known: those that cleave mRNA codons at the ribosomal A site and those that cleave any RNA site specifically. RelE of Escherichia coli cleaves mRNA at the ribosomal A site in vivo and in vitro...

  15. Regulatory RNAs in the Less Studied Streptococcal Species: from Nomenclature to Identification

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    Mohamed Amine Zorgani

    2016-07-01

    Full Text Available Streptococcal species are Gram-positive bacteria involved in severe and invasive diseases in humans and animals. Although this group includes different pathogenic species involved in life-threatening infections for humans, it also includes beneficial species, such as Streptococcus thermophilus, which is used in yogurt production. In bacteria virulence factors are controlled by various regulatory networks including regulatory RNAs. For clearness and to develop logical thinking, we start this review with a revision of regulatory RNAs nomenclature. Previous reviews are mostly dealing with Streptococcus pyogenes and Streptococcus pneumoniae regulatory RNAs. We especially focused our analysis on regulatory RNAs in Streptococcus agalactiae, Streptococcus mutans, Streptococcus thermophilus and other less studied Streptococcus species. Although S. agalactiae RNome remains largely unknown, sRNAs (small RNAs are supposed to mediate regulation during environmental adaptation and host infection. In the case of S. mutans, sRNAs are suggested to be involved in competence regulation, carbohydrate metabolism and Toxin-Antitoxin systems. A new category of miRNA-size small RNAs (msRNAs was also identified for the first time in this species. The analysis of S. thermophilus sRNome shows that many sRNAs are associated to the bacterial immune system known as CRISPR-Cas system. Only few of the other different Streptococcus species have been the subject of studies pointed toward the characterization of regulatory RNAs. Finally, understanding bacterial sRNome can constitute one step forward to the elaboration of new strategies in therapy such as substitution of antibiotics in the management of S. agalactiae neonatal infections, prevention of S. mutans dental caries or use of S. thermophilus CRISPR-Cas system in genome editing applications.

  16. [Bacterial SXT/R391 family from integrating conjugative elements--a review].

    Science.gov (United States)

    Luo, Peng; Hu, Chaoqun

    2014-05-04

    SXT/R391 family has the most abundant types and members in integrating conjugative elements (ICE). SXT/ R391 elements are comprised of conservative core genes and genes in variable regions. The functions of conservative core genes of SXT/R391 include integration and excision, self-transfer through conjugation, and regulation of its expression. The genes in the variable regions often encode for drug and heavy metal resistances, forming of biofilm, adjustment of bacterial motility, and toxin-antitoxin systems that prevent SXT/R391 deletion from hosts. Some genes in variable region of SXT/R391 also encode for restriction-modification system, helicase, and endonuclease. The activity of SXT/R391 is positively regulated by activator SetCD, and negatively regulated by repressor SetR. SXT/R391 cannot be easily deleted from the primary donors in the process of transfer. SXT/R391 prevent the acquirement of closely related and homogeneous elements but cannot prevent the acquirement of heterogenetic ICE, which leads to the generation of hybrid ICE under the action of recombination system encoded by SXT/R391 themselves. SXT/R391 have high transferable frequency and wide host range, and until now more than 40 different SXT/R391 elements have been discovered in various bacteria, especially in Vibrio species, which mainly distribute in coastal areas in Asia and Africa. It suggests that marine environments are likely the main reservoir for SXT/R391 and these elements probably spread from marine environmental strains to clinical strains, under increasing selective pressure. Due to the hazard caused by the prevalence and the transfer of SXT/R391, medical microbiologist and health departments should be fully alert to the spread of the elements.

  17. Structure of the Escherichia coli Antitoxin MqsA (YgiT/b3021) Bound to Its Gene Promoter Reveals Extensive Domain Rearrangements and the Specificity of Transcriptional Regulation

    Energy Technology Data Exchange (ETDEWEB)

    B Brown; T Wood; W Peti; R Page

    2011-12-31

    Bacterial cultures, especially biofilms, produce a small number of persister cells, a genetically identical subpopulation of wild type cells that are metabolically dormant, exhibit multidrug tolerance, and are highly enriched in bacterial toxins. The gene most highly up-regulated in Escherichia coli persisters is mqsR, a ribonuclease toxin that, along with mqsA, forms a novel toxin-antitoxin (TA) system. Like all known TA systems, both the MqsR-MqsA complex and MqsA alone regulate their own transcription. Despite the importance of TA systems in persistence and biofilms, very little is known about how TA modules, and antitoxins in particular, bind and recognize DNA at a molecular level. Here, we report the crystal structure of MqsA bound to a 26-bp fragment from the mqsRA promoter. We show that MqsA binds DNA predominantly via its C-terminal helix-turn-helix domain, with direct binding of recognition helix residues Asn{sup 97} and Arg{sup 010} to the DNA major groove. Unexpectedly, the structure also revealed that the MqsA N-terminal domain interacts with the DNA phosphate backbone. This results in a more than 105{sup o} rotation of the N-terminal domains between the free and complexed states, an unprecedented rearrangement for an antitoxin. The structure also shows that MqsA bends the DNA by more than 55{sup o} in order to achieve symmetrical binding. Finally, using a combination of biochemical and NMR studies, we show that the DNA sequence specificity of MqsA is mediated by direct readout.

  18. Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential.

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    Carl J Yeoman

    Full Text Available BACKGROUND: Gardnerella vaginalis is described as a common vaginal bacterial species whose presence correlates strongly with bacterial vaginosis (BV. Here we report the genome sequencing and comparative analyses of three strains of G. vaginalis. Strains 317 (ATCC 14019 and 594 (ATCC 14018 were isolated from the vaginal tracts of women with symptomatic BV, while Strain 409-05 was isolated from a healthy, asymptomatic individual with a Nugent score of 9. PRINCIPAL FINDINGS: Substantial genomic rearrangement and heterogeneity were observed that appeared to have resulted from both mobile elements and substantial lateral gene transfer. These genomic differences translated to differences in metabolic potential. All strains are equipped with significant virulence potential, including genes encoding the previously described vaginolysin, pili for cytoadhesion, EPS biosynthetic genes for biofilm formation, and antimicrobial resistance systems, We also observed systems promoting multi-drug and lantibiotic extrusion. All G. vaginalis strains possess a large number of genes that may enhance their ability to compete with and exclude other vaginal colonists. These include up to six toxin-antitoxin systems and up to nine additional antitoxins lacking cognate toxins, several of which are clustered within each genome. All strains encode bacteriocidal toxins, including two lysozyme-like toxins produced uniquely by strain 409-05. Interestingly, the BV isolates encode numerous proteins not found in strain 409-05 that likely increase their pathogenic potential. These include enzymes enabling mucin degradation, a trait previously described to strongly correlate with BV, although commonly attributed to non-G. vaginalis species. CONCLUSIONS: Collectively, our results indicate that all three strains are able to thrive in vaginal environments, and therein the BV isolates are capable of occupying a niche that is unique from 409-05. Each strain has significant virulence

  19. The third replicon of members of the Burkholderia cepacia Complex, plasmid pC3, plays a role in stress tolerance.

    Science.gov (United States)

    Agnoli, Kirsty; Frauenknecht, Carmen; Freitag, Roman; Schwager, Stephan; Jenul, Christian; Vergunst, Annette; Carlier, Aurelien; Eberl, Leo

    2014-02-01

    The metabolically versatile Burkholderia cepacia complex (Bcc) occupies a variety of niches, including the plant rhizosphere and the cystic fibrosis lung (where it is often fatal to the patient). Bcc members have multipartite genomes, of which the third replicon, pC3 (previously chromosome 3), has been shown to be a nonessential megaplasmid which confers virulence and both antifungal and proteolytic activity on several strains. In this study, pC3 curing was extended to cover strains of 16 of the 17 members of the Bcc, and the phenotypes conferred by pC3 were determined. B. cenocepacia strains H111, MCO-3, and HI2424 were previously cured of pC3; however, this had not proved possible in the epidemic strain K56-2. Here, we investigated the mechanism of this unexpected stability and found that efficient toxin-antitoxin systems are responsible for maintaining pC3 of strain K56-2. Identification of these systems allowed neutralization of the toxins and the subsequent deletion of K56-2pC3. The cured strain was found to exhibit reduced antifungal activity and was attenuated in both the zebrafish and the Caenorhabditis elegans model of infection. We used a PCR screening method to examine the prevalence of pC3 within 110 Bcc isolates and found that this replicon was absent in only four cases, suggesting evolutionary fixation. It is shown that plasmid pC3 increases the resistance of B. cenocepacia H111 to various stresses (oxidative, osmotic, high-temperature, and chlorhexidine-induced stresses), explaining the prevalence of this replicon within the Bcc.

  20. Analysis of virus genomes from glacial environments reveals novel virus groups with unusual host interactions

    Science.gov (United States)

    Bellas, Christopher M.; Anesio, Alexandre M.; Barker, Gary

    2015-01-01

    Microbial communities in glacial ecosystems are diverse, active, and subjected to strong viral pressures and infection rates. In this study we analyse putative virus genomes assembled from three dsDNA viromes from cryoconite hole ecosystems of Svalbard and the Greenland Ice Sheet to assess the potential hosts and functional role viruses play in these habitats. We assembled 208 million reads from the virus-size fraction and developed a procedure to select genuine virus scaffolds from cellular contamination. Our curated virus library contained 546 scaffolds up to 230 Kb in length, 54 of which were circular virus consensus genomes. Analysis of virus marker genes revealed a wide range of viruses had been assembled, including bacteriophages, cyanophages, nucleocytoplasmic large DNA viruses and a virophage, with putative hosts identified as Cyanobacteria, Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Firmicutes, eukaryotic algae and amoebae. Whole genome comparisons revealed the majority of circular genome scaffolds (CGS) formed 12 novel groups, two of which contained multiple phage members with plasmid-like properties, including a group of phage-plasmids possessing plasmid-like partition genes and toxin-antitoxin addiction modules to ensure their replication and a satellite phage-plasmid group. Surprisingly we also assembled a phage that not only encoded plasmid partition genes, but a clustered regularly interspaced short palindromic repeat (CRISPR)/Cas adaptive bacterial immune system. One of the spacers was an exact match for another phage in our virome, indicating that in a novel use of the system, the lysogen was potentially capable of conferring immunity on its bacterial host against other phage. Together these results suggest that highly novel and diverse groups of viruses are present in glacial environments, some of which utilize very unusual life strategies and genes to control their replication and maintain a long-term relationship with their hosts

  1. Plasmids of Carotenoid-Producing Paracoccus spp. (Alphaproteobacteria) - Structure, Diversity and Evolution

    Science.gov (United States)

    Maj, Anna; Dziewit, Lukasz; Czarnecki, Jakub; Wlodarczyk, Miroslawa; Baj, Jadwiga; Skrzypczyk, Grazyna; Giersz, Dorota; Bartosik, Dariusz

    2013-01-01

    Plasmids are components of many bacterial genomes. They enable the spread of a large pool of genetic information via lateral gene transfer. Many bacterial strains contain mega-sized replicons and these are particularly common in Alphaproteobacteria. Considerably less is known about smaller alphaproteobacterial plasmids. We analyzed the genomes of 14 such plasmids residing in 4 multireplicon carotenoid-producing strains of the genus Paracoccus (Alphaproteobacteria): P. aestuarii DSM 19484, P. haeundaensis LG P-21903, P. marcusii DSM 11574 and P. marcusii OS22. Comparative analyses revealed mosaic structures of the plasmids and recombinational shuffling of diverse genetic modules involved in (i) plasmid replication, (ii) stabilization (including toxin-antitoxin systems of the relBE/parDE, tad-ata, higBA, mazEF and toxBA families) and (iii) mobilization for conjugal transfer (encoding relaxases of the MobQ, MobP or MobV families). A common feature of the majority of the plasmids is the presence of AT-rich sequence islets (located downstream of exc1-like genes) containing genes, whose homologs are conserved in the chromosomes of many bacteria (encoding e.g. RelA/SpoT, SMC-like proteins and a retron-type reverse transcriptase). The results of this study have provided insight into the diversity and plasticity of plasmids of Paracoccus spp., and of the entire Alphaproteobacteria. Some of the identified plasmids contain replication systems not described previously in this class of bacteria. The composition of the plasmid genomes revealed frequent transfer of chromosomal genes into plasmids, which significantly enriches the pool of mobile DNA that can participate in lateral transfer. Many strains of Paracoccus spp. have great biotechnological potential, and the plasmid vectors constructed in this study will facilitate genetic studies of these bacteria. PMID:24260361

  2. Toxin inhibition in C. crescentus VapBC1 is mediated by a flexible pseudo-palindromic protein motif and modulated by DNA binding.

    Science.gov (United States)

    Bendtsen, Kirstine L; Xu, Kehan; Luckmann, Majbritt; Winther, Kristoffer S; Shah, Shiraz A; Pedersen, Christian N S; Brodersen, Ditlev E

    2017-03-17

    Expression of bacterial type II toxin-antitoxin (TA) systems is regulated at the transcriptional level through direct binding of the antitoxin to pseudo-palindromic sequences on operator DNA. In this context, the toxin functions as a co-repressor by stimulating DNA binding through direct interaction with the antitoxin. Here, we determine crystal structures of the complete 90 kDa heterooctameric VapBC1 complex from Caulobacter crescentus CB15 both in isolation and bound to its cognate DNA operator sequence at 1.6 and 2.7 Å resolution, respectively. DNA binding is associated with a dramatic architectural rearrangement of conserved TA interactions in which C-terminal extended structures of the antitoxin VapB1 swap positions to interlock the complex in the DNA-bound state. We further show that a pseudo-palindromic protein sequence in the antitoxin is responsible for this interaction and required for binding and inactivation of the VapC1 toxin dimer. Sequence analysis of 4127 orthologous VapB sequences reveals that such palindromic protein sequences are widespread and unique to bacterial and archaeal VapB antitoxins suggesting a general principle governing regulation of VapBC TA systems. Finally, a structure of C-terminally truncated VapB1 bound to VapC1 reveals discrete states of the TA interaction that suggest a structural basis for toxin activation in vivo. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. Three classes of plasmid (47-63 kb) carry the type B neurotoxin gene cluster of group II Clostridium botulinum.

    Science.gov (United States)

    Carter, Andrew T; Austin, John W; Weedmark, Kelly A; Corbett, Cindi; Peck, Michael W

    2014-08-01

    Pulsed-field gel electrophoresis and DNA sequence analysis of 26 strains of Group II (nonproteolytic) Clostridium botulinum type B4 showed that 23 strains carried their neurotoxin gene cluster on a 47-63 kb plasmid (three strains lacked any hybridization signal for the neurotoxin gene, presumably having lost their plasmid). Unexpectedly, no neurotoxin genes were found on the chromosome. This apparent constraint on neurotoxin gene transfer to the chromosome stands in marked contrast to Group I C. botulinum, in which neurotoxin gene clusters are routinely found in both locations. The three main classes of type B4 plasmid identified in this study shared different regions of homology, but were unrelated to any Group I or Group III plasmid. An important evolutionary aspect firmly links plasmid class to geographical origin, with one class apparently dominant in marine environments, whereas a second class is dominant in European terrestrial environments. A third class of plasmid is a hybrid between the other two other classes, providing evidence for contact between these seemingly geographically separated populations. Mobility via conjugation has been previously demonstrated for the type B4 plasmid of strain Eklund 17B, and similar genes associated with conjugation are present in all type B4 plasmids now described. A plasmid toxin-antitoxin system pemI gene located close to the neurotoxin gene cluster and conserved in each type B4 plasmid class may be important in understanding the mechanism which regulates this unique and unexpected bias toward plasmid-borne neurotoxin genes in Group II C. botulinum type B4.

  4. Transition State Charge Stabilization and Acid-Base Catalysis of mRNA Cleavage by the Endoribonuclease RelE.

    Science.gov (United States)

    Dunican, Brian F; Hiller, David A; Strobel, Scott A

    2015-12-01

    The bacterial toxin RelE is a ribosome-dependent endoribonuclease. It is part of a type II toxin-antitoxin system that contributes to antibiotic resistance and biofilm formation. During amino acid starvation, RelE cleaves mRNA in the ribosomal A-site, globally inhibiting protein translation. RelE is structurally similar to microbial RNases that employ general acid-base catalysis to facilitate RNA cleavage. The RelE active site is atypical for acid-base catalysis, in that it is enriched with positively charged residues and lacks the prototypical histidine-glutamate catalytic pair, making the mechanism of mRNA cleavage unclear. In this study, we use a single-turnover kinetic analysis to measure the effect of pH and phosphorothioate substitution on the rate constant for cleavage of mRNA by wild-type RelE and seven active-site mutants. Mutation and thio effects indicate a major role for stabilization of increased negative change in the transition state by arginine 61. The wild-type RelE cleavage rate constant is pH-independent, but the reaction catalyzed by many of the mutants is strongly dependent on pH, suggestive of general acid-base catalysis. pH-rate curves indicate that wild-type RelE operates with the pK(a) of at least one catalytic residue significantly downshifted by the local environment. Mutation of any single active-site residue is sufficient to disrupt this microenvironment and revert the shifted pK(a) back above neutrality. pH-rate curves are consistent with K54 functioning as a general base and R81 as a general acid. The capacity of RelE to effect a large pK(a) shift and facilitate a common catalytic mechanism by uncommon means furthers our understanding of other atypical enzymatic active sites.

  5. Identification of IncA/C Plasmid Replication and Maintenance Genes and Development of a Plasmid Multilocus Sequence Typing Scheme.

    Science.gov (United States)

    Hancock, Steven J; Phan, Minh-Duy; Peters, Kate M; Forde, Brian M; Chong, Teik Min; Yin, Wai-Fong; Chan, Kok-Gan; Paterson, David L; Walsh, Timothy R; Beatson, Scott A; Schembri, Mark A

    2017-02-01

    Plasmids of incompatibility group A/C (IncA/C) are becoming increasingly prevalent within pathogenic Enterobacteriaceae They are associated with the dissemination of multiple clinically relevant resistance genes, including blaCMY and blaNDM Current typing methods for IncA/C plasmids offer limited resolution. In this study, we present the complete sequence of a blaNDM-1-positive IncA/C plasmid, pMS6198A, isolated from a multidrug-resistant uropathogenic Escherichia coli strain. Hypersaturated transposon mutagenesis, coupled with transposon-directed insertion site sequencing (TraDIS), was employed to identify conserved genetic elements required for replication and maintenance of pMS6198A. Our analysis of TraDIS data identified roles for the replicon, including repA, a toxin-antitoxin system; two putative partitioning genes, parAB; and a putative gene, 053 Construction of mini-IncA/C plasmids and examination of their stability within E. coli confirmed that the region encompassing 053 contributes to the stable maintenance of IncA/C plasmids. Subsequently, the four major maintenance genes (repA, parAB, and 053) were used to construct a new plasmid multilocus sequence typing (PMLST) scheme for IncA/C plasmids. Application of this scheme to a database of 82 IncA/C plasmids identified 11 unique sequence types (STs), with two dominant STs. The majority of blaNDM-positive plasmids examined (15/17; 88%) fall into ST1, suggesting acquisition and subsequent expansion of this blaNDM-containing plasmid lineage. The IncA/C PMLST scheme represents a standardized tool to identify, track, and analyze the dissemination of important IncA/C plasmid lineages, particularly in the context of epidemiological studies. Copyright © 2017 American Society for Microbiology.

  6. Transcriptome mapping of pAR060302, a blaCMY-2-positive broad-host-range IncA/C plasmid.

    Science.gov (United States)

    Lang, Kevin S; Danzeisen, Jessica L; Xu, Wayne; Johnson, Timothy J

    2012-05-01

    The multidrug resistance-encoding plasmids belonging to the IncA/C incompatibility group have recently emerged among Escherichia coli and Salmonella enterica strains in the United States. These plasmids have a unique genetic structure compared to other enterobacterial plasmid types, a broad host range, and a propensity to acquire large numbers of antimicrobial resistance genes via their accessory regions. Using E. coli strain DH5α harboring the prototype IncA/C plasmid pAR060302, we sought to define the baseline transcriptome of IncA/C plasmids under laboratory growth and in the face of selective pressure. The effects of ampicillin, florfenicol, or streptomycin exposure were compared to those on cells left untreated at logarithmic phase using Illumina platform-based RNA sequencing (RNA-Seq). Under growth in Luria-Bertani broth lacking antibiotics, much of the backbone of pAR060302 was transcriptionally inactive, including its putative transfer regions. A few plasmid backbone genes of interest were highly transcribed, including genes of a putative toxin-antitoxin system and an H-NS-like transcriptional regulator. In contrast, numerous genes within the accessory regions of pAR060302 were highly transcribed, including the resistance genes floR, bla(CMY-2), aadA, and aacA. Treatment with ampicillin or streptomycin resulted in no genes being differentially expressed compared to controls lacking antibiotics, suggesting that many of the resistance-associated genes are not differentially expressed due to exposure to these antibiotics. In contrast, florfenicol treatment resulted in the upregulation of floR and numerous chromosomal genes. Overall, the transcriptome mapping of pAR060302 suggests that it mitigates the fitness costs of carrying resistance-associated genes through global regulation with its transcriptional regulators.

  7. Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights.

    Science.gov (United States)

    Bertelli, Claire; Aeby, Sébastien; Chassot, Bérénice; Clulow, James; Hilfiker, Olivier; Rappo, Samuel; Ritzmann, Sébastien; Schumacher, Paolo; Terrettaz, Céline; Benaglio, Paola; Falquet, Laurent; Farinelli, Laurent; Gharib, Walid H; Goesmann, Alexander; Harshman, Keith; Linke, Burkhard; Miyazaki, Ryo; Rivolta, Carlo; Robinson-Rechavi, Marc; van der Meer, Jan Roelof; Greub, Gilbert

    2015-01-01

    With the widespread availability of high-throughput sequencing technologies, sequencing projects have become pervasive in the molecular life sciences. The huge bulk of data generated daily must be analyzed further by biologists with skills in bioinformatics and by "embedded bioinformaticians," i.e., bioinformaticians integrated in wet lab research groups. Thus, students interested in molecular life sciences must be trained in the main steps of genomics: sequencing, assembly, annotation and analysis. To reach that goal, a practical course has been set up for master students at the University of Lausanne: the "Sequence a genome" class. At the beginning of the academic year, a few bacterial species whose genome is unknown are provided to the students, who sequence and assemble the genome(s) and perform manual annotation. Here, we report the progress of the first class from September 2010 to June 2011 and the results obtained by seven master students who specifically assembled and annotated the genome of Estrella lausannensis, an obligate intracellular bacterium related to Chlamydia. The draft genome of Estrella is composed of 29 scaffolds encompassing 2,819,825 bp that encode for 2233 putative proteins. Estrella also possesses a 9136 bp plasmid that encodes for 14 genes, among which we found an integrase and a toxin/antitoxin module. Like all other members of the Chlamydiales order, Estrella possesses a highly conserved type III secretion system, considered as a key virulence factor. The annotation of the Estrella genome also allowed the characterization of the metabolic abilities of this strictly intracellular bacterium. Altogether, the students provided the scientific community with the Estrella genome sequence and a preliminary understanding of the biology of this recently-discovered bacterial genus, while learning to use cutting-edge technologies for sequencing and to perform bioinformatics analyses.

  8. Analysis of non-typeable Haemophilous influenzae VapC1 mutations reveals structural features required for toxicity and flexibility in the active site.

    Directory of Open Access Journals (Sweden)

    Brooke Hamilton

    Full Text Available Bacteria have evolved mechanisms that allow them to survive in the face of a variety of stresses including nutrient deprivation, antibiotic challenge and engulfment by predator cells. A switch to dormancy represents one strategy that reduces energy utilization and can render cells resistant to compounds that kill growing bacteria. These persister cells pose a problem during treatment of infections with antibiotics, and dormancy mechanisms may contribute to latent infections. Many bacteria encode toxin-antitoxin (TA gene pairs that play an important role in dormancy and the formation of persisters. VapBC gene pairs comprise the largest of the Type II TA systems in bacteria and they produce a VapC ribonuclease toxin whose activity is inhibited by the VapB antitoxin. Despite the importance of VapBC TA pairs in dormancy and persister formation, little information exists on the structural features of VapC proteins required for their toxic function in vivo. Studies reported here identified 17 single mutations that disrupt the function of VapC1 from non-typeable H. influenzae in vivo. 3-D modeling suggests that side chains affected by many of these mutations sit near the active site of the toxin protein. Phylogenetic comparisons and secondary mutagenesis indicate that VapC1 toxicity requires an alternative active site motif found in many proteobacteria. Expression of the antitoxin VapB1 counteracts the activity of VapC1 mutants partially defective for toxicity, indicating that the antitoxin binds these mutant proteins in vivo. These findings identify critical chemical features required for the biological function of VapC toxins and PIN-domain proteins.

  9. Removal of hepatitis C virus-infected cells by a zymogenized bacterial toxin.

    Directory of Open Access Journals (Sweden)

    Assaf Shapira

    Full Text Available Hepatitis C virus (HCV infection is a major cause of chronic liver disease and has become a global health threat. No HCV vaccine is currently available and treatment with antiviral therapy is associated with adverse side effects. Moreover, there is no preventive therapy for recurrent hepatitis C post liver transplantation. The NS3 serine protease is necessary for HCV replication and represents a prime target for developing anti HCV therapies. Recently we described a therapeutic approach for eradication of HCV infected cells that is based on protein delivery of two NS3 protease-activatable recombinant toxins we named "zymoxins". These toxins were inactivated by fusion to rationally designed inhibitory peptides via NS3-cleavable linkers. Once delivered to cells where NS3 protease is present, the inhibitory peptide is removed resulting in re-activation of cytotoxic activity. The zymoxins we described suffered from two limitations: they required high levels of protease for activation and had basal activities in the un-activated form that resulted in a narrow potential therapeutic window. Here, we present a solution that overcame the major limitations of the "first generation zymoxins" by converting MazF ribonuclease, the toxic component of the E. coli chromosomal MazEF toxin-antitoxin system, into an NS3-activated zymoxin that is introduced to cells by means of gene delivery. We constructed an expression cassette that encodes for a single polypeptide that incorporates both the toxin and a fragment of its potent natural antidote, MazE, linked via an NS3-cleavable linker. While covalently paired to its inhibitor, the ribonuclease is well tolerated when expressed in naïve, healthy cells. In contrast, activating proteolysis that is induced by even low levels of NS3, results in an eradication of NS3 expressing model cells and HCV infected cells. Zymoxins may thus become a valuable tool in eradicating cells infected by intracellular pathogens that

  10. Horizontal Gene Transfer of the Secretome Drives the Evolution of Bacterial Cooperation and Virulence

    Science.gov (United States)

    Nogueira, Teresa; Rankin, Daniel J.; Touchon, Marie; Taddei, François; Brown, Sam P.; Rocha, Eduardo P.C.

    2009-01-01

    Summary Background Microbes engage in a remarkable array of cooperative behaviors, secreting shared proteins that are essential for foraging, shelter, microbial warfare, and virulence. These proteins are costly, rendering populations of cooperators vulnerable to exploitation by nonproducing cheaters arising by gene loss or migration. In such conditions, how can cooperation persist? Results Our model predicts that differential gene mobility drives intragenomic variation in investment in cooperative traits. More mobile loci generate stronger among-individual genetic correlations at these loci (higher relatedness) and thereby allow the maintenance of more cooperative traits via kin selection. By analyzing 21 Escherichia genomes, we confirm that genes coding for secreted proteins—the secretome—are very frequently lost and gained and are associated with mobile elements. We show that homologs of the secretome are overrepresented among human gut metagenomics samples, consistent with increased relatedness at secretome loci across multiple species. The biosynthetic cost of secreted proteins is shown to be under intense selective pressure, even more than for highly expressed proteins, consistent with a cost of cooperation driving social dilemmas. Finally, we demonstrate that mobile elements are in conflict with their chromosomal hosts over the chimeric ensemble's social strategy, with mobile elements enforcing cooperation on their otherwise selfish hosts via the cotransfer of secretome genes with “mafia strategy” addictive systems (toxin-antitoxin and restriction-modification). Conclusion Our analysis matches the predictions of our model suggesting that horizontal transfer promotes cooperation, as transmission increases local genetic relatedness at mobile loci and enforces cooperation on the resident genes. As a consequence, horizontal transfer promoted by agents such as plasmids, phages, or integrons drives microbial cooperation. PMID:19800234

  11. Identification of Fic-1 as an enzyme that inhibits bacterial DNA replication by AMPylating GyrB, promoting filament formation.

    Science.gov (United States)

    Lu, Canhua; Nakayasu, Ernesto S; Zhang, Li-Qun; Luo, Zhao-Qing

    2016-01-26

    The morphology of bacterial cells is important for virulence, evasion of the host immune system, and coping with environmental stresses. The widely distributed Fic proteins (filamentation induced by cAMP) are annotated as proteins involved in cell division because of the presence of the HPFx[D/E]GN[G/K]R motif. We showed that the presence of Fic-1 from Pseudomonas fluorescens significantly reduced the yield of plasmid DNA when expressed in Escherichia coli or P. fluorescens. Fic-1 interacted with GyrB, a subunit of DNA gyrase, which is essential for bacterial DNA replication. Fic-1 catalyzed the AMPylation of GyrB at Tyr(109), a residue critical for binding ATP, and exhibited auto-AMPylation activity. Mutation of the Fic-1 auto-AMPylated site greatly reduced AMPylation activity toward itself and toward GyrB. Fic-1-dependent AMPylation of GyrB triggered the SOS response, indicative of DNA replication stress or DNA damage. Fic-1 also promoted the formation of elongated cells when the SOS response was blocked. We identified an α-inhibitor protein that we named anti-Fic-1 (AntF), encoded by a gene immediately upstream of Fic-1. AntF interacted with Fic-1, inhibited the AMPylation activity of Fic-1 for GyrB in vitro, and blocked Fic-1-mediated inhibition of DNA replication in bacteria, suggesting that Fic-1 and AntF comprise a toxin-antitoxin module. Our work establishes Fic-1 as an AMPylating enzyme that targets GyrB to inhibit DNA replication and may target other proteins to regulate bacterial morphology.

  12. Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis.

    Science.gov (United States)

    Sonnenschein, Eva C; Nielsen, Kristian F; D'Alvise, Paul; Porsby, Cisse H; Melchiorsen, Jette; Heilmann, Jens; Kalatzis, Panos G; López-Pérez, Mario; Bunk, Boyke; Spröer, Cathrin; Middelboe, Mathias; Gram, Lone

    2017-02-01

    Tropodithietic acid (TDA)-producing Ruegeria mobilis strains of the Roseobacter clade have primarily been isolated from marine aquaculture and have probiotic potential due to inhibition of fish pathogens. We hypothesized that TDA producers with additional novel features are present in the oceanic environment. We isolated 42 TDA-producing R. mobilis strains during a global marine research cruise. While highly similar on the 16S ribosomal RNA gene level (99-100% identity), the strains separated into four sub-clusters in a multilocus sequence analysis. They were further differentiated to the strain level by average nucleotide identity using pairwise genome comparison. The four sub-clusters could not be associated with a specific environmental niche, however, correlated with the pattern of sub-typing using co-isolated phages, the number of prophages in the genomes and the distribution in ocean provinces. Major genomic differences within the sub-clusters include prophages and toxin-antitoxin systems. In general, the genome of R. mobilis revealed adaptation to a particle-associated life style and querying TARA ocean data confirmed that R. mobilis is more abundant in the particle-associated fraction than in the free-living fraction occurring in 40% and 6% of the samples, respectively. Our data and the TARA data, although lacking sufficient data from the polar regions, demonstrate that R. mobilis is a globally distributed marine bacterial species found primarily in the upper open oceans. It has preserved key phenotypic behaviors such as the production of TDA, but contains diverse sub-clusters, which could provide new capabilities for utilization in aquaculture.

  13. A Nonsynonymous SNP Catalog of Mycobacterium tuberculosis Virulence Genes and Its Use for Detecting New Potentially Virulent Sublineages.

    Science.gov (United States)

    Mikheecheva, Natalya E; Zaychikova, Marina V; Melerzanov, Alexander V; Danilenko, Valery N

    2017-04-01

    Mycobacterium tuberculosis is divided into several distinct lineages, and various genetic markers such as IS-elements, VNTR, and SNPs are used for lineage identification. We propose an M. tuberculosis classification approach based on functional polymorphisms in virulence genes. An M. tuberculosis virulence genes catalog has been established, including 319 genes from various protein groups, such as proteases, cell wall proteins, fatty acid and lipid metabolism proteins, sigma factors, toxin-antitoxin systems. Another catalog of 1,573 M. tuberculosis isolates of different lineages has been developed. The developed SNP-calling program has identified 3,563 nonsynonymous SNPs. The constructed SNP-based phylogeny reflected the evolutionary relationship between lineages and detected new sublineages. SNP analysis of sublineage F15/LAM4/KZN revealed four lineage-specific mutations in cyp125, mce3B, vapC25, and vapB34. The Ural lineage has been divided into two geographical clusters based on different SNPs in virulence genes. A new sublineage, B0/N-90, was detected inside the Beijing-B0/W-148 by SNPs in irtB, mce3F and vapC46. We have found 27 members of B0/N-90 among the 227 available genomes of the Beijing-B0/W-148 sublineage. Whole-genome sequencing of strain B9741, isolated from an HIV-positive patient, was demonstrated to belong to the new B0/N-90 group. A primer set for PCR detection of B0/N-90 lineage-specific mutations has been developed. The prospective use of mce3 mutant genes as genetically engineered vaccine is discussed. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  14. Back to the roots

    DEFF Research Database (Denmark)

    Harms, Alexander; Gerdes, Kenn

    2016-01-01

    In this issue of Molecular Cell, Jankevicius et al. (2016) characterize the DarTG toxin-antitoxin module in which the DarT toxin ADP-ribosylates single-stranded DNA and the DarG antitoxin counteracts DarT by direct binding and by enzymatic removal of the ADP-ribosylation.......In this issue of Molecular Cell, Jankevicius et al. (2016) characterize the DarTG toxin-antitoxin module in which the DarT toxin ADP-ribosylates single-stranded DNA and the DarG antitoxin counteracts DarT by direct binding and by enzymatic removal of the ADP-ribosylation....

  15. Dynamic Metabolic Adjustments and Genome Plasticity Are Implicated in the Heat Shock Response of the Extremely Thermoacidophilic Archaeon Sulfolobus solfataricus†

    Science.gov (United States)

    Tachdjian, Sabrina; Kelly, Robert M.

    2006-01-01

    Approximately one-third of the open reading frames encoded in the Sulfolobus solfataricus genome were differentially expressed within 5 min following an 80 to 90°C temperature shift at pH 4.0. This included many toxin-antitoxin loci and insertion elements, implicating a connection between genome plasticity and metabolic regulation in the early stages of stress response. PMID:16740961

  16. Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes

    Directory of Open Access Journals (Sweden)

    Makarova Kira S

    2012-11-01

    Full Text Available Abstract Background The virus-host arms race is a major theater for evolutionary innovation. Archaea and bacteria have evolved diverse, elaborate antivirus defense systems that function on two general principles: i immune systems that discriminate self DNA from nonself DNA and specifically destroy the foreign, in particular viral, genomes, whereas the host genome is protected, or ii programmed cell suicide or dormancy induced by infection. Presentation of the hypothesis Almost all genomic loci encoding immunity systems such as CRISPR-Cas, restriction-modification and DNA phosphorothioation also encompass suicide genes, in particular those encoding known and predicted toxin nucleases, which do not appear to be directly involved in immunity. In contrast, the immunity systems do not appear to encode antitoxins found in typical toxin-antitoxin systems. This raises the possibility that components of the immunity system themselves act as reversible inhibitors of the associated toxin proteins or domains as has been demonstrated for the Escherichia coli anticodon nuclease PrrC that interacts with the PrrI restriction-modification system. We hypothesize that coupling of diverse immunity and suicide/dormancy systems in prokaryotes evolved under selective pressure to provide robustness to the antivirus response. We further propose that the involvement of suicide/dormancy systems in the coupled antivirus response could take two distinct forms: 1 induction of a dormancy-like state in the infected cell to ‘buy time’ for activation of adaptive immunity; 2 suicide or dormancy as the final recourse to prevent viral spread triggered by the failure of immunity. Testing the hypothesis This hypothesis entails many experimentally testable predictions. Specifically, we predict that Cas2 protein present in all cas operons is a mRNA-cleaving nuclease (interferase that might be activated at an early stage of virus infection to enable incorporation of virus

  17. System Budgets

    DEFF Research Database (Denmark)

    Jeppesen, Palle

    1996-01-01

    The lecture note is aimed at introducing system budgets for optical communication systems. It treats optical fiber communication systems (six generations), system design, bandwidth effects, other system impairments and optical amplifiers.......The lecture note is aimed at introducing system budgets for optical communication systems. It treats optical fiber communication systems (six generations), system design, bandwidth effects, other system impairments and optical amplifiers....

  18. System Identification

    NARCIS (Netherlands)

    Keesman, K.J.

    2011-01-01

    Summary System Identification Introduction.- Part I: Data-based Identification.- System Response Methods.- Frequency Response Methods.- Correlation Methods.- Part II: Time-invariant Systems Identification.- Static Systems Identification.- Dynamic Systems Identification.- Part III: Time-varying

  19. Developing Universal Genetic Tools for Rapid and Efficient Deletion Mutation in Vibrio Species Based on Suicide T-Vectors Carrying a Novel Counterselectable Marker, vmi480.

    Directory of Open Access Journals (Sweden)

    Peng Luo

    Full Text Available Despite that Vibrio spp. have a significant impact on the health of humans and aquatic animals, the molecular basis of their pathogenesis is little known, mainly due to the limited genetic tools for the functional research of genes in Vibrio. In some cases, deletion of target DNAs in Vibrio can be achieved through the use of suicide vectors. However, these strategies are time-consuming and lack universality, and the widely used counterselectable gene sacB does not work well in Vibrio cells. In this study, we developed universal genetic tools for rapid and efficient deletion mutations in Vibrio species based on suicide T-Vectors carrying a novel counterselectable marker, vmi480. We explored two uncharacterized genes, vmi480 and vmi470, in a genomic island from Vibrio mimicus VM573 and confirmed that vmi480 and vmi470 constitute a two-component toxin-antitoxin system through deletion and expression of vmi480 and vmi470. The product of vmi480 exhibited strong toxicity to Escherichia coli cells. Based on vmi480 and the PBAD or PTAC promoter system, we constructed two suicide T-vectors, pLP11 and pLP12, and each of these vectors contained a multiple cloning region with two AhdI sites. Both vectors linearized by AhdI digestion could be stored and directly ligated with purified PCR products without a digestion step. By using pLP11 and pLP12 coupled with a highly efficient conjugation system provided by E. coli β2163, six genes from four representative Vibrio species were easily deleted. By using the counterselective marker vmi480, we obtained 3-12 positive colonies (deletion mutants among no more than 20 colonies randomly selected on counterselection plates. The strategy does not require the digestion of PCR products and suicide vectors every time, and it avoids large-scale screening colonies on counterselective plates. These results demonstrate that we successfully developed universal genetic tools for rapid and efficient gene deletion in Vibrio

  20. Mobility and generation of mosaic non-autonomous transposons by Tn3-derived inverted-repeat miniature elements (TIMEs.

    Directory of Open Access Journals (Sweden)

    Magdalena Szuplewska

    Full Text Available Functional transposable elements (TEs of several Pseudomonas spp. strains isolated from black shale ore of Lubin mine and from post-flotation tailings of Zelazny Most in Poland, were identified using a positive selection trap plasmid strategy. This approach led to the capture and characterization of (i 13 insertion sequences from 5 IS families (IS3, IS5, ISL3, IS30 and IS1380, (ii isoforms of two Tn3-family transposons--Tn5563a and Tn4662a (the latter contains a toxin-antitoxin system, as well as (iii non-autonomous TEs of diverse structure, ranging in size from 262 to 3892 bp. The non-autonomous elements transposed into AT-rich DNA regions and generated 5- or 6-bp sequence duplications at the target site of transposition. Although these TEs lack a transposase gene, they contain homologous 38-bp-long terminal inverted repeat sequences (IRs, highly conserved in Tn5563a and many other Tn3-family transposons. The simplest elements of this type, designated TIMEs (Tn3 family-derived Inverted-repeat Miniature Elements (262 bp, were identified within two natural plasmids (pZM1P1 and pLM8P2 of Pseudomonas spp. It was demonstrated that TIMEs are able to mobilize segments of plasmid DNA for transposition, which results in the generation of more complex non-autonomous elements, resembling IS-driven composite transposons in structure. Such transposon-like elements may contain different functional genetic modules in their core regions, including plasmid replication systems. Another non-autonomous element "captured" with a trap plasmid was a TIME derivative containing a predicted resolvase gene and a res site typical for many Tn3-family transposons. The identification of a portable site-specific recombination system is another intriguing example confirming the important role of non-autonomous TEs of the TIME family in shuffling genetic information in bacterial genomes. Transposition of such mosaic elements may have a significant impact on diversity and

  1. Sequences of two related multiple antibiotic resistance virulence plasmids sharing a unique IS26-related molecular signature isolated from different Escherichia coli pathotypes from different hosts.

    Directory of Open Access Journals (Sweden)

    Carola Venturini

    Full Text Available Enterohemorrhagic Escherichia coli (EHEC and atypical enteropathogenic E. coli (aEPEC are important zoonotic pathogens that increasingly are becoming resistant to multiple antibiotics. Here we describe two plasmids, pO26-CRL125 (125 kb from a human O26:H- EHEC, and pO111-CRL115 (115kb from a bovine O111 aEPEC, that impart resistance to ampicillin, kanamycin, neomycin, streptomycin, sulfathiazole, trimethoprim and tetracycline and both contain atypical class 1 integrons with an identical IS26-mediated deletion in their 3´-conserved segment. Complete sequence analysis showed that pO26-CRL125 and pO111-CRL115 are essentially identical except for a 9.7 kb fragment, present in the backbone of pO26-CRL125 but absent in pO111-CRL115, and several indels. The 9.7 kb fragment encodes IncI-associated genes involved in plasmid stability during conjugation, a putative transposase gene and three imperfect repeats. Contiguous sequence identical to regions within these pO26-CRL125 imperfect repeats was identified in pO111-CRL115 precisely where the 9.7 kb fragment is missing, suggesting it may be mobile. Sequences shared between the plasmids include a complete IncZ replicon, a unique toxin/antitoxin system, IncI stability and maintenance genes, a novel putative serine protease autotransporter, and an IncI1 transfer system including a unique shufflon. Both plasmids carry a derivate Tn21 transposon with an atypical class 1 integron comprising a dfrA5 gene cassette encoding resistance to trimethoprim, and 24 bp of the 3´-conserved segment followed by Tn6026, which encodes resistance to ampicillin, kanymycin, neomycin, streptomycin and sulfathiazole. The Tn21-derivative transposon is linked to a truncated Tn1721, encoding resistance to tetracycline, via a region containing the IncP-1α oriV. Absence of the 5 bp direct repeats flanking Tn3-family transposons, indicates that homologous recombination events played a key role in the formation of this complex

  2. Gradient systems and mechanical systems

    Institute of Scientific and Technical Information of China (English)

    Fengxiang Mei; Huibin Wu

    2016-01-01

    All types of gradient systems and their properties are discussed. Two problems connected with gradient sys-tems and mechanical systems are studied. One is the direct problem of transforming a mechanical system into a gradi-ent system, and the other is the inverse problem, which is transforming a gradient system into a mechanical system.

  3. Thermal systems; Systemes thermiques

    Energy Technology Data Exchange (ETDEWEB)

    Lalot, S. [Valenciennes Univ. et du Hainaut Cambresis, LME, 59 (France); Lecoeuche, S. [Ecole des Mines de Douai, Dept. GIP, 59 - Douai (France)]|[Lille Univ. des Sciences et Technologies, 59 - Villeneuve d' Ascq (France); Ahmad, M.; Sallee, H.; Quenard, D. [CSTB, 38 - Saint Martin d' Heres (France); Bontemps, A. [Universite Joseph Fourier, LEGI/GRETh, 38 - Grenoble (France); Gascoin, N.; Gillard, P.; Bernard, S. [Laboratoire d' Energetique, Explosion, Structure, 18 - Bourges (France); Gascoin, N.; Toure, Y. [Laboratoire Vision et Robotique, 18 - Bourges (France); Daniau, E.; Bouchez, M. [MBDA, 18 - Bourges (France); Dobrovicescu, A.; Stanciu, D. [Bucarest Univ. Polytechnique, Faculte de Genie Mecanique (Romania); Stoian, M. [Reims Univ. Champagne Ardenne, Faculte des Sciences, UTAP/LTM, 51 (France); Bruch, A.; Fourmigue, J.F.; Colasson, S. [CEA Grenoble, Lab. Greth, 38 (France); Bontemps, A. [Universite Joseph Fourier, LEGI/GRETh, 38 - Grenoble (France); Voicu, I.; Mare, T.; Miriel, J. [Institut National des Sciences Appliquees (INSA), LGCGM, IUT, 35 - Rennes (France); Galanis, N. [Sherbrooke Univ., Genie Mecanique, QC (Canada); Nemer, M.; Clodic, D. [Ecole des Mines de Paris, Centre Energetique et Procedes, 75 (France); Lasbet, Y.; Auvity, B.; Castelain, C.; Peerhossaini, H. [Nantes Univ., Ecole Polytechnique, Lab. de Thermocinetiquede Nantes, UMR-CNRS 6607, 44 (France)

    2005-07-01

    This session about thermal systems gathers 26 articles dealing with: neural model of a compact heat exchanger; experimental study and numerical simulation of the thermal behaviour of test-cells with walls made of a combination of phase change materials and super-insulating materials; hydraulic and thermal modeling of a supercritical fluid with pyrolysis inside a heated channel: pre-dimensioning of an experimental study; energy analysis of the heat recovery devices of a cryogenic system; numerical simulation of the thermo-hydraulic behaviour of a supercritical CO{sub 2} flow inside a vertical tube; mixed convection inside dual-tube exchangers; development of a nodal approach with homogenization for the simulation of the brazing cycle of a heat exchanger; chaotic exchanger for the cooling of low temperature fuel cells; structural optimization of the internal fins of a cylindrical generator; a new experimental approach for the study of the local boiling inside the channels of exchangers with plates and fins; experimental study of the flow regimes of boiling hydrocarbons on a bundle of staggered tubes; energy study of heat recovery exchangers used in Claude-type refrigerating systems; general model of Carnot engine submitted to various operating constraints; the free pistons Stirling cogeneration system; natural gas supplied cogeneration system with polymer membrane fuel cell; influence of the CRN coating on the heat flux inside the tool during the wood unrolling process; transport and mixture of a passive scalar injected inside the wake of a Ahmed body; control of a laser welding-brazing process by infrared thermography; 2D self-adaptative method for contours detection: application to the images of an aniso-thermal jet; exergy and exergy-economical study of an 'Ericsson' engine-based micro-cogeneration system; simplified air-conditioning of telephone switching equipments; parametric study of the 'low-energy' individual dwelling; brief synthesis of

  4. Variable Persister Gene Interactions with (pppGpp for Persister Formation in Escherichia coli

    Directory of Open Access Journals (Sweden)

    Shuang Liu

    2017-09-01

    Full Text Available Persisters comprise a group of phenotypically heterogeneous metabolically quiescent bacteria with multidrug tolerance and contribute to the recalcitrance of chronic infections. Although recent work has shown that toxin-antitoxin (TA system HipAB depends on stringent response effector (pppGppin persister formation, whether other persister pathways are also dependent on stringent response has not been explored. Here we examined the relationship of (pppGpp with 15 common persister genes (dnaK, clpB, rpoS, pspF, tnaA, sucB, ssrA, smpB, recA, umuD, uvrA, hipA, mqsR, relE, dinJ using Escherichia coli as a model. By comparing the persister levels of wild type with their single gene knockout and double knockout mutants with relA, we divided their interactions into five types, namely A “dependent” (dnaK, recA, B “positive reinforcement” (rpoS, pspF, ssrA, recA, C “antagonistic” (clpB, sucB, umuD, uvrA, hipA, mqsR, relE, dinJ, D “epistasis” (clpB, rpoS, tnaA, ssrA, smpB, hipA, and E “irrelevant” (dnaK, clpB, rpoS, tnaA, sucB, smpB, umuD, uvrA, hipA, mqsR, relE, dinJ. We found that the persister gene interactions are intimately dependent on bacterial culture age, cell concentrations (diluted versus undiluted culture, and drug classifications, where the same gene may belong to different groups with varying antibiotics, culture age or cell concentrations. Together, this study represents the first attempt to systematically characterize the intricate relationships among the different mechanisms of persistence and as such provide new insights into the complexity of the persistence phenomenon at the level of persister gene network interactions.

  5. Microevolutionary events involving narrow host plasmids influences local fixation of vancomycin-resistance in Enterococcus populations.

    Directory of Open Access Journals (Sweden)

    Ana R Freitas

    Full Text Available Vancomycin-resistance in enterococci (VRE is associated with isolates within ST18, ST17, ST78 Enterococcus faecium (Efm and ST6 Enterococcus faecalis (Efs human adapted lineages. Despite of its global spread, vancomycin resistance rates in enterococcal populations greatly vary temporally and geographically. Portugal is one of the European countries where Tn1546 (vanA is consistently found in a variety of environments. A comprehensive multi-hierarchical analysis of VRE isolates (75 Efm and 29 Efs from Portuguese hospitals and aquatic surroundings (1996-2008 was performed to clarify the local dynamics of VRE. Clonal relatedness was established by PFGE and MLST while plasmid characterization comprised the analysis of known relaxases, rep initiator proteins and toxin-antitoxin systems (TA by PCR-based typing schemes, RFLP comparison, hybridization and sequencing. Tn1546 variants were characterized by PCR overlapping/sequencing. Intra- and inter-hospital dissemination of Efm ST18, ST132 and ST280 and Efs ST6 clones, carrying rolling-circle (pEFNP1/pRI1 and theta-replicating (pCIZ2-like, Inc18, pHTβ-like, two pRUM-variants, pLG1-like, and pheromone-responsive plasmids was documented. Tn1546 variants, mostly containing ISEf1 or IS1216, were located on plasmids (30-150 kb with a high degree of mosaicism and heterogeneous RFLP patterns that seem to have resulted from the interplay between broad host Inc18 plasmids (pIP501, pRE25, pEF1, and narrow host RepA_N plasmids (pRUM, pAD1-like. TAs of Inc18 (ω-ε-ζ and pRUM (Axe-Txe plasmids were infrequently detected. Some plasmid chimeras were persistently recovered over years from different clonal lineages. This work represents the first multi-hierarchical analysis of VRE, revealing a frequent recombinatorial diversification of a limited number of interacting clonal backgrounds, plasmids and transposons at local scale. These interactions provide a continuous process of parapatric clonalization driving a full

  6. Microevolutionary Events Involving Narrow Host Plasmids Influences Local Fixation of Vancomycin-Resistance in Enterococcus Populations

    Science.gov (United States)

    Freitas, Ana R.; Novais, Carla; Tedim, Ana P.; Francia, María Victoria; Baquero, Fernando; Peixe, Luísa; Coque, Teresa M.

    2013-01-01

    Vancomycin-resistance in enterococci (VRE) is associated with isolates within ST18, ST17, ST78 Enterococcus faecium (Efm) and ST6 Enterococcus faecalis (Efs) human adapted lineages. Despite of its global spread, vancomycin resistance rates in enterococcal populations greatly vary temporally and geographically. Portugal is one of the European countries where Tn1546 (vanA) is consistently found in a variety of environments. A comprehensive multi-hierarchical analysis of VRE isolates (75 Efm and 29 Efs) from Portuguese hospitals and aquatic surroundings (1996–2008) was performed to clarify the local dynamics of VRE. Clonal relatedness was established by PFGE and MLST while plasmid characterization comprised the analysis of known relaxases, rep initiator proteins and toxin-antitoxin systems (TA) by PCR-based typing schemes, RFLP comparison, hybridization and sequencing. Tn1546 variants were characterized by PCR overlapping/sequencing. Intra- and inter-hospital dissemination of Efm ST18, ST132 and ST280 and Efs ST6 clones, carrying rolling-circle (pEFNP1/pRI1) and theta-replicating (pCIZ2-like, Inc18, pHTβ-like, two pRUM-variants, pLG1-like, and pheromone-responsive) plasmids was documented. Tn1546 variants, mostly containing ISEf1 or IS1216, were located on plasmids (30–150 kb) with a high degree of mosaicism and heterogeneous RFLP patterns that seem to have resulted from the interplay between broad host Inc18 plasmids (pIP501, pRE25, pEF1), and narrow host RepA_N plasmids (pRUM, pAD1-like). TAs of Inc18 (ω-ε-ζ) and pRUM (Axe-Txe) plasmids were infrequently detected. Some plasmid chimeras were persistently recovered over years from different clonal lineages. This work represents the first multi-hierarchical analysis of VRE, revealing a frequent recombinatorial diversification of a limited number of interacting clonal backgrounds, plasmids and transposons at local scale. These interactions provide a continuous process of parapatric clonalization driving a full

  7. The molecular physiological and genetic mechanisms underlying the superb efficacy of quinolones%喹诺酮类药物作用的生理和遗传的分子机制

    Institute of Scientific and Technical Information of China (English)

    龙泉鑫; 何颖; 谢建平

    2012-01-01

    氟喹诺酮类药物是目前使用最广泛的广谱抗生素,占据了全球抗生素类药物市场约18%的份额.其杀菌快速,而且具备大量的衍生物库,为药物更新换代提供了良好的基础.但这些衍生物在杀菌的速度、代谢过程中对氧需求、对蛋白合成的依赖性等方面的差异很大.从药物作用后细菌分子遗传层面的应答特征揭示各类衍生物的深层次作用机制,可以为寻找更有效的新喹诺酮类药物提供坚实基础.SOS应答、毒素-抗毒素系统,细菌程序性死亡、染色体片段化以及活性氧簇等新机制可能不同程度参与了喹诺酮类药物的杀菌过程.本文重点介绍喹诺酮作用的“二步特征”.该特征的引入有助于理解不同喹诺酮类药物的杀菌特征,也有助于开发新的喹诺酮类药物.%The fluoroquinolones are the most widely used broad-spectrum antibiotics, accounting for 18% of global antibacterial market share. They can kill bacteria rapidly with variety of derivatives available. Different quinolones vary significantly in rate and spectrum of killing, oxygen requirement for metabolism and reliance upon protein synthesis. Further understanding the sophisticated mechanisms of action of this important antibiotic family based on the molecular genetic response of bacteria can facilitate the discovery of better quinolone derivatives. Factors such as SOS response, bacterial toxin-antitoxin system, programmed death, chromosome fragmentation and reactive oxygen have been implicated in the action to some extent. "Two steps characteristic" of quinolones killing is also emphasized, which might inspire future better quinolones modification.

  8. Data Systems vs. Information Systems

    OpenAIRE

    Amatayakul, Margret K.

    1982-01-01

    This paper examines the current status of “hospital information systems” with respect to the distinction between data systems and information systems. It is proposed that the systems currently existing are incomplete data dystems resulting in ineffective information systems.

  9. Data Systems vs. Information Systems

    OpenAIRE

    Amatayakul, Margret K.

    1982-01-01

    This paper examines the current status of “hospital information systems” with respect to the distinction between data systems and information systems. It is proposed that the systems currently existing are incomplete data dystems resulting in ineffective information systems.

  10. Multibody Systems

    DEFF Research Database (Denmark)

    Wagner, Falko Jens

    1999-01-01

    Multibody Systems is one area, in which methods for solving DAEs are of special interst. This chapter is about multibody systems, why they result in DAE systems and what kind of problems that can arise when dealing with multibody systems and formulating their corresponding DAE system....

  11. Lymph system

    Science.gov (United States)

    Lymphatic system ... neck, under the arms, and groin. The lymph system includes the: Tonsils Adenoids Spleen Thymus ... JE, Flynn JA, Solomon BS, Stewart RW. Lymphatic system. In: Ball JW, Dains JE, Flynn JA, Solomon ...

  12. Conjugative plasmids of Neisseria gonorrhoeae.

    Directory of Open Access Journals (Sweden)

    Emilia Pachulec

    Full Text Available Many clinical isolates of the human pathogen Neisseria gonorrhoeae contain conjugative plasmids. The host range of these plasmids is limited to Neisseria species, but presence of a tetracycline (tetM determinant inserted in several of these plasmids is an important cause of the rapid spread of tetracycline resistance. Previously plasmids with different backbones (Dutch and American type backbones and with and without different tetM determinants (Dutch and American type tetM determinants have been identified. Within the isolates tested, all plasmids with American or Dutch type tetM determinants contained a Dutch type plasmid backbone. This demonstrated that tetM determinants should not be used to differentiate between conjugal plasmid backbones. The nucleotide sequences of conjugative plasmids with Dutch type plasmid backbones either not containing the tetM determinant (pEP5233 or containing Dutch (pEP5289 or American (pEP5050 type tetM determinants were determined. Analysis of the backbone sequences showed that they belong to a novel IncP1 subfamily divergent from the IncP1alpha, beta, gamma, delta and epsilon subfamilies. The tetM determinants were inserted in a genetic load region found in all these plasmids. Insertion was accompanied by the insertion of a gene with an unknown function, and rearrangement of a toxin/antitoxin gene cluster. The genetic load region contains two toxin/antitoxins of the Zeta/Epsilon toxin/antitoxin family previously only found in Gram positive organisms and the virulence associated protein D of the VapD/VapX toxin/antitoxin family. Remarkably, presence of VapX of pJD1, a small cryptic neisserial plasmid, in the acceptor strain strongly increased the conjugation efficiency, suggesting that it functions as an antitoxin for the conjugative plasmid. The presence of the toxin and antitoxin on different plasmids might explain why the host range of this IncP1 plasmid is limited to Neisseria species. The isolated plasmids

  13. Molecular mechanisms underlying bacterial persisters

    DEFF Research Database (Denmark)

    Maisonneuve, Etienne; Gerdes, Kenn

    2014-01-01

    All bacteria form persisters, cells that are multidrug tolerant and therefore able to survive antibiotic treatment. Due to the low frequencies of persisters in growing bacterial cultures and the complex underlying molecular mechanisms, the phenomenon has been challenging to study. However, recent...... 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...... induced persistence. In several different organisms, toxin-antitoxin modules function as effectors of ppGpp-induced persistence....

  14. RNA decay by messenger RNA interferases

    DEFF Research Database (Denmark)

    Christensen-Dalsgaard, Mikkel; Overgaard, Martin; Winther, Kristoffer Skovbo

    2008-01-01

    Two abundant toxin-antitoxin (TA) gene families, relBE and mazEF, encode mRNA cleaving enzymes whose ectopic overexpression abruptly inhibits translation and thereby induces a bacteriostatic condition. Here we describe and discuss protocols for the overproduction, purification, and analysis of mRNA...... cleaving enzymes such as RelE of Escherichia coli and the corresponding antitoxin RelB. In particular, we describe a set of plasmid vectors useful for the detailed analysis of cleavage sites in model mRNAs....

  15. Systems effectiveness

    CERN Document Server

    Habayeb, A R

    1987-01-01

    Highlights three principal applications of system effectiveness: hardware system evaluation, organizational development and evaluation, and conflict analysis. The text emphasizes the commonality of the system effectiveness discipline. The first part of the work presents a framework for system effectiveness, partitioning and hierarchy of hardware systems. The second part covers the structure, hierarchy, states, functions and activities of organizations. Contains an extended Appendix on mathematical concepts and also several project suggestions.

  16. Bitcoin System

    Directory of Open Access Journals (Sweden)

    Jan Lánský

    2017-06-01

    Full Text Available Cryptocurrency systems are purely digital and decentralized systems that use cryptographic principles to confirm transactions. Bitcoin is the first and also the most widespread cryptocurrency. The aim of this article is to introduce Bitcoin system using a language understandable also to readers without computer science education. This article captures the Bitcoin system from three perspectives: internal structure, network and users. Emphasis is placed on brief and clear definitions (system components and their mutual relationships. A new system view of the stated terms constitutes author’s own contribution.

  17. Intelligent Systems

    Data.gov (United States)

    National Aeronautics and Space Administration — The autonomous systems (AS) project, led by NASA Ames, is developing software for system operation automation. AS technology will help astronauts make more decisions...

  18. Systems Engineering

    Science.gov (United States)

    Pellerano, Fernando

    2015-01-01

    This short course provides information on what systems engineering is and how the systems engineer guides requirements, interfaces with the discipline leads, and resolves technical issues. There are many system-wide issues that either impact or are impacted by the thermal subsystem. This course will introduce these issues and illustrate them with real life examples.

  19. Retrofitting Systems

    DEFF Research Database (Denmark)

    Rose, Jørgen

    1997-01-01

    This report gives an overview of the different retrofitting possibilities that are available today. The report looks at both external and internal systems for external wall constructions, roof constructions, floor constructions and foundations. All systems are described in detail in respect to use...... and methods, and the efficiency of the different systems are discussed....

  20. Operating systems

    CERN Document Server

    Tsichritzis, Dionysios C; Rheinboldt, Werner

    1974-01-01

    Operating Systems deals with the fundamental concepts and principles that govern the behavior of operating systems. Many issues regarding the structure of operating systems, including the problems of managing processes, processors, and memory, are examined. Various aspects of operating systems are also discussed, from input-output and files to security, protection, reliability, design methods, performance evaluation, and implementation methods.Comprised of 10 chapters, this volume begins with an overview of what constitutes an operating system, followed by a discussion on the definition and pr

  1. Cryogenic Systems

    Science.gov (United States)

    Hosoyama, Kenji

    2002-02-01

    In this lecture we discuss the principle of method of cooling to a very low temperature, i.e. cryogenic. The "gas molecular model" will be introduced to explain the mechanism cooling by the expansion engine and the Joule-Thomson expansion valve. These two expansion processes are normally used in helium refrigeration systems to cool the process gas to cryogenic temperature. The reverse Carnot cycle will be discussed in detail as an ideal refrigeration cycle. First the fundamental process of liquefaction and refrigeration cycles will be discussed, and then the practical helium refrigeration system. The process flow of the system and the key components; -compressor, expander, and heat exchanger- will be discussed. As an example of an actual refrigeration system, we will use the cryogenic system for the KEKB superconducting RF cavity. We will also discuss the liquid helium distribution system, which is very important, especially for the cryogenic systems used in accelerator applications. 1 Principles of Cooling and Fundamental Cooling Cycle 2 Expansion engine, Joule-Thomson expansion, kinetic molecular theory, and enthalpy 3 Liquefaction Systems 4 Refrigeration Systems 5 Practical helium liquefier/refrigeration system 6 Cryogenic System for TRISTAN Superconducting RF Cavity

  2. Expert System

    DEFF Research Database (Denmark)

    Hildebrandt, Thomas Troels; Cattani, Gian Luca

    2016-01-01

    An expert system is a computer system for inferring knowledge from a knowledge base, typically by using a set of inference rules. When the concept of expert systems was introduced at Stanford University in the early 1970s, the knowledge base was an unstructured set of facts. Today the knowledge...... base of expert systems is often given in terms of an ontology, extracted and built from various data sources by employing natural language-processing and statistics. To emphasize such capabilities, the term “expert” is now often replaced by “cognitive,” “knowledge,” “knowledge-based,” or “intelligent......” system. With very few exceptions, general-purpose expert systems have failed to emerge so far. However, expert systems are applied in specialized domains, particularly in healthcare. The increasing availability of large quantities of data to organizations today provides a valuable opportunity...

  3. Recommender systems

    CERN Document Server

    Kembellec, Gérald; Saleh, Imad

    2014-01-01

    Acclaimed by various content platforms (books, music, movies) and auction sites online, recommendation systems are key elements of digital strategies. If development was originally intended for the performance of information systems, the issues are now massively moved on logical optimization of the customer relationship, with the main objective to maximize potential sales. On the transdisciplinary approach, engines and recommender systems brings together contributions linking information science and communications, marketing, sociology, mathematics and computing. It deals with the understan

  4. Material Systems

    DEFF Research Database (Denmark)

    Jensen, Mads Brath; Mortensen, Henrik Rubæk; Mullins, Michael;

    2009-01-01

    This paper describes and reflects upon the results of an investigative project which explores the setting up of a material system - a parametric and generative assembly consisting of and taking into consideration material properties, manufacturing constraints and geometric behavior. The project...... approaches the subject through the construction of a logic-driven system aiming to explore the possibilities of a material system that fulfills spatial, structural and performative requirements concurrently and how these are negotiated in situations where they might be conflicting....

  5. Material Systems

    DEFF Research Database (Denmark)

    Jensen, Mads Brath; Mortensen, Henrik Rubæk; Mullins, Michael

    2009-01-01

    This paper describes and reflects upon the results of an investigative project which explores the setting up of a material system - a parametric and generative assembly consisting of and taking into consideration material properties, manufacturing constraints and geometric behavior. The project...... approaches the subject through the construction of a logic-driven system aiming to explore the possibilities of a material system that fulfills spatial, structural and performative requirements concurrently and how these are negotiated in situations where they might be conflicting....

  6. Intelligent systems

    CERN Document Server

    Irwin, J David

    2011-01-01

    Technology has now progressed to the point that intelligent systems are replacing humans in the decision making processes as well as aiding in the solution of very complex problems. In many cases intelligent systems are already outperforming human activities. Artificial neural networks are not only capable of learning how to classify patterns, such images or sequence of events, but they can also effectively model complex nonlinear systems. Their ability to classify sequences of events is probably more popular in industrial applications where there is an inherent need to model nonlinear system

  7. Energetic Systems

    Data.gov (United States)

    Federal Laboratory Consortium — The Energetic Systems Division provides full-spectrum energetic engineering services (project management, design, analysis, production support, in-service support,...

  8. Systemic darwinism.

    Science.gov (United States)

    Winther, Rasmus Grønfeldt

    2008-08-19

    Darwin's 19th century evolutionary theory of descent with modification through natural selection opened up a multidimensional and integrative conceptual space for biology. We explore three dimensions of this space: explanatory pattern, levels of selection, and degree of difference among units of the same type. Each dimension is defined by a respective pair of poles: law and narrative explanation, organismic and hierarchical selection, and variational and essentialist thinking. As a consequence of conceptual debates in the 20th century biological sciences, the poles of each pair came to be seen as mutually exclusive opposites. A significant amount of 21st century research focuses on systems (e.g., genomic, cellular, organismic, and ecological/global). Systemic Darwinism is emerging in this context. It follows a "compositional paradigm" according to which complex systems and their hierarchical networks of parts are the focus of biological investigation. Through the investigation of systems, Systemic Darwinism promises to reintegrate each dimension of Darwin's original logical space. Moreover, this ideally and potentially unified theory of biological ontology coordinates and integrates a plurality of mathematical biological theories (e.g., self-organization/structure, cladistics/history, and evolutionary genetics/function). Integrative Systemic Darwinism requires communal articulation from a plurality of perspectives. Although it is more general than these, it draws on previous advances in Systems Theory, Systems Biology, and Hierarchy Theory. Systemic Darwinism would greatly further bioengineering research and would provide a significantly deeper and more critical understanding of biological reality.

  9. cardiovascular system

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    6.1 Cardiac arrhythmias 2006037 Electroanatomical systems guided circumferential pulmonary veins ablation for atrial fibrillation: initial experience from comparison between the EnSite -NavX and CARTO system LIU Xu(刘旭 ), et al. Dept Cardiol, Shanghai Chest Hosp, Shanghai, 200030, China. Chin J Cardiol 2005; 33 (22): 975 -978.

  10. Linear Systems.

    Science.gov (United States)

    The report documents a series of seminars at Rome Air Development Center with the content equivalent to an intense course in Linear Systems . Material...is slanted toward the practicing engineer and introduces some of the fundamental concepts and techniques for analyzing linear systems . Techniques for

  11. Immune System

    NARCIS (Netherlands)

    Kuper, C.F.; Ruehl-Fehlert, C.; Elmore, S.A.; Parker, G.A.

    2013-01-01

    Cells of the immune system are found in every organ, from the classic lymphoid organs to tissues such as liver, mucosae, and omental adipose tissue. Toxicity to the immune system may be from a direct or indirect injury to lymphoid organs. The morphological responses range from lymphocyte depletion t

  12. Caste System

    OpenAIRE

    Hoff, Karla

    2016-01-01

    In standard economics, individuals are rational actors and economic forces undermine institutions that impose large inefficiencies. The persistence of the caste system is evidence of the need for psychologically more realistic models of decision-making in economics. The caste system divides South Asian society into hereditary groups whose lowest ranks are represented as innately polluted. ...

  13. Creative Systems

    DEFF Research Database (Denmark)

    Manelius, Anne-Mette; Beim, Anne

    2007-01-01

    Opsamling af diskussioner på konferencen og udstillingen Creative Systems i september/oktober 2007. Konferencen og Udstillingen Creative Systems sætter fokus på systemer som en positiv drivkraft i den kreative skabelsesproces. CINARK inviterede fire internationale kapaciteter, som indenfor hver...... deres felt har beskæftiget sig med udviklingen af systemer. Kieran Timberlake, markant amerikansk tegnestue; Mark West, Professor på University of Manitoba, Canada, og pioner indenfor anvendelse af tekstilforskalling til betonstøbninger; Matilda McQuaid, Arkitekturhistoriker og kurator på udstillingen...... om Extreme Textiles på amerikanske Cooper Hewit Design Museum, samt Professor Ludger Hovestadt, ved ETH, Zürich der fokuserer på udvikling og anvendelse af logaritmiske systemtilgange. Udstillingen diskuterede ud fra deres meget forskellige arbejder, det kreative potentiale i anvendelsen af systemer...

  14. Power system

    Science.gov (United States)

    Hickam, Christopher Dale

    2008-03-18

    A power system includes a prime mover, a transmission, and a fluid coupler having a selectively engageable lockup clutch. The fluid coupler may be drivingly connected between the prime mover and the transmission. Additionally, the power system may include a motor/generator drivingly connected to at least one of the prime mover and the transmission. The power-system may also include power-system controls configured to execute a control method. The control method may include selecting one of a plurality of modes of operation of the power system. Additionally, the control method may include controlling the operating state of the lockup clutch dependent upon the mode of operation selected. The control method may also include controlling the operating state of the motor/generator dependent upon the mode of operation selected.

  15. Reactive Systems

    DEFF Research Database (Denmark)

    Aceto, Luca; Ingolfsdottir, Anna; Larsen, Kim Guldstrand

    A reactive system comprises networks of computing components, achieving their goals through interaction among themselves and their environment. Thus even relatively small systems may exhibit unexpectedly complex behaviours. As moreover reactive systems are often used in safety critical systems......, the need for mathematically based formal methodology is increasingly important. There are many books that look at particular methodologies for such systems. This book offers a more balanced introduction for graduate students and describes the various approaches, their strengths and weaknesses, and when...... they are best used. Milner's CCS and its operational semantics are introduced, together with the notions of behavioural equivalences based on bisimulation techniques and with recursive extensions of Hennessy-Milner logic. In the second part of the book, the presented theories are extended to take timing issues...

  16. Dynamical systems

    CERN Document Server

    Sternberg, Shlomo

    2010-01-01

    Celebrated mathematician Shlomo Sternberg, a pioneer in the field of dynamical systems, created this modern one-semester introduction to the subject for his classes at Harvard University. Its wide-ranging treatment covers one-dimensional dynamics, differential equations, random walks, iterated function systems, symbolic dynamics, and Markov chains. Supplementary materials offer a variety of online components, including PowerPoint lecture slides for professors and MATLAB exercises.""Even though there are many dynamical systems books on the market, this book is bound to become a classic. The the

  17. Physical Systems

    CERN Document Server

    Belkind, Ori

    2012-01-01

    Based on the concept of a physical system, this book offers a new philosophical interpretation of classical mechanics and the Special Theory of Relativity. According to Belkind's view the role of physical theory is to describe the motions of the parts of a physical system in relation to the motions of the whole. This approach provides a new perspective into the foundations of physical theory, where motions of parts and wholes of physical systems are taken to be fundamental, prior to spacetime, material properties and laws of motion. He defends this claim with a constructive project, deriving b

  18. Creative systems

    DEFF Research Database (Denmark)

    Beim, Anne

    2007-01-01

    At udvikle systemer har altid været et væsentligt element i den arkitektoniske skabelsesproces. Systemer er ikke nødvendigvis begrænsninger, men kan ses som positive faktorer i skabelses og fremstillinsprocessen. Center for Industriel Arkitektur, Cinark, har afholdt en international konference, en...... workshop og en udstilling under overskriften; Creative Systems. Artiklen præsenterer de fire oplægsholdere Matilda McQuaid, Mark West, Stephen Kieran og Ludger Hovestadt og en række diskussionstemaer....

  19. The SOS response is permitted in Escherichia coli strains deficient in the expression of the mazEF pathway.

    Science.gov (United States)

    Kalderon, Ziva; Kumar, Sathish; Engelberg-Kulka, Hanna

    2014-01-01

    The Escherichia coli (E. coli) SOS response is the largest, most complex, and best characterized bacterial network induced by DNA damage. It is controlled by a complex network involving the RecA and LexA proteins. We have previously shown that the SOS response to DNA damage is inhibited by various elements involved in the expression of the E. coli toxin-antitoxin mazEF pathway. Since the mazEF module is present on the chromosomes of most E. coli strains, here we asked: Why is the SOS response found in so many E. coli strains? Is the mazEF module present but inactive in those strains? We examined three E. coli strains used for studies of the SOS response, strains AB1932, BW25113, and MG1655. We found that each of these strains is either missing or inhibiting one of several elements involved in the expression of the mazEF-mediated death pathway. Thus, the SOS response only takes place in E. coli cells in which one or more elements of the E. coli toxin-antitoxin module mazEF or its downstream pathway is not functioning.

  20. Screening for Escherichia coli K-12 genes conferring glyoxal resistance or sensitivity by transposon insertions.

    Science.gov (United States)

    Lee, Changhan; Kim, Jihong; Kwon, Minsuk; Lee, Kihyun; Min, Haeyoung; Kim, Seong Hun; Kim, Dongkyu; Lee, Nayoung; Kim, Jiyeun; Kim, Doyun; Ko, Changmin; Park, Chankyu

    2016-09-01

    Glyoxal (GO) belongs to the reactive electrophilic species generated in vivo in all organisms. In order to identify targets of GO and their response mechanisms, we attempted to screen for GO-sensitive mutants by random insertions of TnphoA-132. The genes responsible for GO susceptibility were functionally classified as the following: (i) tRNA modification; trmE, gidA and truA, (ii) DNA repair; recA and recC, (iii) toxin-antitoxin; mqsA and (iv) redox metabolism; yqhD and caiC In addition, an insertion in the crp gene, encoding the cAMP responsive transcription factor, exhibits a GO-resistant phenotype, which is consistent with the phenotype of adenylate cyclase (cya) mutant showing GO resistance. This suggests that global regulation involving cAMP is operated in a stress response to GO. To further characterize the CRP-regulated genes directly associated with GO resistance, we created double mutants deficient in both crp and one of the candidate genes including yqhD, gloA and sodB The results indicate that these genes are negatively regulated by CRP as confirmed by real-time RT-PCR. We propose that tRNA as well as DNA are the targets of GO and that toxin/antitoxin, antioxidant and cAMP are involved in cellular response to GO.

  1. Recommender Systems

    CERN Document Server

    Lü, Linyuan; Yeung, Chi Ho; Zhang, Yi-Cheng; Zhang, Zi-Ke; Zhou, Tao

    2012-01-01

    The ongoing rapid expansion of the Internet greatly increases the necessity of effective recommender systems for filtering the abundant information. Extensive research for recommender systems is conducted by a broad range of communities including social and computer scientists, physicists, and interdisciplinary researchers. Despite substantial theoretical and practical achievements, unification and comparison of different approaches are lacking, which impedes further advances. In this article, we review recent developments in recommender systems and discuss the major challenges. We compare and evaluate available algorithms and examine their roles in the future developments. In addition to algorithms, physical aspects are described to illustrate macroscopic behavior of recommender systems. Potential impacts and future directions are discussed. We emphasize that recommendation has a great scientific depth and combines diverse research fields which makes it of interests for physicists as well as interdisciplinar...

  2. Avionics Systems

    Directory of Open Access Journals (Sweden)

    P.M. Soundar Rajan

    2013-03-01

    Full Text Available ‘Avionics’ systems, over the decades, have grown from simple communication radios and navigation equipments to complex integrated equipments primarily infiuenced by dominance of digital technology. Continuous growth in integrated circuit technology, functional integration of complete system on chip, very high speed communication channels and fault tolerant communication protocols have brought remarkable advancements in avionics systems. Further Mechanical and Pneumatic functional blocks are being replaced by digital systems progressively and decisively. New generation aircraft are being built around powerful avionics assets to provide stress free cockpit to the pilot.Defence Science Journal, 2013, 63(2, pp.129-130, DOI:http://dx.doi.org/10.14429/dsj.63.4269

  3. AEG System -

    Data.gov (United States)

    Department of Transportation — The AEG System is used to create, revise, approve, and distribute text of the AEGS and Flight Standard Board (FSB)/Type Rating Report. The MMEL specifies under what...

  4. Bubble systems

    CERN Document Server

    Avdeev, Alexander A

    2016-01-01

    This monograph presents a systematic analysis of bubble system mathematics, using the mechanics of two-phase systems in non-equilibrium as the scope of analysis. The author introduces the thermodynamic foundations of bubble systems, ranging from the fundamental starting points to current research challenges. This book addresses a range of topics, including description methods of multi-phase systems, boundary and initial conditions as well as coupling requirements at the phase boundary. Moreover, it presents a detailed study of the basic problems of bubble dynamics in a liquid mass: growth (dynamically and thermally controlled), collapse, bubble pulsations, bubble rise and breakup. Special emphasis is placed on bubble dynamics in turbulent flows. The analysis results are used to write integral equations governing the rate of vapor generation (condensation) in non-equilibrium flows, thus creating a basis for solving a number of practical problems. This book is the first to present a comprehensive theory of boil...

  5. Health systems

    DEFF Research Database (Denmark)

    Büchner, Vera Antonia; Hinz, Vera; Schreyögg, Jonas

    2016-01-01

    This study investigates potential changes in hospital performance after health system entry, while differentiating between hospital technical and cost efficiency and hospital profitability. In the first stage we obtained (bootstrapped) data envelopment analysis (DEA) efficiency scores. Then......, genetic matching is used as a novel matching procedure in this context along with a difference-in-difference approach within a panel regression framework. With the genetic matching procedure, independent and health system hospitals are matched along a number of environmental and organizational...... characteristics. The results show that health system entry increases hospital technical and cost efficiency by between 0.6 and 3.4 % in four alternative post-entry periods, indicating that health system entry has not a transitory but rather a permanent effect on hospital efficiency. Regarding hospital...

  6. Bitcoin System

    National Research Council Canada - National Science Library

    Jan Lánský

    2017-01-01

    .... Bitcoin is the first and also the most widespread cryptocurrency. The aim of this article is to introduce Bitcoin system using a language understandable also to readers without computer science education...

  7. Systems failure.

    OpenAIRE

    Macleod, Anna

    1998-01-01

    Systems Failure A solo exhibition of new work by Anna Macleod developed in conversation with curator Liz Burns. The Dock, Carrick on Shannon, Co Leitrim. Ireland. 12th February – 17th April 2010. The works for the exhibition Systems Failure include drawings, prints and small constructions that examine the delicate balance that exists between need and aspects of failure rooted in the relationship between humanity and land use. The work seeks to question the relationship between scient...

  8. Nanorobotic Systems

    Directory of Open Access Journals (Sweden)

    Lixin Dong

    2008-11-01

    Full Text Available Two strategies towards the realization of nanotechnology have been presented, i.e., top-down and bottom up. The former one is mainly based on nanofabrication and includes technologies such as nano-lithography, nano-imprint, and etching. Presently, they are still 2D fabrication processes with low resolution. The later one is an assembly-based technique. At present, it includes such items as self-assembly, dip-pen lithography, and directed self-assembly. These techniques can generate regular nano patterns in large scales. To fabricate 3D complex nano devices there are still no effective ways by so far. Here we show our effort on the development of a nano laboratory, a prototype nanomanufacturing system, based on nanorobotic manipulations. In which, we take a hybrid strategy as shown in Fig. 1. In this system, nano fabrication and nano assembly can be performed in an arbitrary order to construct nano building blocks and finally nano devices. The most important feature in this system is that the products can be fed back into the system to shrink the system part by part leading to nanorobots. Property characterization can be performed in each intermediate process. Due to the nanorobotic manipulation system, dynamic measurement can be performed rather than conventional static observations.

  9. System-of-Systems Complexity

    Directory of Open Access Journals (Sweden)

    Hermann Kopetz

    2013-11-01

    Full Text Available The global availability of communication services makes it possible to interconnect independently developed systems, called constituent systems, to provide new synergistic services and more efficient economic processes. The characteristics of these new Systems-of-Systems are qualitatively different from the classic monolithic systems. In the first part of this presentation we elaborate on these differences, particularly with respect to the autonomy of the constituent systems, to dependability, continuous evolution, and emergence. In the second part we look at a SoS from the point of view of cognitive complexity. Cognitive complexity is seen as a relation between a model of an SoS and the observer. In order to understand the behavior of a large SoS we have to generate models of adequate simplicity, i.e, of a cognitive complexity that can be handled by the limited capabilities of the human mind. We will discuss the importance of properly specifying and placing the relied-upon message interfaces between the constituent systems that form an open SoS and discuss simplification strategies that help to reduce the cognitive complexity.

  10. Systems Studies

    Energy Technology Data Exchange (ETDEWEB)

    Graham, R.L.

    1998-03-17

    The Systems Studies Activity had two objectives: (1) to investigate nontechnical barriers to the deployment of biomass production and supply systems and (2) to enhance and extend existing systems models of bioenergy supply and use. For the first objective, the Activity focused on existing bioenergy markets. Four projects were undertaken: a comparative analysis of bioenergy in Sweden and Austria; a one-day workshop on nontechnical barriers jointly supported by the Production Systems Activity; the development and testing of a framework for analyzing barriers and drivers to bioenergy markets; and surveys of wood pellet users in Sweden, Austria and the US. For the second objective, two projects were undertaken. First, the Activity worked with the Integrated BioEnergy Systems (TBS) Activity of TEA Bioenergy Task XIII to enhance the BioEnergy Assessment Model (BEAM). This model is documented in the final report of the IBS Activity. The Systems Studies Activity contributed to enhancing the feedstock portion of the model by developing a coherent set of willow, poplar, and switchgrass production modules relevant to both the US and the UK. The Activity also developed a pretreatment module for switchgrass. Second, the Activity sponsored a three-day workshop on modeling bioenergy systems with the objectives of providing an overview of the types of models used to evaluate bioenergy and promoting communication among bioenergy modelers. There were nine guest speakers addressing different types of models used to evaluate different aspects of bioenergy, ranging from technoeconomic models based on the ASPEN software to linear programming models to develop feedstock supply curves for the US. The papers from this workshop have been submitted to Biomass and Bioenergy and are under editorial review.

  11. Systemic trauma.

    Science.gov (United States)

    Goldsmith, Rachel E; Martin, Christina Gamache; Smith, Carly Parnitzke

    2014-01-01

    Substantial theoretical, empirical, and clinical work examines trauma as it relates to individual victims and perpetrators. As trauma professionals, it is necessary to acknowledge facets of institutions, cultures, and communities that contribute to trauma and subsequent outcomes. Systemic trauma-contextual features of environments and institutions that give rise to trauma, maintain it, and impact posttraumatic responses-provides a framework for considering the full range of traumatic phenomena. The current issue of the Journal of Trauma & Dissociation is composed of articles that incorporate systemic approaches to trauma. This perspective extends conceptualizations of trauma to consider the influence of environments such as schools and universities, churches and other religious institutions, the military, workplace settings, hospitals, jails, and prisons; agencies and systems such as police, foster care, immigration, federal assistance, disaster management, and the media; conflicts involving war, torture, terrorism, and refugees; dynamics of racism, sexism, discrimination, bullying, and homophobia; and issues pertaining to conceptualizations, measurement, methodology, teaching, and intervention. Although it may be challenging to expand psychological and psychiatric paradigms of trauma, a systemic trauma perspective is necessary on both scientific and ethical grounds. Furthermore, a systemic trauma perspective reflects current approaches in the fields of global health, nursing, social work, and human rights. Empirical investigations and intervention science informed by this paradigm have the potential to advance scientific inquiry, lower the incidence of a broader range of traumatic experiences, and help to alleviate personal and societal suffering.

  12. Turbine system

    Energy Technology Data Exchange (ETDEWEB)

    McMahan, Kevin Weston; Dillard, Daniel Jackson

    2016-05-03

    A turbine system is disclosed. The turbine system includes a transition duct having an inlet, an outlet, and a passage extending between the inlet and the outlet and defining a longitudinal axis, a radial axis, and a tangential axis. The outlet of the transition duct is offset from the inlet along the longitudinal axis and the tangential axis. The turbine system further includes a turbine section connected to the transition duct. The turbine section includes a plurality of shroud blocks at least partially defining a hot gas path, a plurality of buckets at least partially disposed in the hot gas path, and a plurality of nozzles at least partially disposed in the hot gas path. At least one of a shroud block, a bucket, or a nozzle includes means for withstanding high temperatures.

  13. System Description:

    DEFF Research Database (Denmark)

    Schürmann, Carsten; Poswolsky, Adam

    2009-01-01

    Delphin is a functional programming language [Adam Poswolsky and Carsten Schürmann. Practical programming with higher-order encodings and dependent types. In European Symposium on Programming (ESOP), 2008] utilizing dependent higher-order datatypes. Delphin's two-level type-system cleanly separates...... data from computation, allowing for decidable type checking. The data level is LF [Robert Harper, Furio Honsell, and Gordon Plotkin. A framework for defining logics. Journal of the Association for Computing Machinery, 40(1):143-184, January 1993], which allows for the specification of deductive systems...

  14. Lubrication system

    Energy Technology Data Exchange (ETDEWEB)

    Wadding, C.; Lagasse, N.L.; Milo, G.T.; Vankamerik, J.G.

    1986-02-11

    This patent describes a lubrication system for controlling the flow of lubricant as a function of the altitude at which a gas turbine engine is operating. This lubrication system is comprised of: 1.) A source of lubricant under pressure; 2.) A unit requiring lubrication; 3.) A movable valve in fluid communication with the source and with the unit for regulating the flow of lubricant from the source to the unit; and 4.) An altitude sensor associated with the movable valve for positioning the movable valve to control the flow of lubricant from the source to the unit, as a function of the altitude at which the engine is operating.

  15. Microbiology System

    Science.gov (United States)

    1992-01-01

    Technology originating in a NASA-sponsored study of the measurement of microbial growth in zero gravity led to the development of Biomerieux Vitek, Inc.'s VITEK system. VITEK provides a physician with accurate diagnostic information and identifies the most effective medication. Test cards are employed to identify organisms and determine susceptibility to antibiotics. A photo-optical scanner scans the card and monitors changes in the growth of cells contained within the card. There are two configurations - VITEK and VITEK JR as well as VIDAS, a companion system that detects bacteria, viruses, etc. from patient specimens. The company was originally created by McDonnell Douglas, the NASA contractor.

  16. [Systemic scleroderma].

    Science.gov (United States)

    Hunzelmann, N

    2013-04-01

    Systemic scleroderma is a chronic autoimmune disease affecting the skin, internal organs and the musculoskeletal system. The presence of Raynaud phenomenon, anti-nuclear antibodies and pathologic capillaroscopy are early signs of the disease. Limited cutaneous SSc, diffuse cutaneous SSc and SSc-overlap syndromes are the main clinical subtypes. Multidisciplinary care is mandatory. Follow-up examinations should be performed at least annually in order to recognize in a timely fashion treatable organ involvement such as pulmonary arterial hypertension. Besides symptomatic treatment of organ involvement, immunosuppressive therapy is indicated for a progressive inflammatory course.

  17. Computer systems

    Science.gov (United States)

    Olsen, Lola

    1992-01-01

    In addition to the discussions, Ocean Climate Data Workshop hosts gave participants an opportunity to hear about, see, and test for themselves some of the latest computer tools now available for those studying climate change and the oceans. Six speakers described computer systems and their functions. The introductory talks were followed by demonstrations to small groups of participants and some opportunities for participants to get hands-on experience. After this familiarization period, attendees were invited to return during the course of the Workshop and have one-on-one discussions and further hands-on experience with these systems. Brief summaries or abstracts of introductory presentations are addressed.

  18. Irrigation System

    Science.gov (United States)

    1984-01-01

    Under contract with Marshall Space Flight Center, Midwest Research Institute compiled a Lubrication Handbook intended as a reference source for designers and manufacturers of aerospace hardware and crews responsible for maintenance of such equipment. Engineers of Lindsay Manufacturing Company learned of this handbook through NASA Tech Briefs and used it for supplemental information in redesigning gear boxes for their center pivot agricultural irrigation system.

  19. Immune System

    Science.gov (United States)

    ... and mature there to become B cells or leave for the thymus gland, where they mature to become T cells. B lymphocytes and T lymphocytes have separate jobs to do: B lymphocytes are like the body's military intelligence system, seeking out their targets and sending defenses to ...

  20. Bricks / Systems

    DEFF Research Database (Denmark)

    and systems. The basis for this theme is the work conducted at the Utzon(x) Research Group at Aalborg University, in combination with the rich tradition and implementation of masonry work in Denmark, which has attracted increasing attention from architectural practitioners and researchers alike. How should...

  1. Multiagent systems

    National Research Council Canada - National Science Library

    Sycara, Katia P

    1998-01-01

    ... of such multiagent systems (MASs) are a core set of issues and research questions that have been studied over the years by the distributed AT community. In this article, I present some of the critical notions in MASs and the research work that has addressed them. I organize these notions around the concept of problem-solving coherence,...

  2. System Dynamics

    Science.gov (United States)

    Morecroft, John

    System dynamics is an approach for thinking about and simulating situations and organisations of all kinds and sizes by visualising how the elements fit together, interact and change over time. This chapter, written by John Morecroft, describes modern system dynamics which retains the fundamentals developed in the 1950s by Jay W. Forrester of the MIT Sloan School of Management. It looks at feedback loops and time delays that affect system behaviour in a non-linear way, and illustrates how dynamic behaviour depends upon feedback loop structures. It also recognises improvements as part of the ongoing process of managing a situation in order to achieve goals. Significantly it recognises the importance of context, and practitioner skills. Feedback systems thinking views problems and solutions as being intertwined. The main concepts and tools: feedback structure and behaviour, causal loop diagrams, dynamics, are practically illustrated in a wide variety of contexts from a hot water shower through to a symphony orchestra and the practical application of the approach is described through several real examples of its use for strategic planning and evaluation.

  3. Systems chemistry

    NARCIS (Netherlands)

    Ludlow, R. Frederick; Otto, Sijbren

    2008-01-01

    The study of complex mixtures of interacting synthetic molecules has historically not received much attention from chemists, even though research into complexity is well established in the neighbouring fields. However, with the huge recent interest in systems biology and the availability of modern a

  4. Transport system

    NARCIS (Netherlands)

    Drenth, K.F.

    1999-01-01

    The transport system comprises at least one road surface (2) and at least one vehicle (4) on wheels (6). The road surface (2) has a substantially bowl-shaped cross section and the vehicle (4) is designed so that the wheels (6) run directly on the road surface (2) while the road surface (2) acts as a

  5. Solar system

    CERN Document Server

    Homer, Charlene

    2007-01-01

    Thrill young astronomers with a journey through our Solar System. Find out all about the Inner and Outer Planets, the Moon, Stars, Constellations, Asteroids, Meteors and Comets. Using simplified language and vocabulary, concepts such as planetary orbits, the asteroid belt, the lunar cycle and phases of the moon, and shooting stars are all explored.

  6. Quorum Systems

    DEFF Research Database (Denmark)

    Förster, Klaus-Tycho

    2017-01-01

    What happens if a single server is no longer powerful enough to service all your customers? The obvious choice is to add more servers and to use the majority approach (e.g. Paxos, Chapter 2) to guarantee consistency. However, even if you buy one million servers, a client still has to access more ...... study the theory behind overlapping sets, known as quorum systems....

  7. Immune System

    Science.gov (United States)

    A properly functioning immune system is essential to good health. It defends the body against infectious agents and in some cases tumor cells. Individuals with immune deficiencies resulting from genetic defects, diseases (e.g., AIDS, leukemia), or drug therapies are more suscepti...

  8. Systems Chronotherapeutics

    Science.gov (United States)

    Innominato, Pasquale F.; Dallmann, Robert; Rand, David A.; Lévi, Francis A.

    2017-01-01

    Chronotherapeutics aim at treating illnesses according to the endogenous biologic rhythms, which moderate xenobiotic metabolism and cellular drug response. The molecular clocks present in individual cells involve approximately fifteen clock genes interconnected in regulatory feedback loops. They are coordinated by the suprachiasmatic nuclei, a hypothalamic pacemaker, which also adjusts the circadian rhythms to environmental cycles. As a result, many mechanisms of diseases and drug effects are controlled by the circadian timing system. Thus, the tolerability of nearly 500 medications varies by up to fivefold according to circadian scheduling, both in experimental models and/or patients. Moreover, treatment itself disrupted, maintained, or improved the circadian timing system as a function of drug timing. Improved patient outcomes on circadian-based treatments (chronotherapy) have been demonstrated in randomized clinical trials, especially for cancer and inflammatory diseases. However, recent technological advances have highlighted large interpatient differences in circadian functions resulting in significant variability in chronotherapy response. Such findings advocate for the advancement of personalized chronotherapeutics through interdisciplinary systems approaches. Thus, the combination of mathematical, statistical, technological, experimental, and clinical expertise is now shaping the development of dedicated devices and diagnostic and delivery algorithms enabling treatment individualization. In particular, multiscale systems chronopharmacology approaches currently combine mathematical modeling based on cellular and whole-body physiology to preclinical and clinical investigations toward the design of patient-tailored chronotherapies. We review recent systems research works aiming to the individualization of disease treatment, with emphasis on both cancer management and circadian timing system–resetting strategies for improving chronic disease control and

  9. Exploring Enterprise, System of Systems, and System and Software Architectures

    Science.gov (United States)

    2016-06-13

    2009 Carnegie Mellon University Exploring Enterprise, System of Systems, and System and Software Architectures Software Engineering Institute...TITLE AND SUBTITLE Exploring Enterprise, System of Systems, and System and Software Architectures 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c...Carnegie Mellon University, Software Engineering Institute,Pittsburgh,PA,15213 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/MONITORING AGENCY

  10. Systemic Architecture

    DEFF Research Database (Denmark)

    Poletto, Marco; Pasquero, Claudia

    2012-01-01

    design protocols developed to describe the city as a territory of self-organization. Collecting together nearly a decade of design experiments by the authors and their practice, ecoLogicStudio, the book discusses key disciplinary definitions such as ecologic urbanism, algorithmic architecture, bottom......This is a manual investigating the subject of urban ecology and systemic development from the perspective of architectural design. It sets out to explore two main goals: to discuss the contemporary relevance of a systemic practice to architectural design, and to share a toolbox of informational......-up or tactical design, behavioural space and the boundary of the natural and the artificial realms within the city and architecture. A new kind of "real-time world-city" is illustrated in the form of an operational design manual for the assemblage of proto-architectures, the incubation of proto...

  11. Decentralized Systems.

    Science.gov (United States)

    1980-12-31

    source of interrupts can be generated at each element. These interrupts can be used to sample local state information I or to maintain a measure of...adjoining identifiers or system words. 2.7.2 Synonymous Symbols For convience some operators have a number of different representations They are...of this perfor- Sr tance measure for the programs sampled . The programs executed included the Sieve of Eratosthenes described in section 2.1, a

  12. Imaging System

    Science.gov (United States)

    1995-01-01

    The 1100C Virtual Window is based on technology developed under NASA Small Business Innovation (SBIR) contracts to Ames Research Center. For example, under one contract Dimension Technologies, Inc. developed a large autostereoscopic display for scientific visualization applications. The Virtual Window employs an innovative illumination system to deliver the depth and color of true 3D imaging. Its applications include surgery and Magnetic Resonance Imaging scans, viewing for teleoperated robots, training, and in aviation cockpit displays.

  13. Blackboard Systems.

    Science.gov (United States)

    1986-06-01

    article stated that although the importance of context, syntax, semantics, and phonological rules in the recognition of speech was accepted, no system had...of, from the lowest to the highest level: parametric, segmental, phonetic , phonemic, syllabic, lexical, phrasal, and conceptual levels (see Figure 3...from classification (classifying acoustic segments into phonetic classes), to recognition (recognizing words) to generation and 42SCe (25] for a

  14. Systemic Assurance

    Science.gov (United States)

    2015-07-31

    simulations, cyber-physical robotic systems, and extremely large commercial Java programs. An important goal is to develop incrementally compostable...randomness and stochastic behavior, both as integral to algorithm design and as a consequence of multi- threading , (3) Concurrency and distribution, as the...should be involved in all four threads of the effort: Baseline Analysis of Codified Best Practices The baselining analysis for existing practices has

  15. Security system

    Science.gov (United States)

    Baumann, Mark J.; Kuca, Michal; Aragon, Mona L.

    2016-02-02

    A security system includes a structure having a structural surface. The structure is sized to contain an asset therein and configured to provide a forceful breaching delay. The structure has an opening formed therein to permit predetermined access to the asset contained within the structure. The structure includes intrusion detection features within or associated with the structure that are activated in response to at least a partial breach of the structure.

  16. Gasification system

    Science.gov (United States)

    Haldipur, Gaurang B.; Anderson, Richard G.; Cherish, Peter

    1983-01-01

    A method and system for injecting coal and process fluids into a fluidized bed gasification reactor. Three concentric tubes extend vertically upward into the fluidized bed. Coal particulates in a transport gas are injected through an inner tube, and an oxygen rich mixture of oxygen and steam are injected through an inner annulus about the inner tube. A gaseous medium relatively lean in oxygen content, such as steam, is injected through an annulus surrounding the inner annulus.

  17. Propulsion Systems

    Science.gov (United States)

    2011-03-31

    definition we are choosing x to be aligned with the direction of flight. Thus, accounting for the possible rotation of the axes, the acceleration in...Monopropellants. In a monopropellant system, like the name suggests, there is one propellant which decomposes exothermically as it passes through a catalytic...it comes into contact with the catalyst bed. Subsequently, the ammonia decomposes into nitrogen and hydrogen in an endothermic reaction lowering the

  18. Law system and legislation system

    OpenAIRE

    Boshno, Svetlana

    2013-01-01

    This paper is a continuation of publication of the «Jurisprudence» textbook by Svetlana Vladimirovna Boshno. Law system is a key element of general theory of law. The major fundamentals of its construction are subject matter and method of legal regulation. Of great importance is the division of legal regulation methods into mandative and dispositive ones. The paper articulates the concepts of institute and branch of law demonstrated through various examples. An important classification of bra...

  19. Linear systems

    CERN Document Server

    Bourlès, Henri

    2013-01-01

    Linear systems have all the necessary elements (modeling, identification, analysis and control), from an educational point of view, to help us understand the discipline of automation and apply it efficiently. This book is progressive and organized in such a way that different levels of readership are possible. It is addressed both to beginners and those with a good understanding of automation wishing to enhance their knowledge on the subject. The theory is rigorously developed and illustrated by numerous examples which can be reproduced with the help of appropriate computation software. 60 exe

  20. Dynamical systems

    CERN Document Server

    Birkhoff, George D

    1927-01-01

    His research in dynamics constitutes the middle period of Birkhoff's scientific career, that of maturity and greatest power. -Yearbook of the American Philosophical Society The author's great book€¦is well known to all, and the diverse active modern developments in mathematics which have been inspired by this volume bear the most eloquent testimony to its quality and influence. -Zentralblatt MATH In 1927, G. D. Birkhoff wrote a remarkable treatise on the theory of dynamical systems that would inspire many later mathematicians to do great work. To a large extent, Birkhoff was writing about his o

  1. Nuclear systems

    CERN Document Server

    Todreas, Neil E

    2011-01-01

    Principal Characteristics of Power ReactorsIntroductionPower CyclesPrimary Coolant SystemsReactor CoresFuel AssembliesAdvanced Water- and Gas-Cooled Reactors (Generation III And III+)Advanced Thermal and Fast Neutron Spectrum Reactors (Generation IV)ReferencesProblemsThermal Design Principles and ApplicationIntroductionOverall Plant Characteristics Influenced by Thermal Hydraulic ConsiderationsEnergy Production and Transfer ParametersThermal Design LimitsThermal Design MarginFigures of Merit for Core Thermal PerformanceThe Inverted Fuel ArrayThe Equivalent Annulus ApproximationReferencesProble

  2. Expert Systems: What Is an Expert System?

    Science.gov (United States)

    Duval, Beverly K.; Main, Linda

    1994-01-01

    Describes expert systems and discusses their use in libraries. Highlights include parts of an expert system; expert system shells; an example of how to build an expert system; a bibliography of 34 sources of information on expert systems in libraries; and a list of 10 expert system shells used in libraries. (Contains five references.) (LRW)

  3. Expert Systems: What Is an Expert System?

    Science.gov (United States)

    Duval, Beverly K.; Main, Linda

    1994-01-01

    Describes expert systems and discusses their use in libraries. Highlights include parts of an expert system; expert system shells; an example of how to build an expert system; a bibliography of 34 sources of information on expert systems in libraries; and a list of 10 expert system shells used in libraries. (Contains five references.) (LRW)

  4. Systemic Planning

    DEFF Research Database (Denmark)

    Leleur, Steen

    This book presents principles and methodology for planning in a complex world. It sets out a so-called systemic approach to planning, among other things, by applying “hard” and “soft” methodologies and methods in combination. The book is written for Ph.D and graduate students in engineering......, business and other fields, and it is useful for all professionals, across a wide range of employment areas, who share an interest in renewing planning practice. Such an endeavour is seen as both important and timely, recognising that many complex planning tasks necessitate organisations – be they public...... or private – to engage in planning to prepare proactive decision-making....

  5. Model Systems

    Directory of Open Access Journals (Sweden)

    Francisco Rodríguez-Trelles

    1998-12-01

    Full Text Available Current efforts to study the biological effects of global change have focused on ecological responses, particularly shifts in species ranges. Mostly ignored are microevolutionary changes. Genetic changes may be at least as important as ecological ones in determining species' responses. In addition, such changes may be a sensitive indicator of global changes that will provide different information than that provided by range shifts. We discuss potential candidate systems to use in such monitoring programs. Studies of Drosophila subobscura suggest that its chromosomal inversion polymorphisms are responding to global warming. Drosophila inversion polymorphisms can be useful indicators of the effects of climate change on populations and ecosystems. Other species also hold the potential to become important indicators of global change. Such studies might significantly influence ecosystem conservation policies and research priorities.

  6. Cognitive Systems

    DEFF Research Database (Denmark)

    and its relation and potential over current artificial intelligence architectures. Machine learning models that learn from data and previous knowledge will play an increasingly important role in all levels of cognition as large real world digital environments (such as the Internet) usually are too complex...... to be modeled within a limited set of predefined specifications. There will inevitably be a need for robust decisions and behaviors in novel situations that include handling of conflicts and ambiguities based on the capability and knowledge of the artificial cognitive system. Further, there is a need......, cognitive psychology, and semantics. However, machine learning for signal processing plays a key role at all the levels of the cognitive processes, and we expect this to be a new emerging trend in our community in the coming years. Current examples of the use of machine learning for signal processing...

  7. Systemic Planning

    DEFF Research Database (Denmark)

    Leleur, Steen

    This book presents principles and methodology for planning in a complex world. It sets out a so-called systemic approach to planning, among other things, by applying “hard” and “soft” methodologies and methods in combination. The book is written for Ph.D and graduate students in engineering......, business and other fields, and it is useful for all professionals, across a wide range of employment areas, who share an interest in renewing planning practice. Such an endeavour is seen as both important and timely, recognising that many complex planning tasks necessitate organisations – be they public...... or private – to engage in planning to prepare proactive decision-making....

  8. Turbocompound system

    Energy Technology Data Exchange (ETDEWEB)

    Fox, L.D.

    1986-05-06

    A turbocompound system is described for improving the performance of an internal combustion engine without substantially increasing an end viewed profile of the engine to which it is mounted in use. The system consists of: (a) an exhaust driven turbocharger means having an exhaust manifold means extending in an axial direction for collecting exhaust gases from engine cylinders and delivering the gases to an outlet end thereof, exhaust turbine means for extracting energy from the exhaust gases, the exhaust turbine means being provided with an inlet connected to the outlet end of the manifold and an outlet for discharging the exhaust gases, compressor means coupled to the exhaust turbine means for providing a supply of charge air under pressure to an air outlet thereof for delivery to air intake means of an internal combustion engine in use; (b) a power turbine means for extracting additional energy from the exhaust gases, the power turbine means having an intake connected to the outlet of the exhaust turbine means, and mounting means on a side of the power turbine means facing in a direction parallel to the axial direction of the exhaust manifold means that is constructed for being mounted, in use, on an end of an engine adjacent one end of a crankshaft of the engine; and (c) coupling means connected to the power turbine means for transferring mechanical energy produced by the power turbine means, the coupling means extending from the power turbine means to a power take-off end in a direction parallel to the axial length of the exhaust manifold means by an amount that is sufficient for enabling the power take-off end to be connected, in use, to an opposite end of the engine crankshaft from the one end thereof in a manner for transferring the mechanical energy produced by the power turbine means adjacent the one end of the crankshaft to the opposite end of the crankshaft without having to pass therethrough.

  9. Systems engineering simplified

    CERN Document Server

    Cloutier, Robert; Bone, Mary Alice

    2015-01-01

    IntroductionOverviewDiscussion of Common TerminologyThe Case for Systems EngineeringA Brief History of Systems EngineeringSystem ExamplesSummaryThe System Life CycleManaging System Development-The Vee ModelSystem ProductionSystem Utilization and SupportSystem Retirement and DisposalOther Systems Engineering Development ModelsSpiral ModelAgile Model for Systems EngineeringSystem of InterestAbstraction and DecompositionIntegrationDeveloping and Managing RequirementsCyclone Requiremen

  10. Cardiovascular System

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    7.1 Heart failure2007175 Effects of recombinant human brain natriuretic peptide on aldosterone and endothelin-1 in treatment of heart failure. FU Yao(付尧),et al. Dept Cardiol, 1st Affili Hosp, China Med Univ, Shenyang 110001. Chin Cir J 2007;22(1):35-37. Obiective To study the efficacy and the effects of recombinant human brain natriuretic peptide(rhBNP) on aldosterone and endothelin-1 in the treatment of congestive heart failure(CHF).Methods A randomized, open, controlled clinical trial was conducted in 35 patients with CHF. Eighteen received rhBNP and 17 were treated with nitroglycerin as controls. The changes hemodynamic indexes, the plasma concentrations of K+, Na+, aldo-sterone(ALD) and endothelin-1 (ET-1) in order to examine the efficacy and mechanism of rhBNP. Results Between experiment and control groups significant differences were found in the decreasing of PCWP, PAP and plasma concentration of Na+, ALD, ET-1, and in the increasing of plasma concentration of K+ (P<0.05~0.01). Conclusion The mechanism of rhBNP may be associated with the overactivation of renin-angiotension-aldosterone system, and the inhibited production of endothelin-1.

  11. Systems Biology and Health Systems Complexity in;

    NARCIS (Netherlands)

    Donald Combs, C.; Barham, S.R.; Sloot, P.M.A.

    2016-01-01

    Systems biology addresses interactions in biological systems at different scales of biological organization, from the molecular to the cellular, organ, organism, societal, and ecosystem levels. This chapter expands on the concept of systems biology, explores its implications for individual patients

  12. System safety education focused on system management

    Science.gov (United States)

    Grose, V. L.

    1971-01-01

    System safety is defined and characteristics of the system are outlined. Some of the principle characteristics include role of humans in hazard analysis, clear language for input and output, system interdependence, self containment, and parallel analysis of elements.

  13. Respiratory System

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    8.1 Respiratory failure2007204 Comparison of the effects of BiPAP ventilation combined with lung recruitment maneuvers and low tidal volume A/C ventilation in patients with acute respiratory distress syndrome. WANG Xiaozhi(王晓芝),et al. Dept Respir & Intensive Care Unit, Binzhou Med Coll, Binzhou 256603. Chin J Tuberc Respir Dis 2007;30(1):44-47. Objective To compare the effects of BiPAP ventilation combined with lung recruitment maneuvers(LRM) with low tidal volume A/C ventilation in patients with acute respiratory distress syndrome (ARDS). Methods A prospective, randomized comparison of BiPAP mechanical ventilation combined with lung recruitment maneuvers(test group) with low tidal volume A/C ventilation (control group) was conducted in 28 patients with ARDS. FiO2/PaO2 ratio, respiratory system compliance(Cs), central venous pressure (CVP), duration of ventilation support were recorded at 0 h, 48 h and 72 h separately. The ventilation associated lung injury and mortality at 28 d were also recorded. Results The FiO2/PaO2 ratio were (298±16) and (309±16) cm H2O, Cs were (38.4±2.2) and (42.0±1.3) ml/cm H2O, CVP were (13.8±0.8) and (11.6±0.7) cm H2O in the test group at 48 h and 72 h separately. In the control group, FiO2/PaO2 ratio were (212±12) and (246±17) cm H2O, Cs were (29.5±1.3) and (29.0±1.0) ml/cm H2O, CVP were 18.6±1.1 and (16.8±1.0) cm H2O. The results were better in the test group as compared with the control group (t=10.03-29. 68, all P<0.01). The duration of ventilation support in the test group was shorter than the control group [(14±3) d vs (19±3)d, t=4.80, P<0.01]. The mortality in 28 d and ventilation associated lung injury were similar in the two groups. Conclusion The results show that combination of LRM with BiPAP mode ventilation, as compared with the control group, contributes to the improved FiO2/PaO2 ratio, pulmonary compliance, stable homodynamic and shorter duration of ventilation support in patients with ARDs.

  14. Quality management system

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Mu Sung

    2009-08-15

    This book deals with ISO9001 quality management system which includes summary of this system such as classification of quality, principle of quality management, and definition, requirement and procedure of quality management system, introduction of ISO9001 system like model of ISO9001 quality management system, ISO certificate system, structure of ISO9001 standard, requirement of ISO9001 quality management system, process approach and documentation of system, propel cases of ISO9001 quality management system.

  15. Systems theory of interconnected port contact systems

    NARCIS (Netherlands)

    Eberard, D.; Maschke, B.M.; Schaft, A.J. van der

    2005-01-01

    Port-based network modeling of a large class of complex physical systems leads to dynamical systems known as port-Hamiltonian systems. The key ingredient of any port-Hamiltonian system is a power-conserving interconnection structure (mathematically formalized by the geometric notion of a Dirac struc

  16. Protecting Information in Systems of Systems

    NARCIS (Netherlands)

    Trivellato, Daniel; Zannone, Nicola; Etalle, Sandro

    2011-01-01

    Systems of Systems (SoS) are dynamic, distributed coalitions of autonomous and heterogeneous systems that collaborate to achieve a common goal. While offering several advantages in terms of scalability and flexibility, the SoS paradigm has a strong impact on system interoperability and on the securi

  17. Advanced Systems Theory Applied to AMB Systems

    NARCIS (Netherlands)

    Balini, H.M.N.K.

    2011-01-01

    In this thesis we look at the application of advanced systems theoretic algorithms for an experimental Active Magnetic Bearing System (AMB). These systems are inherently unstable and therefore require a feedback controller. Accurate modeling of these systems with input-output data is hindered due to

  18. Square conservation systems and Hamiltonian systems

    Institute of Scientific and Technical Information of China (English)

    王斌; 曾庆存; 季仲贞

    1995-01-01

    The internal and external relationships between the square conservation scheme and the symplectic scheme are revealed by a careful study on the interrelation between the square conservation system and the Hamiltonian system in the linear situation, thus laying a theoretical basis for the application and extension of symplectic schemes to square conservations systems, and of those schemes with quadratic conservation properties to Hamiltonian systems.

  19. A Security Framework for Systems of Systems

    NARCIS (Netherlands)

    Trivellato, Daniel; Zannone, Nicola; Etalle, Sandro

    2011-01-01

    Systems of systems consist of a wide variety of dynamic, distributed coalitions of autonomous and heterogeneous systems that collaborate to achieve a common goal. While offering several advantages in terms of scalability and flexibility, this new paradigm has a strong impact on system

  20. Understanding Patterns for System of Systems Integration

    DEFF Research Database (Denmark)

    Kazman, Rick; Schmid, Klaus; Nielsen, Claus Ballegård

    2013-01-01

    of systems integration patterns. These characteristics at the same time support the architecting process by highlighting important issues a SoS architect needs to consider. We discuss the consolidated template and illustrate it with an example pattern. We also discuss the integration of this novel pattern......Architecting systems of systems is well known to be a formidable challenge. A major aspect in this is defining the integration among the systems that constitute the system of systems. In this paper, we aim to support the SoS architect by systematically developing a way to characterize system...

  1. Concept and System of Personification Control System

    Institute of Scientific and Technical Information of China (English)

    Bai,Fengshuang; Yin,Yixin; Tu,Xuyan; Zhang,Ying

    2006-01-01

    This paper provides the system and conception of the Personification Control System (PCS) on the basis of Intelligent Control System based on Artificial life (ICS/AL), Artificial Emotion, Humanoid Control, and Intelligent Control System based on Field bus. According to system science and deciding of organize of biology, the Pyramid System of PCS are created. Then Pyramid System of PCS which is made up of PCS1/H, PCS1/S, PCS1/O, PCS1/C and PCS1/G is described.

  2. Networked control of microgrid system of systems

    Science.gov (United States)

    Mahmoud, Magdi S.; Rahman, Mohamed Saif Ur; AL-Sunni, Fouad M.

    2016-08-01

    The microgrid has made its mark in distributed generation and has attracted widespread research. However, microgrid is a complex system which needs to be viewed from an intelligent system of systems perspective. In this paper, a network control system of systems is designed for the islanded microgrid system consisting of three distributed generation units as three subsystems supplying a load. The controller stabilises the microgrid system in the presence of communication infractions such as packet dropouts and delays. Simulation results are included to elucidate the effectiveness of the proposed control strategy.

  3. D0 Cryo System Control System Autodialer

    Energy Technology Data Exchange (ETDEWEB)

    Urbin, J.; /Fermilab

    1990-04-17

    The DO cryogenic system is controlled by a TI565-PLC based control system. This allows the system to be unmanned when in steady state operation. System experts will need to be contacted when system parameters exceed normal operating points and reach alarm setpoints. The labwide FIRUS system provides one alarm monitor and communication link. An autodialer provides a second and more flexible alarm monitor and communication link. The autodialer monitors contact points in the control system and after receiving indication of an alarm accesses a list of experts which it calls until it receives an acknowledgement. There are several manufacturers and distributors of autodialer systems. This EN explains the search process the DO cryo group used to fmd an autodialer system that fit the cryo system's needs and includes information and specs for the unit we chose.

  4. Integrated library systems.

    Science.gov (United States)

    Goldstein, C M

    1983-07-01

    The development of integrated library systems is discussed. The four major discussion points are (1) initial efforts; (2) network resources; (3) minicomputer-based systems; and (4) beyond library automation. Four existing systems are cited as examples of current systems.

  5. Freshwater systems; Frisch gezapft

    Energy Technology Data Exchange (ETDEWEB)

    Meyer, J.P.

    2008-06-09

    Increasingly, providers of solar systems are also offering freshwater systems, although these are more costly than combined storage systems. The contribution discusses the pros and cons of these systems as well as the freshwater quality. (orig.)

  6. System design specification Brayton Isotope Power System (BIPS) Flight System (FS), and Ground Demonstration System (GDS)

    Energy Technology Data Exchange (ETDEWEB)

    1976-06-14

    The system design specification for ground demonstration, development, and flight qualification of a Brayton Isotope Power System (BIPS) is presented. The requirements for both a BIPS conceptual Flight System (FS) and a Ground Demonstration System (GDS) are defined.

  7. Situation awareness with systems of systems

    CERN Document Server

    Tretmans, Jan; Borth, Michael

    2013-01-01

    This book discusses various aspects, challenges, and solutions for developing systems-of-systems for situation awareness, using applications in the domain of maritime safety and security.  Topics include advanced, multi-objective visualization methods for situation awareness, stochastic outlier selection, rule-based anomaly detection, an ontology-based event model for semantic reasoning, new methods for semi-automatic generation of adapters bridging communication gaps, security policies for systems-of-systems, trust assessment, and methods to deal with the dynamics of systems-of-systems in run-time monitoring, testing, and diagnosis. Architectural considerations for designing information-centric systems-of-systems such as situation awareness systems, and an integrated demonstrator implementing many of the investigated aspects, complete the book.

  8. System of systems modeling and analysis.

    Energy Technology Data Exchange (ETDEWEB)

    Campbell, James E.; Anderson, Dennis James; Longsine, Dennis E. (Intera, Inc., Austin, TX); Shirah, Donald N.

    2005-01-01

    This report documents the results of an LDRD program entitled 'System of Systems Modeling and Analysis' that was conducted during FY 2003 and FY 2004. Systems that themselves consist of multiple systems (referred to here as System of Systems or SoS) introduce a level of complexity to systems performance analysis and optimization that is not readily addressable by existing capabilities. The objective of the 'System of Systems Modeling and Analysis' project was to develop an integrated modeling and simulation environment that addresses the complex SoS modeling and analysis needs. The approach to meeting this objective involved two key efforts. First, a static analysis approach, called state modeling, has been developed that is useful for analyzing the average performance of systems over defined use conditions. The state modeling capability supports analysis and optimization of multiple systems and multiple performance measures or measures of effectiveness. The second effort involves time simulation which represents every system in the simulation using an encapsulated state model (State Model Object or SMO). The time simulation can analyze any number of systems including cross-platform dependencies and a detailed treatment of the logistics required to support the systems in a defined mission.

  9. Computer System Design System-on-Chip

    CERN Document Server

    Flynn, Michael J

    2011-01-01

    The next generation of computer system designers will be less concerned about details of processors and memories, and more concerned about the elements of a system tailored to particular applications. These designers will have a fundamental knowledge of processors and other elements in the system, but the success of their design will depend on the skills in making system-level tradeoffs that optimize the cost, performance and other attributes to meet application requirements. This book provides a new treatment of computer system design, particularly for System-on-Chip (SOC), which addresses th

  10. Smart electromechanical systems the central nervous system

    CERN Document Server

    Kurbanov, Vugar

    2017-01-01

    This book describes approaches to solving the problems of developing the central nervous system of robots (CNSR) based on smart electromechanical systems (SEMS) modules, principles of construction of the various modules of the central nervous system and variants of mathematical software CNSR in control systems for intelligent robots. It presents the latest advances in theory and practice at the Russian Academy of Sciences. Developers of intelligent robots to solve modern problems in robotics are increasingly addressing the use of the bionic approach to create robots that mimic the complexity and adaptability of biological systems. These have smart electromechanical system (SEMS), which are used in various cyber-physical systems (CPhS), and allow the functions of calculation, control, communications, information storage, monitoring, measurement and control of parameters and environmental parameters to be integrated. The behavior of such systems is based on the information received from the central nervous syst...

  11. Linking Political Systems and War Systems

    DEFF Research Database (Denmark)

    Harste, Gorm

    2009-01-01

    Decisive parts of the Western political system have demonstrated a seemingly surprising misinterpretation of military might. As Madelaine Albright has suggested, the mighty perceived themselves as "almighty". Political power seems to have invested in instrumental coercive power relations and found...... military coercion to be the appropriate mean. Using the system theory and the theory of systemic risks displayed by the German sociologist Niklas Luhmann the article demonstrates how military systems due to their own autonomy and autopoiesis do not fit into the idea of political government....... The Clausewitzian ideal of a political system that could continue its power games by means of war was moderated by Clausewitz' own analysis of "friction". How can a political system be so blind towards the possibilities of another system? What are the risks of systemic blind spots? The argument of the paper...

  12. Situation Awareness with Systems of Systems

    NARCIS (Netherlands)

    Laar, P. van de; Tretmans, J.; Borth, M.

    2013-01-01

    This book discusses various aspects, challenges, and solutions for developing systems-of-systems for situation awareness, using applications in the domain of maritime safety and security. Topics include advanced, multi-objective visualization methods for situation awareness, stochastic outlier

  13. Linking Political Systems and War Systems

    DEFF Research Database (Denmark)

    Harste, Gorm

    2009-01-01

    Decisive parts of the Western political system have demonstrated a seemingly surprising misinterpretation of military might. As Madelaine Albright has suggested, the mighty perceived themselves as "almighty". Political power seems to have invested in instrumental coercive power relations and found...... military coercion to be the appropriate mean. Using the system theory and the theory of systemic risks displayed by the German sociologist Niklas Luhmann the article demonstrates how military systems due to their own autonomy and autopoiesis do not fit into the idea of political government....... The Clausewitzian ideal of a political system that could continue its power games by means of war was moderated by Clausewitz' own analysis of "friction". How can a political system be so blind towards the possibilities of another system? What are the risks of systemic blind spots? The argument of the paper...

  14. Engine Auxiliary System Guideline: Lubricating Oil Systems

    OpenAIRE

    Linna, Joni

    2015-01-01

    This thesis was done for Wärtsilä Technical Services organization, the purpose of this work was to gather and structure information about the lubricating oil systems from the company’s internal databases, interviews with system specialists and from different literature sources covering Ship Power and Power Plant products. The outcome was a guideline, covering typical power plant and marine system descriptions, all components used in the lubricating oil system with their functional description...

  15. COMPARISON TRADITIONAL SYSTEMS OF TUNNEL FORMWORK SYSTEM

    OpenAIRE

    ERKAN, İbrahim Hakkı; Yılmaz, Ülkü Sultan; Türken, Hakan

    2011-01-01

    Tunnel formwork systems became the most widespread construction technology preferred in recent years in Turkey due to rapidity and economy. In this study, before all else, a brief information was given about the types and construction techniques of tunnel formwork systems. Then a reinforced concrete building sample was firstly modeled as it was constructed with the tunnel formwork system and secondly modeled as it was formed by a frame system with shear walls constructed by the traditional re...

  16. LCLS XTOD Attenuator System System Concept Report

    Energy Technology Data Exchange (ETDEWEB)

    Kishiyama, K; Roeben, M; Trent, J; Ryutov, D; Shen, S

    2006-04-12

    The attenuator system for the Linac Coherent Light Source (LCLS) X-ray Transport, Optics and Diagnostics (XTOD) system has been configured and analyzed by the Lawrence Livermore National Laboratory's New Technologies Engineering Division (NTED) as requested by the SLAC/LCLS program. The system layout, performance analyses and selection of the vacuum components are presented in this System Conceptual Review (SCR) report. Also included are the plans for prototype, procurement, mechanical integration, and the cost estimates.

  17. Designing information systems

    CERN Document Server

    Blethyn, Stanley G

    2014-01-01

    Designing Information Systems focuses on the processes, methodologies, and approaches involved in designing information systems. The book first describes systems, management and control, and how to design information systems. Discussions focus on documents produced from the functional construction function, users, operators, analysts, programmers and others, process management and control, levels of management, open systems, design of management information systems, and business system description, partitioning, and leveling. The text then takes a look at functional specification and functiona

  18. Modeling learning technology systems as business systems

    NARCIS (Netherlands)

    Avgeriou, Paris; Retalis, Symeon; Papaspyrou, Nikolaos

    2003-01-01

    The design of Learning Technology Systems, and the Software Systems that support them, is largely conducted on an intuitive, ad hoc basis, thus resulting in inefficient systems that defectively support the learning process. There is now justifiable, increasing effort in formalizing the engineering o

  19. Non linear system become linear system

    Directory of Open Access Journals (Sweden)

    Petre Bucur

    2007-01-01

    Full Text Available The present paper refers to the theory and the practice of the systems regarding non-linear systems and their applications. We aimed the integration of these systems to elaborate their response as well as to highlight some outstanding features.

  20. Expert Systems for auditing management information systems

    Directory of Open Access Journals (Sweden)

    Gheroghe Popescu

    2007-05-01

    Full Text Available Expert systems are built with the help of: specialised programming languages or expert system generators (shell. But this structure was reached after tens of years of work and research, because expert systems are nothing but pragmatic capitalisation of the results of research carried out in artificial intelligence and theory of knowledge.

  1. General Systems Theory and Instructional Systems Design.

    Science.gov (United States)

    Salisbury, David F.

    1990-01-01

    Describes basic concepts in the field of general systems theory (GST) and identifies commonalities that exist between GST and instructional systems design (ISD). Models and diagrams that depict system elements in ISD are presented, and two matrices that show how GST has been used in ISD literature are included. (11 references) (LRW)

  2. The complement system in systemic autoimmune disease

    NARCIS (Netherlands)

    Chen, Min; Daha, Mohamed R.; Kallenberg, Cees G. M.

    2010-01-01

    Complement is part of the innate immune system. Its major function is recognition and elimination of pathogens via direct killing and/or stimulation of phagocytosis. Activation of the complement system is, however, also involved in the pathogenesis of the systemic autoimmune diseases. Activation via

  3. Optical system defect propagation in ABCD systems

    DEFF Research Database (Denmark)

    McKinley, W.G.; Yura, H.T.; Hanson, Steen Grüner

    1988-01-01

    We describe how optical system defects (tilt/jitter, decenter, and despace) propagate through an arbitrary paraxial optical system that can be described by an ABCD ray transfer matrix. A pedagogical example is given that demonstrates the effect of alignment errors on a typical optical system....... © 1988 Optical Society of America...

  4. Observing System Evaluations Using GODAE Systems

    Science.gov (United States)

    2009-09-01

    Journal of Marine Systems 35...dimensional temperature fields: A first approach based on simulated observations. Journal of Marine Systems 46:85-98. Langland, R.H., and N.L. Baker...capabilities of multisatellite altimeter missions: First results with real data in the Mediterranean Sea. Journal of Marine Systems 65:190-211.

  5. Modeling learning technology systems as business systems

    NARCIS (Netherlands)

    Avgeriou, Paris; Retalis, Symeon; Papaspyrou, Nikolaos

    2003-01-01

    The design of Learning Technology Systems, and the Software Systems that support them, is largely conducted on an intuitive, ad hoc basis, thus resulting in inefficient systems that defectively support the learning process. There is now justifiable, increasing effort in formalizing the engineering

  6. Biomedical signals and systems

    CERN Document Server

    Tranquillo, Joseph V

    2013-01-01

    Biomedical Signals and Systems is meant to accompany a one-semester undergraduate signals and systems course. It may also serve as a quick-start for graduate students or faculty interested in how signals and systems techniques can be applied to living systems. The biological nature of the examples allows for systems thinking to be applied to electrical, mechanical, fluid, chemical, thermal and even optical systems. Each chapter focuses on a topic from classic signals and systems theory: System block diagrams, mathematical models, transforms, stability, feedback, system response, control, time

  7. Psychology of system design

    CERN Document Server

    Meister, D

    2014-01-01

    This is a book about systems, including: systems in which humans control machines; systems in which humans interact with humans and the machine component is relatively unimportant; systems which are heavily computerized and those that are not; and governmental, industrial, military and social systems. The book deals with both traditional systems like farming, fishing and the military, and with systems just now tentatively emerging, like the expert and the interactive computer system. The emphasis is on the system concept and its implications for analysis, design and evaluation of these many di

  8. Operating System Security

    CERN Document Server

    Jaeger, Trent

    2008-01-01

    Operating systems provide the fundamental mechanisms for securing computer processing. Since the 1960s, operating systems designers have explored how to build "secure" operating systems - operating systems whose mechanisms protect the system against a motivated adversary. Recently, the importance of ensuring such security has become a mainstream issue for all operating systems. In this book, we examine past research that outlines the requirements for a secure operating system and research that implements example systems that aim for such requirements. For system designs that aimed to

  9. Lighting system with thermal management system

    Science.gov (United States)

    Arik, Mehmet; Weaver, Stanton; Stecher, Thomas; Seeley, Charles; Kuenzler, Glenn; Wolfe, Jr., Charles; Utturkar, Yogen; Sharma, Rajdeep; Prabhakaran, Satish; Icoz, Tunc

    2013-05-07

    Lighting systems having unique configurations are provided. For instance, the lighting system may include a light source, a thermal management system and driver electronics, each contained within a housing structure. The light source is configured to provide illumination visible through an opening in the housing structure. The thermal management system is configured to provide an air flow, such as a unidirectional air flow, through the housing structure in order to cool the light source. The driver electronics are configured to provide power to each of the light source and the thermal management system.

  10. Lighting system with thermal management system

    Energy Technology Data Exchange (ETDEWEB)

    Arik, Mehmet; Weaver, Stanton Earl; Stecher, Thomas Elliot; Seeley, Charles Erklin; Kuenzler, Glenn Howard; Wolfe, Jr, Charles Franklin; Utturkar, Yogen Vishwas; Sharma, Rajdeep; Prabhakaran, Satish; Icoz, Tunc

    2016-10-11

    Lighting systems having unique configurations are provided. For instance, the lighting system may include a light source, a thermal management system and driver electronics, each contained within a housing structure. The light source is configured to provide illumination visible through an opening in the housing structure. The thermal management system is configured to provide an air flow, such as a unidirectional air flow, through the housing structure in order to cool the light source. The driver electronics are configured to provide power to each of the light source and the thermal management system.

  11. Systems Measures of Water Distribution System Resilience

    Energy Technology Data Exchange (ETDEWEB)

    Klise, Katherine A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Murray, Regan [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Walker, La Tonya Nicole [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-01-01

    Resilience is a concept that is being used increasingly to refer to the capacity of infrastructure systems to be prepared for and able to respond effectively and rapidly to hazardous events. In Section 2 of this report, drinking water hazards, resilience literature, and available resilience tools are presented. Broader definitions, attributes and methods for measuring resilience are presented in Section 3. In Section 4, quantitative systems performance measures for water distribution systems are presented. Finally, in Section 5, the performance measures and their relevance to measuring the resilience of water systems to hazards is discussed along with needed improvements to water distribution system modeling tools.

  12. Intelligent test integration system

    Science.gov (United States)

    Sztipanovits, J.; Padalkar, S.; Rodriguez-Moscoso, J.; Kawamura, K.; Purves, B.; Williams, R.; Biglari, H.

    1988-01-01

    A new test technology is described which was developed for space system integration. The ultimate purpose of the system is to support the automatic generation of test systems in real time, distributed computing environments. The Intelligent Test Integration System (ITIS) is a knowledge based layer above the traditional test system components which can generate complex test configurations from the specification of test scenarios.

  13. Autonomous photovoltaic lighting system

    OpenAIRE

    Ahmed A. A. Hafez; Montesinos Miracle, Daniel; Sudrià Andreu, Antoni

    2012-01-01

    This paper introduces a comparison between the conventional and Photovoltaic (PV) lighting systems. A simple sizing procedure for a PV stand-alone system was advised. The paper also proposes a novel PV lighting system. The proposed system is simple, compact and reliable. The system operation was investigated by thoroughly mathematical and simulation work.

  14. Mapping biological systems to network systems

    CERN Document Server

    Rathore, Heena

    2016-01-01

    The book presents the challenges inherent in the paradigm shift of network systems from static to highly dynamic distributed systems – it proposes solutions that the symbiotic nature of biological systems can provide into altering networking systems to adapt to these changes. The author discuss how biological systems – which have the inherent capabilities of evolving, self-organizing, self-repairing and flourishing with time – are inspiring researchers to take opportunities from the biology domain and map them with the problems faced in network domain. The book revolves around the central idea of bio-inspired systems -- it begins by exploring why biology and computer network research are such a natural match. This is followed by presenting a broad overview of biologically inspired research in network systems -- it is classified by the biological field that inspired each topic and by the area of networking in which that topic lies. Each case elucidates how biological concepts have been most successfully ...

  15. Operating System Performance Analyzer for Embedded Systems

    Directory of Open Access Journals (Sweden)

    Shahzada Khayyam Nisar

    2011-11-01

    Full Text Available RTOS provides a number of services to an embedded system designs such as case management, memory management, and Resource Management to build a program. Choosing the best OS for an embedded system is based on the available OS for system designers and their previous knowledge and experience. This can cause an imbalance between the OS and embedded systems. RTOS performance analysis is critical in the design and integration of embedded software to ensure that limits the application meet at runtime. To select an appropriate operating system for an embedded system for a particular application, the OS services to be analyzed. These OS services are identified by parameters to establish performance metrics. Performance Metrics selected include context switching, Preemption time and interrupt latency. Performance Metrics are analyzed to choose the right OS for an embedded system for a particular application.

  16. Systems Architecture for a Nationwide Healthcare System.

    Science.gov (United States)

    Abin, Jorge; Nemeth, Horacio; Friedmann, Ignacio

    2015-01-01

    From a national level to give Internet technology support, the Nationwide Integrated Healthcare System in Uruguay requires a model of Information Systems Architecture. This system has multiple healthcare providers (public and private), and a strong component of supplementary services. Thus, the data processing system should have an architecture that considers this fact, while integrating the central services provided by the Ministry of Public Health. The national electronic health record, as well as other related data processing systems, should be based on this architecture. The architecture model described here conceptualizes a federated framework of electronic health record systems, according to the IHE affinity model, HL7 standards, local standards on interoperability and security, as well as technical advice provided by AGESIC. It is the outcome of the research done by AGESIC and Systems Integration Laboratory (LINS) on the development and use of the e-Government Platform since 2008, as well as the research done by the team Salud.uy since 2013.

  17. Autonomic Nervous System Disorders

    Science.gov (United States)

    Your autonomic nervous system is the part of your nervous system that controls involuntary actions, such as the beating of your heart ... breathing and swallowing Erectile dysfunction in men Autonomic nervous system disorders can occur alone or as the result ...

  18. Calo trigger acquisition system

    CERN Multimedia

    Franchini, Matteo

    2016-01-01

    Calo trigger acquisition system - Evolution of the acquisition system from a multiple boards system (upper, orange cables) to a single board one (below, light blue cables) where all the channels are collected in a single board.

  19. Brain and Nervous System

    Science.gov (United States)

    ... Your 1- to 2-Year-Old Brain and Nervous System KidsHealth > For Parents > Brain and Nervous System Print ... brain is quite the juggler. Anatomy of the Nervous System If you think of the brain as a ...

  20. for hybrid dynamical systems

    Directory of Open Access Journals (Sweden)

    Wassim M. Haddad

    2001-01-01

    Full Text Available In this paper we develop a unified dynamical systems framework for a general class of systems possessing left-continuous flows; that is, left-continuous dynamical systems. These systems are shown to generalize virtually all existing notions of dynamical systems and include hybrid, impulsive, and switching dynamical systems as special cases. Furthermore, we generalize dissipativity, passivity, and nonexpansivity theory to left-continuous dynamical systems. Specifically, the classical concepts of system storage functions and supply rates are extended to left-continuous dynamical systems providing a generalized hybrid system energy interpretation in terms of stored energy, dissipated energy over the continuous-time dynamics, and dissipated energy over the resetting events. Finally, the generalized dissipativity notions are used to develop general stability criteria for feedback interconnections of left-continuous dynamical systems. These results generalize the positivity and small gain theorems to the case of left-continuous, hybrid, and impulsive dynamical systems.

  1. Bridge Management Systems

    DEFF Research Database (Denmark)

    Thoft-Christensen, Palle

    In this paper bridge management systems are discussed with special emphasis on management systems for reinforced concrete bridges. Management systems for prestressed concrete bridges, steel bridges, or composite bridges can be developed in a similar way....

  2. Manned systems technology discipline

    Science.gov (United States)

    Bretoi, Remus

    1990-01-01

    Viewgraphs on manned systems technology discipline for Space Station Freedom are presented. Topics covered include: crew-systems interfaces and interactions; crew training; on-board systems maintenance and support; habitability and environment; and computational human factors.

  3. System Software 7 Macintosh

    CERN Multimedia

    1991-01-01

    System 7 is a single-user graphical user interface-based operating system for Macintosh computers and was part of the classic Mac OS line of operating systems. It was introduced on May 13, 1991, by Apple Computer. It succeeded System 6, and was the main Macintosh operating system until it was succeeded by Mac OS 8 in 1997. Features added with the System 7 release included virtual memory, personal file sharing, QuickTime, QuickDraw 3D, and an improved user interface. This is the first real major evolution of the Macintosh system, bringing a significant improvement in the user interface, improved stability and many new features such as the ability to use multiple applications at the same time. "System 7" is the last operating system name of the Macintosh that contains the word "system". Macintosh operating systems were later called "Mac OS" (for Macintosh Operating System).

  4. Game Information System

    CERN Document Server

    Warnars, Spits; Kingdom, United; 10.5121/ijcsit.2010.2310

    2010-01-01

    In this Information system age many organizations consider information system as their weapon to compete or gain competitive advantage or give the best services for non profit organizations. Game Information System as combining Information System and game is breakthrough to achieve organizations’ performance. The Game Information System will run the Information System with game and how game can be implemented to run the Information System. Game is not only for fun and entertainment, but will be a challenge to combine fun and entertainment with Information System. The Challenge to run the information system with entertainment, deliver the entertainment with information system all at once. Game information system can be implemented in many sectors as like the information system itself but in difference’s view. A view of game which people can joy and happy and do their transaction as a fun things.

  5. Central Nervous System Vasculitis

    Science.gov (United States)

    ... Nervous System (CNS) Vasculitis Central Nervous System (CNS) Vasculitis Central nervous system (CNS) vasculitis is inflammation of ... CNS (PACNS). What is the cause of CNS Vasculitis? How the vessels in the brain become inflamed ...

  6. Immune System Quiz

    Science.gov (United States)

    ... Know About Puberty Train Your Temper Quiz: Immune System KidsHealth > For Kids > Quiz: Immune System Print A A A How much do you know about your immune system? Find out by taking this quiz! About KidsHealth ...

  7. What Are Expert Systems?

    Science.gov (United States)

    d'Agapeyeff, A.

    1986-01-01

    Intended for potential business users, this paper describes the main characteristics of expert systems; discusses practical use considerations; presents a taxonomy of the systems; and reviews several expert system development projects in business and industry. (MBR)

  8. The Trinity System

    Energy Technology Data Exchange (ETDEWEB)

    Archer, Billy Joe [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Vigil, Benny Manuel [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-01-13

    This paper describes the Trinity system, the first ASC Advanced Technology System (ATS-1). We describe the Trinity procurement timeline, the ASC computing strategy, the Trinity specific mission needs, and the Trinity system specifications.

  9. Marketing reporting system

    Directory of Open Access Journals (Sweden)

    Hanić Hasan M.

    2004-01-01

    Full Text Available The main components of a developed and good organized marketing information system are: internal reporting system, marketing reporting system, market research system and analytical marketing system. Marketing reporting system provides data and information about changes in business and micro marketing environment. This component of MIS ensures that marketing managers are up-to-date with what is going on, and to be informed about changes in company marketing environment.

  10. Marketing reporting system

    OpenAIRE

    Hanić Hasan M.

    2004-01-01

    The main components of a developed and good organized marketing information system are: internal reporting system, marketing reporting system, market research system and analytical marketing system. Marketing reporting system provides data and information about changes in business and micro marketing environment. This component of MIS ensures that marketing managers are up-to-date with what is going on, and to be informed about changes in company marketing environment.

  11. Small test SDHW systems

    DEFF Research Database (Denmark)

    Vejen, Niels Kristian

    1999-01-01

    Three small test SDHW systems was tested in a laboratory test facility.The three SDHW systems where all based on the low flow principe and a mantle tank but the design of the systems where different.......Three small test SDHW systems was tested in a laboratory test facility.The three SDHW systems where all based on the low flow principe and a mantle tank but the design of the systems where different....

  12. Small test SDHW systems

    DEFF Research Database (Denmark)

    Vejen, Niels Kristian

    1999-01-01

    Three small test SDHW systems was tested in a laboratory test facility.The three SDHW systems where all based on the low flow principe and a mantle tank but the design of the systems where different.......Three small test SDHW systems was tested in a laboratory test facility.The three SDHW systems where all based on the low flow principe and a mantle tank but the design of the systems where different....

  13. Law System in Japan

    OpenAIRE

    Andreea Lorena Ponaru

    2007-01-01

    This article attempts to present and explain the main features of the japanese law system. Japanese Law system was reformed during the domination of Tokugawa shogun family. In 1870, Foreign Governmental Systems Study Office was founded. By judicial sentences many french laws were introduced in Japanese law system. Roma-Tokyo-Berlin Alliance (1936) introduced a strong German influence in the law system. The Japanese judicial system has known five periods. In the first (1869-1888) were introduc...

  14. Battery systems engineering

    CERN Document Server

    Rahn, Christopher D

    2012-01-01

    A complete all-in-one reference on the important interdisciplinary topic of Battery Systems Engineering Focusing on the interdisciplinary area of battery systems engineering, this book provides the background, models, solution techniques, and systems theory that are necessary for the development of advanced battery management systems. It covers the topic from the perspective of basic electrochemistry as well as systems engineering topics and provides a basis for battery modeling for system engineering of electric and hybrid electric vehicle platforms. This original

  15. Airports Geographic Information System -

    Data.gov (United States)

    Department of Transportation — The Airports Geographic Information System maintains the airport and aeronautical data required to meet the demands of the Next Generation National Airspace System....

  16. Control system design method

    Science.gov (United States)

    Wilson, David G [Tijeras, NM; Robinett, III, Rush D.

    2012-02-21

    A control system design method and concomitant control system comprising representing a physical apparatus to be controlled as a Hamiltonian system, determining elements of the Hamiltonian system representation which are power generators, power dissipators, and power storage devices, analyzing stability and performance of the Hamiltonian system based on the results of the determining step and determining necessary and sufficient conditions for stability of the Hamiltonian system, creating a stable control system based on the results of the analyzing step, and employing the resulting control system to control the physical apparatus.

  17. Aeronautical Information System -

    Data.gov (United States)

    Department of Transportation — The Aeronautical Information System (AIS) is a leased weather automated system that provides a means of collecting and distributing aeronautical weather information...

  18. Cognitive Medical Multiagent Systems

    Directory of Open Access Journals (Sweden)

    Barna Iantovics

    2010-01-01

    Full Text Available The development of efficient and flexible agent-based medical diagnosis systems represents a recent research direction. Medical multiagent systems may improve the efficiency of traditionally developed medical computational systems, like the medical expert systems. In our previous researches, a novel cooperative medical diagnosis multiagent system called CMDS (Contract Net Based Medical Diagnosis System was proposed. CMDS system can solve flexibly a large variety of medical diagnosis problems. This paper analyses the increased intelligence of the CMDS system, which motivates its use for different medical problem’s solving.

  19. RECURSIVE SYSTEM IDENTIFICATION

    Institute of Scientific and Technical Information of China (English)

    Han-Fu Chen

    2009-01-01

    Most of existing methods in system identification with possible exception of those for linear systems are off-line in nature, and hence are nonrecursive.This paper demonstrates the recent progress in recursive system identification.The recursive identifi-cation algorithms are presented not only for linear systems (multivariate ARMAX systems) but also for nonlinear systems such as the Hammerstein and Wiener systems, and the non-linear ARX systems.The estimates generated by the algorithms are online updated and converge a.s.to the true values as time tends to infinity.

  20. Neural Systems Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — As part of the Electrical and Computer Engineering Department and The Institute for System Research, the Neural Systems Laboratory studies the functionality of the...

  1. Credit Management System

    Data.gov (United States)

    US Agency for International Development — Credit Management System. Outsourced Internet-based application. CMS stores and processes data related to USAID credit programs. The system provides information...

  2. Antibacterial action of quinolones: from target to network.

    Science.gov (United States)

    Cheng, Guyue; Hao, Haihong; Dai, Menghong; Liu, Zhenli; Yuan, Zonghui

    2013-08-01

    Quinolones are widely used broad-spectrum antibacterials with incomplete elucidated mechanism of action. Here, molecular basis for the antibacterial action of quinolones, from target to network, is fully discussed and updated. Quinolones trap DNA gyrase or topoisomerase IV to form reversible drug-enzyme-DNA cleavage complexes, resulting in bacteriostasis. Cell death arises from chromosome fragmentation in protein synthesis-dependent or -independent pathways according to distinguished quinolone structures. In the former pathway, irreversible oxidative DNA damage caused by reactive oxygen species kills bacteria eventually. Toxin-antitoxin mazEF is triggered as an additional lethal action. Bacteria survive and develop resistance by SOS and other stress responses. Enlarged knowledges of quinolone actions and bacterial response will provide new targets for drug design and approaches to prevent bacterial resistance.

  3. Adenylylation of Gyrase and Topo IV by FicT Toxins Disrupts Bacterial DNA Topology

    Directory of Open Access Journals (Sweden)

    Alexander Harms

    2015-09-01

    Full Text Available Toxin-antitoxin (TA modules are ubiquitous molecular switches controlling bacterial growth via the release of toxins that inhibit cell proliferation. Most of these toxins interfere with protein translation, but a growing variety of other mechanisms hints at a diversity that is not yet fully appreciated. Here, we characterize a group of FIC domain proteins as toxins of the conserved and abundant FicTA family of TA modules, and we reveal that they act by suspending control of cellular DNA topology. We show that FicTs are enzymes that adenylylate DNA gyrase and topoisomerase IV, the essential bacterial type IIA topoisomerases, at their ATP-binding site. This modification inactivates both targets by blocking their ATPase activity, and, consequently, causes reversible growth arrest due to the knotting, catenation, and relaxation of cellular DNA. Our results give insight into the regulation of DNA topology and highlight the remarkable plasticity of FIC domain proteins.

  4. Doc of prophage P1 is inhibited by its antitoxin partner Phd through fold complementation

    DEFF Research Database (Denmark)

    Garcia-Pino, Abel; Christensen-Dalsgaard, Mikkel; Wyns, Lode

    2008-01-01

    evolutionary origin for the phd/doc operon. Doc induces growth arrest of Escherichia coli cells in a reversible manner, by targeting the protein synthesis machinery. Moreover, Doc activates the endogenous E. coli RelE mRNA interferase but does not require this or any other known chromosomal toxin......Prokaryotic toxin-antitoxin modules are involved in major physiological events set in motion under stress conditions. The toxin Doc (death on curing) from the phd/doc module on phage P1 hosts the C-terminal domain of its antitoxin partner Phd (prevents host death) through fold complementation....... This Phd domain is intrinsically disordered in solution and folds into an alpha-helix upon binding to Doc. The details of the interactions reveal the molecular basis for the inhibitory action of the antitoxin. The complex resembles the Fic (filamentation induced by cAMP) proteins and suggests a possible...

  5. The Role of Reactive Oxygen Species in Antibiotic-Mediated Killing of Bacteria.

    Science.gov (United States)

    Van Acker, Heleen; Coenye, Tom

    2017-01-12

    Recently, it was proposed that there is a common mechanism behind the activity of bactericidal antibiotics, involving the production of reactive oxygen species (ROS). However, the involvement of ROS in antibiotic-mediated killing has become the subject of much debate. In the present review, we provide an overview of the data supporting the ROS hypothesis; we also present data that explain the contradictory results often obtained when studying antibiotic-induced ROS production. For this latter aspect we will focus on the importance of taking the experimental setup into consideration and on the importance of some technical aspects of the assays typically used. Finally, we discuss the link between ROS production and toxin-antitoxin modules, and present an overview of implications for treatment.

  6. Integrated Systems Health Management for Intelligent Systems

    Science.gov (United States)

    Figueroa, Fernando; Melcher, Kevin

    2011-01-01

    The implementation of an integrated system health management (ISHM) capability is fundamentally linked to the management of data, information, and knowledge (DIaK) with the purposeful objective of determining the health of a system. It is akin to having a team of experts who are all individually and collectively observing and analyzing a complex system, and communicating effectively with each other in order to arrive at an accurate and reliable assessment of its health. In this paper, concepts, procedures, and approaches are presented as a foundation for implementing an intelligent systems ]relevant ISHM capability. The capability stresses integration of DIaK from all elements of a system. Both ground-based (remote) and on-board ISHM capabilities are compared and contrasted. The information presented is the result of many years of research, development, and maturation of technologies, and of prototype implementations in operational systems.

  7. Epilogue: Systems Approaches and Systems Practice

    Science.gov (United States)

    Reynolds, Martin; Holwell, Sue

    Each of the five systems approaches discussed in this volume: system dynamics (SD), the viable systems model (VSM), strategic options development and analysis (SODA), soft systems methodology (SSM) and critical systems heuristics (CSH) has a pedigree. Not in the sense of the sometimes absurd spectacle of animals paraded at dog shows. Rather, their pedigree derives from their systems foundations, their capacity to evolve and their flexibility in use. None of the five approaches has developed out of use in restricted and controlled contexts of either low or high levels of complicatedness. Neither has any one of them evolved as a consequence of being applied only to situations with either presumed stakeholder agreement on purpose, or courteous disagreement amongst stakeholders, or stakeholder coercion. The compilation is not a celebration of abstract ‘methodologies', but of theoretically robust approaches that have a genuine pedigree in practice.

  8. Systems engineering for very large systems

    Science.gov (United States)

    Lewkowicz, Paul E.

    Very large integrated systems have always posed special problems for engineers. Whether they are power generation systems, computer networks or space vehicles, whenever there are multiple interfaces, complex technologies or just demanding customers, the challenges are unique. 'Systems engineering' has evolved as a discipline in order to meet these challenges by providing a structured, top-down design and development methodology for the engineer. This paper attempts to define the general class of problems requiring the complete systems engineering treatment and to show how systems engineering can be utilized to improve customer satisfaction and profit ability. Specifically, this work will focus on a design methodology for the largest of systems, not necessarily in terms of physical size, but in terms of complexity and interconnectivity.

  9. Metadata Management System for Healthcare Information Systems

    OpenAIRE

    Patil, Ketan Shripat

    2011-01-01

    The Utah Department of Health (UDOH) uses multiple and diverse healthcare information systems for managing, maintaining, and sharing the health information. To keep track of the important details about these information systems such as the operational details, data semantics, data exchange standards, and personnel responsible for maintaining and managing it is a monumental task, with several limitations. This report describes the design and implementation of the Metadata Management System (MD...

  10. L-system fractals

    CERN Document Server

    Mishra, Jibitesh

    2007-01-01

    The book covers all the fundamental aspects of generating fractals through L-system. Also it provides insight to various researches in this area for generating fractals through L-system approach & estimating dimensions. Also it discusses various applications of L-system fractals. Key Features: - Fractals generated from L-System including hybrid fractals - Dimension calculation for L-system fractals - Images & codes for L-system fractals - Research directions in the area of L-system fractals - Usage of various freely downloadable tools in this area - Fractals generated from L-System including hybrid fractals- Dimension calculation for L-system fractals- Images & codes for L-system fractals- Research directions in the area of L-system fractals- Usage of various freely downloadable tools in this area

  11. Distributed computer control systems

    Energy Technology Data Exchange (ETDEWEB)

    Suski, G.J.

    1986-01-01

    This book focuses on recent advances in the theory, applications and techniques for distributed computer control systems. Contents (partial): Real-time distributed computer control in a flexible manufacturing system. Semantics and implementation problems of channels in a DCCS specification. Broadcast protocols in distributed computer control systems. Design considerations of distributed control architecture for a thermal power plant. The conic toolset for building distributed systems. Network management issues in distributed control systems. Interprocessor communication system architecture in a distributed control system environment. Uni-level homogenous distributed computer control system and optimal system design. A-nets for DCCS design. A methodology for the specification and design of fault tolerant real time systems. An integrated computer control system - architecture design, engineering methodology and practical experience.

  12. Forming different planetary systems

    Institute of Scientific and Technical Information of China (English)

    Ji-Lin Zhou; Ji-Wei Xie; Hui-Gen Liu; Hui Zhang; Yi-Sui Sun

    2012-01-01

    With the increasing number of detected exoplanet samples,the statistical properties of planetary systems have become much clearer.In this review,we summarize the major statistical results that have been revealed mainly by radial velocity and transiting observations,and try to interpret them within the scope of the classical core-accretion scenario of planet formation,especially in the formation of different orbital architectures for planetary systems around main sequence stars.Based on the different possible formation routes for different planet systems,we tentatively classify them into three major catalogs:hot Jupiter systems,standard systems and distant giant planet systems.The standard systems can be further categorized into three sub-types under different circumstances:solar-like systems,hot Super-Earth systems,and subgiant planet systems.We also review the theory of planet detection and formation in binary systems as well as planets in star clusters.

  13. Site systems engineering: Systems engineering management plan

    Energy Technology Data Exchange (ETDEWEB)

    Grygiel, M.L. [Westinghouse Hanford Co., Richland, WA (United States)

    1996-05-03

    The Site Systems Engineering Management Plan (SEMP) is the Westinghouse Hanford Company (WHC) implementation document for the Hanford Site Systems Engineering Policy, (RLPD 430.1) and Systems Engineering Criteria Document and Implementing Directive, (RLID 430.1). These documents define the US Department of Energy (DOE), Richland Operations Office (RL) processes and products to be used at Hanford to implement the systems engineering process at the site level. This SEMP describes the products being provided by the site systems engineering activity in fiscal year (FY) 1996 and the associated schedule. It also includes the procedural approach being taken by the site level systems engineering activity in the development of these products and the intended uses for the products in the integrated planning process in response to the DOE policy and implementing directives. The scope of the systems engineering process is to define a set of activities and products to be used at the site level during FY 1996 or until the successful Project Hanford Management Contractor (PHMC) is onsite as a result of contract award from Request For Proposal DE-RP06-96RL13200. Following installation of the new contractor, a long-term set of systems engineering procedures and products will be defined for management of the Hanford Project. The extent to which each project applies the systems engineering process and the specific tools used are determined by the project`s management.

  14. Hot Spot Removal System: System description

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-09-01

    Hazardous wastes contaminated with radionuclides, chemicals, and explosives exist across the Department of Energy complex and need to be remediated due to environmental concerns. Currently, an opportunity is being developed to dramatically reduce remediation costs and to assist in the acceleration of schedules associated with these wastes by deploying a Hot Spot Removal System. Removing the hot spot from the waste site will remove risk driver(s) and enable another, more cost effective process/option/remedial alternative (i.e., capping) to be applied to the remainder of the site. The Hot Spot Removal System consists of a suite of technologies that will be utilized to locate and remove source terms. Components of the system can also be used in a variety of other cleanup activities. This Hot Spot Removal System Description document presents technologies that were considered for possible inclusion in the Hot Spot Removal System, technologies made available to the Hot Spot Removal System, industrial interest in the Hot Spot Removal System`s subsystems, the schedule required for the Hot Spot Removal System, the evaluation of the relevant technologies, and the recommendations for equipment and technologies as stated in the Plan section.

  15. SYSTEMS APPROACH FOR CONTEMPORARY COMPLEX TOURISM SYSTEMS

    Directory of Open Access Journals (Sweden)

    Tadeja Jere Jakulin

    2016-09-01

    Full Text Available Systems approach represents thinking outside the box and is connected to the transformation of common linear approach and thinking. Western society followed rules of classical western science, which form many centuries took analysis as mainstream of thinking and researching. One can find perfect and logical explanation for this. In the past, classical science researched matter and reached optimal results with analysis and analytical thinking. Nowadays more and more scientists research intangible world around matter and cooperate with prevailed, fastest growing service industry such as tourism. Following paper presents systems approach in tourism, which defines wideness, co-dependency among tourism system elements, and "big picture" point of view. In a frame of systems methodology, we will show the importance of systems approach in order to understand complexity in the area of tourism. At once an excellent example of the analytical approach will be shown in so called "the tip of the iceberg" theory, where events represent analytical thinking and structure or base of the iceberg represents systems approach. Complexity of the tourism systems will be explained and a model of a common tourism system developed. We claim that the analysis, in the past, caused technological progress; it caused the development of western science, which we now know it. It led to the discoveries but for dealing with contemporary complex challenges is not sufficient. Today a systems approach is suitable enough for dealing with complex question in the area of tourism and of course in global society.

  16. Novel central nervous system drug delivery systems.

    Science.gov (United States)

    Stockwell, Jocelyn; Abdi, Nabiha; Lu, Xiaofan; Maheshwari, Oshin; Taghibiglou, Changiz

    2014-05-01

    For decades, biomedical and pharmaceutical researchers have worked to devise new and more effective therapeutics to treat diseases affecting the central nervous system. The blood-brain barrier effectively protects the brain, but poses a profound challenge to drug delivery across this barrier. Many traditional drugs cannot cross the blood-brain barrier in appreciable concentrations, with less than 1% of most drugs reaching the central nervous system, leading to a lack of available treatments for many central nervous system diseases, such as stroke, neurodegenerative disorders, and brain tumors. Due to the ineffective nature of most treatments for central nervous system disorders, the development of novel drug delivery systems is an area of great interest and active research. Multiple novel strategies show promise for effective central nervous system drug delivery, giving potential for more effective and safer therapies in the future. This review outlines several novel drug delivery techniques, including intranasal drug delivery, nanoparticles, drug modifications, convection-enhanced infusion, and ultrasound-mediated drug delivery. It also assesses possible clinical applications, limitations, and examples of current clinical and preclinical research for each of these drug delivery approaches. Improved central nervous system drug delivery is extremely important and will allow for improved treatment of central nervous system diseases, causing improved therapies for those who are affected by central nervous system diseases.

  17. Recommender Systems for Social Tagging Systems

    CERN Document Server

    Balby Marinho, Leandro

    2012-01-01

    Social Tagging Systems are web applications in which users upload resources (e.g., bookmarks, videos, photos, etc.) and annotate it with a list of freely chosen keywords called tags. This is a grassroots approach to organize a site and help users to find the resources they are interested in. Social tagging systems are open and inherently social; features that have been proven to encourage participation. However, with the large popularity of these systems and the increasing amount of user-contributed content, information overload rapidly becomes an issue. Recommender Systems are well known appl

  18. Power system protection 2 systems and methods

    CERN Document Server

    1995-01-01

    The worldwide growth in demand for electricity has forced the pace of developments in electrical power system design to meet consumer needs for reliable, secure and cheap supplies. Power system protection, as a technology essential to high quality supply, is widely recognised as a specialism of growing and often critical importance, in which power system needs and technological progress have combined to result in rapid developments in policy and practice in recent years. In the United Kingdom, the need for appropriate training in power system protection was recognised in the early 1960s with t

  19. STEP electronic system design

    Science.gov (United States)

    Couch, R. H.; Johnson, J. W.

    1984-01-01

    The STEP electronic system design is discussed. The purpose of the design is outlined. The electronic system design is summarized and it is found that: an effective conceptual system design is developed; the design represents a unique set of capabilities; makes efficient use of available orbiter resources; the system capabilities exceed identified potential experiment needs.

  20. Nonlinear Hamiltonian systems

    DEFF Research Database (Denmark)

    Jørgensen, Michael Finn

    1995-01-01

    It is generally very difficult to solve nonlinear systems, and such systems often possess chaotic solutions. In the rare event that a system is completely solvable, it is said to integrable. Such systems never have chaotic solutions. Using the Inverse Scattering Transform Method (ISTM) two...

  1. Product Service Systems

    DEFF Research Database (Denmark)

    Departing from Product Development models based on physical artefacts. Moving towards integrated Product Development and System Operations models suited Product/Service-systems......Departing from Product Development models based on physical artefacts. Moving towards integrated Product Development and System Operations models suited Product/Service-systems...

  2. Medical imaging systems

    Science.gov (United States)

    Frangioni, John V

    2013-06-25

    A medical imaging system provides simultaneous rendering of visible light and diagnostic or functional images. The system may be portable, and may include adapters for connecting various light sources and cameras in open surgical environments or laparascopic or endoscopic environments. A user interface provides control over the functionality of the integrated imaging system. In one embodiment, the system provides a tool for surgical pathology.

  3. Measuring Systemic Risk

    DEFF Research Database (Denmark)

    Acharya, Viral V.; Heje Pedersen, Lasse; Philippon, Thomas

    We present a simple model of systemic risk and we show that each financial institution's contribution to systemic risk can be measured as its systemic expected shortfall (SES), i.e., its propensity to be undercapitalized when the system as a whole is undercapitalized. SES increases...

  4. Universal Index System

    Science.gov (United States)

    Kelley, Steve; Roussopoulos, Nick; Sellis, Timos; Wallace, Sarah

    1993-01-01

    The Universal Index System (UIS) is an index management system that uses a uniform interface to solve the heterogeneity problem among database management systems. UIS provides an easy-to-use common interface to access all underlying data, but also allows different underlying database management systems, storage representations, and access methods.

  5. Hybrid intelligent engineering systems

    CERN Document Server

    Jain, L C; Adelaide, Australia University of

    1997-01-01

    This book on hybrid intelligent engineering systems is unique, in the sense that it presents the integration of expert systems, neural networks, fuzzy systems, genetic algorithms, and chaos engineering. It shows that these new techniques enhance the capabilities of one another. A number of hybrid systems for solving engineering problems are presented.

  6. Central Dental Evacuation Systems.

    Science.gov (United States)

    1982-05-01

    20 High-Vacuum Oral Evacuation System (HIVAC) for Oral Surgery, Periodontics, and Endodontics Treatment Rooms..................... 20...handpiece. Inlets to this system are required throughout the dental facility for all disciplines of patient treatment where coolant and irrigation liquids...System (HIVAC) for Oral Surgery, Periodontics, and Endodontics Treatment Rooms The HIVAC system is designed to build and sustain high vacuum pressures

  7. CDMA systems capacity engineering

    CERN Document Server

    Kim, Kiseon

    2004-01-01

    This new hands-on resource tackles capacity planning and engineering issues that are crucial to optimizing wireless communication systems performance. Going beyond the system physical level and investigating CDMA system capacity at the service level, this volume is the single-source for engineering and analyzing systems capacity and resources.

  8. System Performance and Testing

    NARCIS (Netherlands)

    Frei, U.; Oversloot, H.

    2004-01-01

    This chapter compares and contrasts the system performance of two widely used solar thermal systems using testing and simulation programs. Solar thermal systems are used in many countries for heating domestically used water. In addition to the simple thermosiphon systems, better designed pumped syst

  9. Expert Systems: An Overview.

    Science.gov (United States)

    Adiga, Sadashiv

    1984-01-01

    Discusses: (1) the architecture of expert systems; (2) features that distinguish expert systems from conventional programs; (3) conditions necessary to select a particular application for the development of successful expert systems; (4) issues to be resolved when building expert systems; and (5) limitations. Examples of selected expert systems…

  10. Information Systems Security Audit

    Directory of Open Access Journals (Sweden)

    Gheorghe Popescu

    2007-12-01

    Full Text Available The article covers:Defining an information system; benefits obtained by introducing new information technologies; IT management;Defining prerequisites, analysis, design, implementation of IS; Information security management system; aspects regarding IS security policy; Conceptual model of a security system; Auditing information security systems and network infrastructure security.

  11. ERP–systems

    OpenAIRE

    Shustova I.

    2016-01-01

    In this work, we analyzed the existing ERP–systems of foreign and domestic manufacturers. Popular ERP–systems in the Republic of Belarus were considered. The leading ERP-systems in the domestic market and their features were described in detail. Finally, we described the steps that must be taken to select the most suitable ERP-system for a particular company.

  12. Type Systems for Bigraphs

    DEFF Research Database (Denmark)

    Elsborg, Ebbe; Hildebrandt, Thomas; Sangiorgi, Davide

    of controls and a set of reaction rules, collectively a bigraphical reactive system (BRS). Possible advantages of developing bigraphical type systems include: a deeper understanding of a type system itself and its properties; transfer of the type systems to the concrete family of calculi that the BRS models...

  13. Product Service Systems

    DEFF Research Database (Denmark)

    Departing from Product Development models based on physical artefacts. Moving towards integrated Product Development and System Operations models suited Product/Service-systems......Departing from Product Development models based on physical artefacts. Moving towards integrated Product Development and System Operations models suited Product/Service-systems...

  14. Information Systems Security Audit

    OpenAIRE

    Gheorghe Popescu; Veronica Adriana Popescu; Cristina Raluca Popescu

    2007-01-01

    The article covers:Defining an information system; benefits obtained by introducing new information technologies; IT management;Defining prerequisites, analysis, design, implementation of IS; Information security management system; aspects regarding IS security policy; Conceptual model of a security system; Auditing information security systems and network infrastructure security.

  15. ERP–systems

    OpenAIRE

    Shustova I.

    2016-01-01

    In this work, we analyzed the existing ERP–systems of foreign and domestic manufacturers. Popular ERP–systems in the Republic of Belarus were considered. The leading ERP-systems in the domestic market and their features were described in detail. Finally, we described the steps that must be taken to select the most suitable ERP-system for a particular company.

  16. An autonomous in vivo dual selection protocol for boolean genetic circuits.

    Science.gov (United States)

    Beneš, David; Sosík, Petr; Rodríguez-Patón, Alfonso

    2015-01-01

    Success in synthetic biology depends on the efficient construction of robust genetic circuitry. However, even the direct engineering of the simplest genetic elements (switches, logic gates) is a challenge and involves intense lab work. As the complexity of biological circuits grows, it becomes more complicated and less fruitful to rely on the rational design paradigm, because it demands many time-consuming trial-and-error cycles. One of the reasons is the context-dependent behavior of small assembly parts (like BioBricks), which in a complex environment often interact in an unpredictable way. Therefore, the idea of evolutionary engineering (artificial directed in vivo evolution) based on screening and selection of randomized combinatorial genetic circuit libraries became popular. In this article we build on the so-called dual selection technique. We propose a plasmid-based framework using toxin-antitoxin pairs together with the relaxase conjugative protein, enabling an efficient autonomous in vivo evolutionary selection of simple Boolean circuits in bacteria (E. coli was chosen for demonstration). Unlike previously reported protocols, both on and off selection steps can run simultaneously in various cells in the same environment without human intervention; and good circuits not only survive the selection process but are also horizontally transferred by conjugation to the neighbor cells to accelerate the convergence rate of the selection process. Our directed evolution strategy combines a new dual selection method with fluorescence-based screening to increase the robustness of the technique against mutations. As there are more orthogonal toxin-antitoxin pairs in E. coli, the approach is likely to be scalable to more complex functions. In silico experiments based on empirical data confirm the high search and selection capability of the protocol.

  17. On generalized Volterra systems

    Science.gov (United States)

    Charalambides, S. A.; Damianou, P. A.; Evripidou, C. A.

    2015-01-01

    We construct a large family of evidently integrable Hamiltonian systems which are generalizations of the KM system. The algorithm uses the root system of a complex simple Lie algebra. The Hamiltonian vector field is homogeneous cubic but in a number of cases a simple change of variables transforms such a system to a quadratic Lotka-Volterra system. We present in detail all such systems in the cases of A3, A4 and we also give some examples from higher dimensions. We classify all possible Lotka-Volterra systems that arise via this algorithm in the An case.

  18. Multiobjective Collaborative Optimization of Systems of Systems

    Science.gov (United States)

    2005-06-01

    operationally independent. (System-ysem 1)..y Design ,I ’"esignReqm ts ... .em (Sy stem 1) S stems F S Funcion Overlap Reqmts...te m...284. Maier, M.W. & Rechtin, E. (2002). The art of systems architecting. (2nd ed.). Boca Raton, FL: CRC Press LLC. Marglin, S. (1967). Public

  19. The Solar System as an Exoplanetary System

    CERN Document Server

    Martin, Rebecca G

    2015-01-01

    With the availability of considerably more data, we revisit the question of how special our Solar System is, compared to observed exoplanetary systems. To this goal, we employ a mathematical transformation that allows for a meaningful, statistical comparison. We find that the masses and densities of the giant planets in our Solar System are very typical, as is the age of the Solar System. While the orbital location of Jupiter is somewhat of an outlier, this is most likely due to strong selection effects towards short-period planets. The eccentricities of the planets in our Solar System are relatively small compared to those in observed exosolar systems, but still consistent with the expectations for an 8-planet system (and could, in addition, reflect a selection bias towards high-eccentricity planets). The two characteristics of the Solar System that we find to be most special are the lack of super-Earths with orbital periods of days to months and the general lack of planets inside of the orbital radius of Me...

  20. Variable Structure Systems and Systems Zeros

    OpenAIRE

    El-Ghezawi, O.M.E.; S. A. Billings; Zinober, A.S.I.

    1981-01-01

    The analysis of variable structure systems in the sliding mode yields the concept of equivalent control which leads naturally to a new method for determining the zeros and zero directions of linear multivariable systems. The analysis presented is conceptually easy and computationally attractive.

  1. Applications of membrane systems in distributed systems

    Institute of Scientific and Technical Information of China (English)

    Aneta Binder; Rudolf Freund; Georg Lojka; Marion Oswald

    2007-01-01

    Based on the biological model of cell-to-cell communication proposed by A. Rustom et al. (Science, 2004, 303: 1007-1010), we investigate the possibilities to apply P systems with dynamic channels transporting membrane vesicles for describing processes in distributed systems.

  2. Performance, Performance System, and High Performance System

    Science.gov (United States)

    Jang, Hwan Young

    2009-01-01

    This article proposes needed transitions in the field of human performance technology. The following three transitions are discussed: transitioning from training to performance, transitioning from performance to performance system, and transitioning from learning organization to high performance system. A proposed framework that comprises…

  3. [Universal coaxial anesthetic system].

    Science.gov (United States)

    Ungerer, M J; le Roux, F P

    1978-02-25

    A true universal co-axial anaesthetic system has been designed. This system may be used either as a Mapleson A circuit during spontaneous ventilation or as a Mapleson D circuit during controlled ventilation. Conversion to either system may be conveniently carried out by interchanging the pop-off valve and fresh gas inlet, without disconnecting the system from the patient. Resistance to flow of both tubes has been measured and was found to be within acceptable limits. The efficiency of this system in a Mapleson A arrangement was compared with that of a conventional Magill circuit during spontaneous breathing in 2 conscious volunteers. It was shown that no significant difference exists between these systems eith regard to rebreathing, and that the universal co-axial system may be used as efficiently and economically as the Magill circuit during spontaneous ventilation. The co-axial system can be easily connected to a circle system, combining the advantages of the two systems.

  4. Dynamical system synchronization

    CERN Document Server

    Luo, Albert C J

    2013-01-01

    Dynamical System Synchronization (DSS) meticulously presents for the first time the theory of dynamical systems synchronization based on the local singularity theory of discontinuous dynamical systems. The book details the sufficient and necessary conditions for dynamical systems synchronizations, through extensive mathematical expression. Techniques for engineering implementation of DSS are clearly presented compared with the existing techniques.  This book also:  Presents novel concepts and methods for dynamical system synchronization Extends beyond the Lyapunov theory for dynamical system synchronization Introduces companion and synchronization of discrete dynamical systems Includes local singularity theory for discontinuous dynamical systems Covers the invariant domains of synchronization Features more than 75 illustrations Dynamical System Synchronization is an ideal book for those interested in better understanding new concepts and methodology for dynamical system synchronization, local singularity...

  5. Intrusion Detection System: Security Monitoring System

    Directory of Open Access Journals (Sweden)

    ShabnamNoorani,

    2015-10-01

    Full Text Available An intrusion detection system (IDS is an ad hoc security solution to protect flawed computer systems. It works like a burglar alarm that goes off if someone tampers with or manages to get past other security mechanisms such as authentication mechanisms and firewalls. An Intrusion Detection System (IDS is a device or a software application that monitors network or system activities for malicious activities or policy violations and produces reports to a management station.Intrusion Detection System (IDS has been used as a vital instrument in defending the network from this malicious or abnormal activity..In this paper we are comparing host based and network based IDS and various types of attacks possible on IDS.

  6. Measuring Systemic Risk

    DEFF Research Database (Denmark)

    Acharya, Viral V.; Heje Pedersen, Lasse; Philippon, Thomas

    2017-01-01

    We present an economic model of systemic risk in which undercapitalization of the financial sector as a whole is assumed to harm the real economy, leading to a systemic risk externality. Each financial institution’s contribution to systemic risk can be measured as its systemic expected shortfall...... of components of SES to predict emerging systemic risk during the financial crisis of 2007–2009....

  7. Photovoltaic systems and applications

    Energy Technology Data Exchange (ETDEWEB)

    1982-01-01

    Abstracts are given of presentations given at a project review meeting held at Albuquerque, NM. The proceedings cover the past accomplishments and current activities of the Photovoltaic Systems Research, Balance-of-System Technology Development and System Application Experiments Projects at Sandia National Laboratories. The status of intermediate system application experiments and residential system analysis is emphasized. Some discussion of the future of the Photovoltaic Program in general, and the Sandia projects in particular is also presented.

  8. HYBRID VEHICLE CONTROL SYSTEM

    Directory of Open Access Journals (Sweden)

    V. Dvadnenko

    2016-06-01

    Full Text Available The hybrid vehicle control system includes a start–stop system for an internal combustion engine. The system works in a hybrid mode and normal vehicle operation. To simplify the start–stop system, there were user new possibilities of a hybrid car, which appeared after the conversion. Results of the circuit design of the proposed system of basic blocks are analyzed.

  9. Systems Theory and Systems Approach to Leadership

    Directory of Open Access Journals (Sweden)

    Dr.Sc. Berim Ramosaj

    2014-06-01

    Full Text Available Systems theory is product of the efforts of many researchers to create an intermediate field of coexistence of all sciences. If not for anything else, because of the magnitude that the use of systemic thinking and systemic approach has taken, it has become undisputed among the theories. Systems theory not only provides a glossary of terms with which researchers from different fields can be understood, but provides a framework for the presentation and interpretation of phenomena and realities. This paper addresses a systematic approach to leadership, as an attempt to dredge leadership and systems theory literature to find the meeting point. Systems approach is not an approach to leadership in terms of a manner of leader’s work, but it’s the leader's determination to factorize in his leadership the external environment and relationships with and among elements. Leader without followers is unable to exercise his leadership and to ensure their conviction he should provide a system, a structure, a purpose, despite the alternative chaos. Systems approach clarifies the thought on the complexity and dynamism of the environment and provides a framework for building ideas. If the general system theory is the skeleton of science (Boulding: 1956, this article aims to replenish it with leadership muscles by prominent authors who have written on systems theory and leadership, as well as through original ideas. In this work analytical methods were used (by analyzing approaches individually as well as synthetic methods (by assaying individual approaches in context of entirety. The work is a critical review of literature as well as a deductive analysis mingled with models proposed by authors through inductive analysis. Meta-analysis has been used to dissect the interaction and interdependence between leadership approaches.

  10. A distribution management system

    Energy Technology Data Exchange (ETDEWEB)

    Verho, P.; Jaerventausta, P.; Kaerenlampi, M.; Paulasaari, H. [Tampere Univ. of Technology (Finland); Partanen, J. [Lappeenranta Univ. of Technology (Finland)

    1996-12-31

    The development of new distribution automation applications is considerably wide nowadays. One of the most interesting areas is the development of a distribution management system (DMS) as an expansion of the traditional SCADA system. At the power transmission level such a system is called an energy management system (EMS). The idea of these expansions is to provide supporting tools for control center operators in system analysis and operation planning. The needed data for new applications is mainly available in some existing systems. Thus the computer systems of utilities must be integrated. The main data source for the new applications in the control center are the AM/FM/GIS (i.e. the network database system), the SCADA, and the customer information system (CIS). The new functions can be embedded in some existing computer system. This means a strong dependency on the vendor of the existing system. An alternative strategy is to develop an independent system which is integrated with other computer systems using well-defined interfaces. The latter approach makes it possible to use the new applications in various computer environments, having only a weak dependency on the vendors of the other systems. In the research project this alternative is preferred and used in developing an independent distribution management system

  11. A System of Systems Approach to the EU Energy System

    Science.gov (United States)

    Jess, Tom; Madani, Kaveh; Mahlooji, Maral; Ristic, Bora

    2016-04-01

    Around the world, measures to prevent dangerous climate change are being adopted and may change energy systems fundamentally. The European Union (EU) is committed to reducing greenhouse gas emission by 20% by 2020 and by 80-95% by 2050. In order to achieve this, EU member states aim to increase the share of renewables in the energy mix to 20% by 2020. This commitment comes as part of a series of other aims, principles, and policies to reform the EU's energy system. Cost-efficiency in the emissions reductions measures as well as strategic goals under the Resource Efficient Europe flagship initiative which would include a more prudent approach to other natural resources such as water and land. Using the "System of Systems Approach", as from Hadian and Madani (2015), energy sources' Relative Aggregate Footprints (RAF) in the EU are evaluated. RAF aggregates across four criteria: carbon footprint, water footprint, land footprint, and economic cost. The four criteria are weighted by resource availability across the EU and for each Member State. This provides an evaluation of the overall resource use efficiency of the EU's energy portfolio and gives insight into the differences in the desirability of energy sources across Member States. Broadly, nuclear, onshore wind, and geothermal are most desirable under equal criteria weights and EU average weighting introduces only small changes in the relative performance of only few technologies. The member state specific weightings show that most countries have similar energy technology preferences. However, the UK deviates most strongly from the average, with an even stronger preference for nuclear and coal. Sweden, Malta and Finland also deviate from the typical preferences indicating the complexity in play in reforming the EU energy system. Reference Hadian S, Madani K (2015) A System of Systems Approach to Energy Sustainability Assessment: Are All Renewables Really Green? Ecological Indicators, 52, 194-206.

  12. Modeling Power Systems as Complex Adaptive Systems

    Energy Technology Data Exchange (ETDEWEB)

    Chassin, David P.; Malard, Joel M.; Posse, Christian; Gangopadhyaya, Asim; Lu, Ning; Katipamula, Srinivas; Mallow, J V.

    2004-12-30

    Physical analogs have shown considerable promise for understanding the behavior of complex adaptive systems, including macroeconomics, biological systems, social networks, and electric power markets. Many of today's most challenging technical and policy questions can be reduced to a distributed economic control problem. Indeed, economically based control of large-scale systems is founded on the conjecture that the price-based regulation (e.g., auctions, markets) results in an optimal allocation of resources and emergent optimal system control. This report explores the state-of-the-art physical analogs for understanding the behavior of some econophysical systems and deriving stable and robust control strategies for using them. We review and discuss applications of some analytic methods based on a thermodynamic metaphor, according to which the interplay between system entropy and conservation laws gives rise to intuitive and governing global properties of complex systems that cannot be otherwise understood. We apply these methods to the question of how power markets can be expected to behave under a variety of conditions.

  13. Intelligent systems technology infrastructure for integrated systems

    Science.gov (United States)

    Lum, Henry

    1991-01-01

    A system infrastructure must be properly designed and integrated from the conceptual development phase to accommodate evolutionary intelligent technologies. Several technology development activities were identified that may have application to rendezvous and capture systems. Optical correlators in conjunction with fuzzy logic control might be used for the identification, tracking, and capture of either cooperative or non-cooperative targets without the intensive computational requirements associated with vision processing. A hybrid digital/analog system was developed and tested with a robotic arm. An aircraft refueling application demonstration is planned within two years. Initially this demonstration will be ground based with a follow-on air based demonstration. System dependability measurement and modeling techniques are being developed for fault management applications. This involves usage of incremental solution/evaluation techniques and modularized systems to facilitate reuse and to take advantage of natural partitions in system models. Though not yet commercially available and currently subject to accuracy limitations, technology is being developed to perform optical matrix operations to enhance computational speed. Optical terrain recognition using camera image sequencing processed with optical correlators is being developed to determine position and velocity in support of lander guidance. The system is planned for testing in conjunction with Dryden Flight Research Facility. Advanced architecture technology is defining open architecture design constraints, test bed concepts (processors, multiple hardware/software and multi-dimensional user support, knowledge/tool sharing infrastructure), and software engineering interface issues.

  14. Micro Information Systems

    DEFF Research Database (Denmark)

    Ulslev Pedersen, Rasmus; Kühn Pedersen, Mogens

    2014-01-01

    such as medical and manufacturing. These new sensor applications have implications for information systems (IS) and, the authors visualize this new class of information systems as fractals growing from an established class of systems; namely that of information systems (IS). The identified applications...... and implications are used as an empirical basis for creating a model for these small new information systems. Such sensor systems are called embedded systems in the technical sciences, and the authors want to couple it with general IS. They call the merger of these two important research areas (IS and embedded...... systems) for micro information systems (micro-IS). It is intended as a new research field within IS research. An initial framework model is established, which seeks to capture both the possibilities and constraints of this new paradigm, while looking simultaneously at the fundamental IS and ICT aspects...

  15. Rover waste assay system

    Energy Technology Data Exchange (ETDEWEB)

    Akers, D.W.; Stoots, C.M.; Kraft, N.C.; Marts, D.J. [Idaho National Engineering Lab., Idaho Falls, ID (United States)

    1997-11-01

    The Rover Waste Assay System (RWAS) is a nondestructive assay system designed for the rapid assay of highly-enriched {sup 235}U contaminated piping, tank sections, and debris from the Rover nuclear rocket fuel processing facility at the Idaho Chemical Processing Plant. A scanning system translates a NaI(Tl) detector/collimator system over the structural components where both relative and calibrated measurements for {sup 137}Cs are made. Uranium-235 concentrations are in operation and is sufficiently automated that most functions are performed by the computer system. These functions include system calibration, problem identification, collimator control, data analysis, and reporting. Calibration of the system was done through a combination of measurements on calibration standards and benchmarked modeling. A description of the system is presented along with the methods and uncertainties associated with the calibration and analysis of the system for components from the Rover facility. 4 refs., 2 figs., 4 tabs.

  16. Enhanced nurse call systems.

    Science.gov (United States)

    2001-04-01

    This Evaluation focuses on high-end computerized nurse call systems--what we call enhanced systems. These are highly flexible systems that incorporate microprocessor and communications technologies to expand the capabilities of the nurse call function. Enhanced systems, which vary in configuration from one installation to the next, typically consist of a basic system that provides standard nurse call functionality and a combination of additional enhancements that provide the added functionality the facility desires. In this study, we examine the features that distinguish enhanced nurse call systems from nonenhanced systems, focusing on their application and benefit to healthcare facilities. We evaluated seven systems to determine how well they help (1) improve patient care, as well as increase satisfaction with the care provided, and (2) improve caregiver efficiency, as well as increase satisfaction with the work environment. We found that all systems meet these objectives, but not all systems perform equally well for all implementations. Our ratings will help facilities identify those systems that offer the most effective features for their intended use. The study also includes a Technology Management Guide to help readers (1) determine whether they'll benefit from the capabilities offered by enhanced systems and (2) target a system for purchase and equip the system for optimum performance and cost-effective operation.

  17. Nonlinearity of colloid systems oxyhydrate systems

    CERN Document Server

    Sucharev, Yuri I

    2008-01-01

    The present monograph is the first systematic study of the non-linear characteristic of gel oxy-hydrate systems involving d- and f- elements. These are the oxyhydrates of rare-earth elements and oxides - hydroxides of d- elements (zirconium, niobium, titanium, etc.) The non-linearity of these gel systems introduces fundamental peculiarities into their structure and, consequently, their properties. The polymer-conformational diversity of energetically congenial gel fragments, which continu-ously transform under the effect of, for instance, system dissipation heat, is central to the au-thor's hy

  18. Embedded systems handbook networked embedded systems

    CERN Document Server

    Zurawski, Richard

    2009-01-01

    Considered a standard industry resource, the Embedded Systems Handbook provided researchers and technicians with the authoritative information needed to launch a wealth of diverse applications, including those in automotive electronics, industrial automated systems, and building automation and control. Now a new resource is required to report on current developments and provide a technical reference for those looking to move the field forward yet again. Divided into two volumes to accommodate this growth, the Embedded Systems Handbook, Second Edition presents a comprehensive view on this area

  19. Generalized L systems

    Institute of Scientific and Technical Information of China (English)

    陆汝钤; 张文妍

    2002-01-01

    This paper proposes the concept of generalized L systems, GL systems for short, which can describe asynchronized concurrent phenomena. We have proved that the GL systems are proper extensions of the traditional L systems. We have also defined a classification of GL systems and proved a sufficient and necessary condition for the equivalence of two subclasses of GL systems: two quivalent, iff k = j and there exists a common divisor g of all mr and a common divisor h of all ni such that i: mi/g = ni/h.

  20. Cooperating systems: Layered MAS

    Science.gov (United States)

    Rochowiak, Daniel

    1990-01-01

    Distributed intelligent systems can be distinguished by the models that they use. The model developed focuses on layered multiagent system conceived of as a bureaucracy in which a distributed data base serves as a central means of communication. The various generic bureaus of such a system is described and a basic vocabulary for such systems is presented. In presenting the bureaus and vocabularies, special attention is given to the sorts of reasonings that are appropriate. A bureaucratic model has a hierarchy of master system and work group that organizes E agents and B agents. The master system provides the administrative services and support facilities for the work groups.

  1. Microelectronic systems 1 checkbook

    CERN Document Server

    Vears, R E

    2013-01-01

    Microelectronic Systems 1 Checkbook provides coverage of the Business and Technician Education Council level 1 unit in Microelectronic Systems. However, it can be regarded as a basic textbook in microelectronic systems for a much wider range of studies. Each topic considered in the text is presented in a way that assumes the reader has little prior knowledge of electronics. The aim of the book is to provide an introduction to the concept of systems, to differentiate analogue and digital systems, and to describe the nature of microprocessor-controlled systems. An introduction to programming is

  2. Metrics for Multiagent Systems

    Science.gov (United States)

    Lass, Robert N.; Sultanik, Evan A.; Regli, William C.

    A Multiagent System (MAS) is a software paradigm for building large scale intelligent distributed systems. Increasingly these systems are being deployed on handheld computing devices that rely on non-traditional communications mediums such as mobile ad hoc networks and satellite links. These systems present new challenges for computer scientists in describing system performance and analyzing competing systems. This chapter surveys existing metrics that can be used to describe MASs and related components. A framework for analyzing MASs is provided and an example of how this framework might be employed is given for the domain of distributed constraint reasoning.

  3. Introducing Systems Approaches

    Science.gov (United States)

    Reynolds, Martin; Holwell, Sue

    Systems Approaches to Managing Change brings together five systems approaches to managing complex issues, each having a proven track record of over 25 years. The five approaches are: System Dynamics (SD) developed originally in the late 1950s by Jay Forrester Viable Systems Model (VSM) developed originally in the late 1960s by Stafford Beer Strategic Options Development and Analysis (SODA: with cognitive mapping) developed originally in the 1970s by Colin Eden Soft Systems Methodology (SSM) developed originally in the 1970s by Peter Checkland Critical Systems Heuristics (CSH) developed originally in the late 1970s by Werner Ulrich

  4. Simulation of Polygeneration Systems

    Directory of Open Access Journals (Sweden)

    Francesco Calise

    2016-11-01

    Full Text Available This Special Issue aims at collecting the recent studies dealing with polygeneration systems, with a special focus on the possible integration of different technologies into a single system, able to convert one or multiple energy sources into energy services (electricity, heat and cooling and other useful products (e.g., desalinized water, hydrogen, glycerin, ammonia, etc.. Renewable sources (solar, wind, hydro, biomass and geothermal, as well as fossil fuels, feeding advanced energy systems such as fuel cells and cogeneration systems, are considered. Special attention is paid to control strategies and to the management of the systems in general. Studies including thermoeconomic analyses and system optimizations are presented.

  5. Continuous system modeling

    Science.gov (United States)

    Cellier, Francois E.

    1991-01-01

    A comprehensive and systematic introduction is presented for the concepts associated with 'modeling', involving the transition from a physical system down to an abstract description of that system in the form of a set of differential and/or difference equations, and basing its treatment of modeling on the mathematics of dynamical systems. Attention is given to the principles of passive electrical circuit modeling, planar mechanical systems modeling, hierarchical modular modeling of continuous systems, and bond-graph modeling. Also discussed are modeling in equilibrium thermodynamics, population dynamics, and system dynamics, inductive reasoning, artificial neural networks, and automated model synthesis.

  6. Smart SDHW systems

    DEFF Research Database (Denmark)

    Andersen, Elsa

    2000-01-01

    The aim of the project is to develop smart solar domestic hot water (SDHW) systems. A smart SDHW is a system in which the domestic water can bee heated both by solar collectors and by an auxiliary energy supply system. The auxiliary energy supply system heats up the hot-water tank from the top...... periods in a laboratory. Numeric models of the systems have been developed. The models are verified with measured temperatures and energy quantities. In order to verify the good test results in the laboratory two of the smart SDHW systems have been installed in practice. Measurements will bee carried out...

  7. Test System Impact on System Availability

    DEFF Research Database (Denmark)

    Pau, L. F.

    1987-01-01

    The specifications are presented for an imperfect automatic test system (ATS) (test frequency distribution, reliability, false alarm rate, nondetection rate) in order to account for the availability, readiness, mean time between unscheduled repairs (MTBUR), reliability, and maintenance of the sys......The specifications are presented for an imperfect automatic test system (ATS) (test frequency distribution, reliability, false alarm rate, nondetection rate) in order to account for the availability, readiness, mean time between unscheduled repairs (MTBUR), reliability, and maintenance...... of the system subject to monitoring and test. A time-dependent Markov model is presented, and applied in three cases, with examples of numerical results provided for preventive maintenance decisions, design of an automatic test system, buffer testing in computers, and data communications....

  8. Information system development activities and inquiring systems

    DEFF Research Database (Denmark)

    Carugati, Andrea

    2008-01-01

    This article presents a framework that maps information system development (ISD) activities on systems for the creation of knowledge. This work addresses the relevant and persisting problem of improving the chances of ISD success. The article builds upon previous research on knowledge aspects...... provides a new way to see the development of a system in terms of the knowledge created in the process. The main practical implication of the framework is that it improves the managers' ability to guide ISD activities as knowledge activities embedded in a knowledge process, a crucial element in development...... of ISD, abandoning the idea of a monolithic approach to knowledge and presenting a pluralistic approach based on the idea that different inquiring systems can support micro-level ISD activities. The article is divided into two parts. The first part presents the theoretical development of the framework...

  9. Information system development activities and inquiring systems

    DEFF Research Database (Denmark)

    Carugati, Andrea

    2008-01-01

    This article presents a framework that maps information system development (ISD) activities on systems for the creation of knowledge. This work addresses the relevant and persisting problem of improving the chances of ISD success. The article builds upon previous research on knowledge aspects...... provides a new way to see the development of a system in terms of the knowledge created in the process. The main practical implication of the framework is that it improves the managers' ability to guide ISD activities as knowledge activities embedded in a knowledge process, a crucial element in development...... of ISD, abandoning the idea of a monolithic approach to knowledge and presenting a pluralistic approach based on the idea that different inquiring systems can support micro-level ISD activities. The article is divided into two parts. The first part presents the theoretical development of the framework...

  10. Business System Planning Project System Requirements Specification

    Energy Technology Data Exchange (ETDEWEB)

    NELSON, R.E.

    2000-09-08

    The purpose of the Business Systems Planning Project System Requirements Specification (SRS) is to provide the outline and contents of the requirements for the CH2M HILL Hanford Group, Inc. (CHG) integrated business and technical information systems. The SRS will translate proposed objectives into the statement of the functions that are to be performed and data and information flows that they require. The requirements gathering methodology will use (1) facilitated group requirement sessions; (2) individual interviews; (3) surveys; and (4) document reviews. The requirements will be verified and validated through coordination of the technical requirement team and CHG Managers. The SRS document used the content and format specified in Lockheed Martin Services, Inc. Organization Standard Software Practices in conjunction with the Institute of Electrical and Electronics Engineers Standard 8340-1984 for Systems Requirements Documents.

  11. Water Fluoridation Reporting System (Public Water Systems)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Water Fluoridation Reporting System (WFRS) has been developed to provide tools to assist states in managing fluoridation programs. WFRS is designed to track all...

  12. System Information Distribution in Massive MIMO Systems

    OpenAIRE

    Sörman, Simon

    2016-01-01

    The 5th generation mobile telecommunication system (5G) is currently being specified and developed, with large expectations on throughput and efficiency. While 4G and more specifically LTE might constitute a basis of the design of the network, there are some parts that should be improved. One thing to improve is the static signalling that occurs very frequently in a 4G network, of which system information such as synchronization signals, detection of network frequencies, operators, configurat...

  13. EPICS system: system structure and user interface

    Energy Technology Data Exchange (ETDEWEB)

    West, R.E.; Bartlett, J.F.; Bobbitt, J.S.; Lahey, T.E.; Kramper, B.J.; MacKinnon, B.A.

    1984-02-01

    This paper present the user's view of and the general organization of the EPICS control system at Fermilab. Various subsystems of the EPICS control system are discussed. These include the user command language, software protection, the device database, remote computer interfaces, and several application utilities. This paper is related to two other papers on EPICS: an overview paper and a detailed implementation paper.

  14. Mathematical System Theory and System Modeling

    OpenAIRE

    1980-01-01

    Choosing models related effectively to the questions to be addressed is a central issue in the craft of systems analysis. Since the mathematical description the analyst chooses constrains the types of issues he candeal with, it is important for these models to be selected so as to yield limitations that are acceptable in view of the questions the systems analysis seeks to answer. In this paper, the author gives an overview of the central issues affecting the question of model choice. To ...

  15. SUBSURFACE EMPLACEMENT TRANSPORTATION SYSTEM

    Energy Technology Data Exchange (ETDEWEB)

    T. Wilson; R. Novotny

    1999-11-22

    The objective of this analysis is to identify issues and criteria that apply to the design of the Subsurface Emplacement Transportation System (SET). The SET consists of the track used by the waste package handling equipment, the conductors and related equipment used to supply electrical power to that equipment, and the instrumentation and controls used to monitor and operate those track and power supply systems. Major considerations of this analysis include: (1) Operational life of the SET; (2) Geometric constraints on the track layout; (3) Operating loads on the track; (4) Environmentally induced loads on the track; (5) Power supply (electrification) requirements; and (6) Instrumentation and control requirements. This analysis will provide the basis for development of the system description document (SDD) for the SET. This analysis also defines the interfaces that need to be considered in the design of the SET. These interfaces include, but are not limited to, the following: (1) Waste handling building; (2) Monitored Geologic Repository (MGR) surface site layout; (3) Waste Emplacement System (WES); (4) Waste Retrieval System (WRS); (5) Ground Control System (GCS); (6) Ex-Container System (XCS); (7) Subsurface Electrical Distribution System (SED); (8) MGR Operations Monitoring and Control System (OMC); (9) Subsurface Facility System (SFS); (10) Subsurface Fire Protection System (SFR); (11) Performance Confirmation Emplacement Drift Monitoring System (PCM); and (12) Backfill Emplacement System (BES).

  16. Business system: Sustainable development and anticipatory system

    Directory of Open Access Journals (Sweden)

    Vojko Potočan

    2002-01-01

    Full Text Available The existence and development of humankind depends mainly upon the co-ordinated operation of all areas and levels of human activity. However, in theory and in practice there is no model of operation, which would provide a harmonized and target oriented development. A partial solution is offered by sustainable development, which tries to define and carry out common goals of mankind with a harmonized implementation of human activities at all levels of its living and behaviour. Companies belong to central institutions of modern society which essentially co–create the sustainability of society. The company’s endeavour by simulation to prepare models of their goals concerning their internal and external environment. On the base of systemic treatment, we can define companies as business system, which can survive in a log-run only on the basis of sustainable development. The business system can also be supported by the application of the anticipatory systems. The anticipatory systems can be, in this sense, understood as an entity of the methodological approach, techniques and modes of work. Their characteristics have, a direct impact on the determination of goals, on the orientation of operation, and hence on the achievement of the business system results.

  17. Operating System for Runtime Reconfigurable Multiprocessor Systems

    Directory of Open Access Journals (Sweden)

    Diana Göhringer

    2011-01-01

    Full Text Available Operating systems traditionally handle the task scheduling of one or more application instances on processor-like hardware architectures. RAMPSoC, a novel runtime adaptive multiprocessor System-on-Chip, exploits the dynamic reconfiguration on FPGAs to generate, start and terminate hardware and software tasks. The hardware tasks have to be transferred to the reconfigurable hardware via a configuration access port. The software tasks can be loaded into the local memory of the respective IP core either via the configuration access port or via the on-chip communication infrastructure (e.g. a Network-on-Chip. Recent-series of Xilinx FPGAs, such as Virtex-5, provide two Internal Configuration Access Ports, which cannot be accessed simultaneously. To prevent conflicts, the access to these ports as well as the hardware resource management needs to be controlled, e.g. by a special-purpose operating system running on an embedded processor. For that purpose and to handle the relations between temporally and spatially scheduled operations, the novel approach of an operating system is of high importance. This special purpose operating system, called CAP-OS (Configuration Access Port-Operating System, which will be presented in this paper, supports the clients using the configuration port with the services of priority-based access scheduling, hardware task mapping and resource management.

  18. Integrated Reporting Information System -

    Data.gov (United States)

    Department of Transportation — The Integrated Reporting Information System (IRIS) is a flexible and scalable web-based system that supports post operational analysis and evaluation of the National...

  19. Levonorgestrel Intrauterine System

    Science.gov (United States)

    Levonorgestrel intrauterine system (Mirena, Skyla) is used to prevent pregnancy. The manufacturer states that Mirena brand intrauterine ... to use an intrauterine system to prevent pregnancy. Levonorgestrel is in a class of medications called hormonal ...

  20. Saturated Switching Systems

    CERN Document Server

    Benzaouia, Abdellah

    2012-01-01

    Saturated Switching Systems treats the problem of actuator saturation, inherent in all dynamical systems by using two approaches: positive invariance in which the controller is designed to work within a region of non-saturating linear behaviour; and saturation technique which allows saturation but guarantees asymptotic stability. The results obtained are extended from the linear systems in which they were first developed to switching systems with uncertainties, 2D switching systems, switching systems with Markovian jumping and switching systems of the Takagi-Sugeno type. The text represents a thoroughly referenced distillation of results obtained in this field during the last decade. The selected tool for analysis and design of stabilizing controllers is based on multiple Lyapunov functions and linear matrix inequalities. All the results are illustrated with numerical examples and figures many of them being modelled using MATLAB®. Saturated Switching Systems will be of interest to academic researchers in con...

  1. Central nervous system

    Science.gov (United States)

    The central nervous system is composed of the brain and spinal cord. Your brain and spinal cord serve as the main "processing center" for your entire nervous system. They control all the workings of your body.

  2. Visitor Registration System

    Data.gov (United States)

    US Agency for International Development — Visitor Registration System (VRS) streamlines visitor check-in and check-out process for expediting visitors into USAID. The system captures visitor information...

  3. Human Resource Accounting System

    Science.gov (United States)

    Cerullo, Michael J.

    1974-01-01

    Main objectives of human resource accounting systems are to satisfy the informational demands made by investors and by operating managers. The paper's main concern is with the internal uses of a human asset system. (Author)

  4. Geographical information systems

    DEFF Research Database (Denmark)

    Möller, Bernd

    2004-01-01

    The chapter gives an introduction to Geographical Information Systems (GIS) with particular focus on their application within environmental management.......The chapter gives an introduction to Geographical Information Systems (GIS) with particular focus on their application within environmental management....

  5. Systemic banking crises

    OpenAIRE

    O. Emre Ergungor; James B. Thomson

    2005-01-01

    Systemic banking crises can have devastating effects on the economies of developing or industrialized countries. This Policy Discussion Paper reviews the factors that weaken banking systems and make them more susceptible to crises.

  6. Inductive Monitoring System (IMS)

    Data.gov (United States)

    National Aeronautics and Space Administration — IMS: Inductive Monitoring System The Inductive Monitoring System (IMS) is a tool that uses a data mining technique called clustering to extract models of normal...

  7. Health System Measurement Project

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Health System Measurement Project tracks government data on critical U.S. health system indicators. The website presents national trend data as well as detailed...

  8. Geographical information systems

    DEFF Research Database (Denmark)

    Möller, Bernd

    2004-01-01

    The chapter gives an introduction to Geographical Information Systems (GIS) with particular focus on their application within environmental management.......The chapter gives an introduction to Geographical Information Systems (GIS) with particular focus on their application within environmental management....

  9. Semiotic labelled deductive systems

    Energy Technology Data Exchange (ETDEWEB)

    Nossum, R.T. [Imperial College of Science, Technology and Medicine, London (United Kingdom)

    1996-12-31

    We review the class of Semiotic Models put forward by Pospelov, as well as the Labelled Deductive Systems developed by Gabbay, and construct an embedding of Semiotic Models into Labelled Deductive Systems.

  10. VT DSL Systems 2006

    Data.gov (United States)

    Vermont Center for Geographic Information — (Link to Metadata) The VT DSL Broadband System dataset (DSL2006) includes polygons depicting the extent of Vermont's DSL broadband system as of 12/31/2006. This data...

  11. Absorption heat pump system

    Science.gov (United States)

    Grossman, G.

    1982-06-16

    The efficiency of an absorption heat pump system is improved by conducting liquid from a second stage evaporator thereof to an auxiliary heat exchanger positioned downstream of a primary heat exchanger in the desorber of the system.

  12. Flight Systems Monitor Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This SBIR Phase I project will develop the Flight System Monitor which will use non-intrusive electrical monitoring (NEMO). The electronic system health of...

  13. Generalized adjoint systems

    CERN Document Server

    Serakos, Demetrios

    2015-01-01

    This book defines and develops the generalized adjoint of an input-output system. It is the result of a theoretical development and examination of the generalized adjoint concept and the conditions under which systems analysis using adjoints is valid. Results developed in this book are useful aids for the analysis and modeling of physical systems, including the development of guidance and control algorithms and in developing simulations. The generalized adjoint system is defined and is patterned similarly to adjoints of bounded linear transformations. Next the elementary properties of the generalized adjoint system are derived. For a space of input-output systems, a generalized adjoint map from this space of systems to the space of generalized adjoints is defined. Then properties of the generalized adjoint map are derived. Afterward the author demonstrates that the inverse of an input-output system may be represented in terms of the generalized adjoint. The use of generalized adjoints to determine bounds for ...

  14. Handbook of systems toxicology

    National Research Council Canada - National Science Library

    Casciano, Daniel A; Sahu, Saura C

    2011-01-01

    "In the first handbook to comprehensively cover the emerging area of systems toxicology, the Handbook of Systems Toxicology provides an authoritative compilation of up-to-date developments presented...

  15. Gleason grading system

    Science.gov (United States)

    ... medlineplus.gov/ency/patientinstructions/000920.htm Gleason grading system To use the sharing features on this page, ... score of between 5 and 7. Gleason Grading System Sometimes, it can be hard to predict how ...

  16. Interstitial hydrogen storage system

    Energy Technology Data Exchange (ETDEWEB)

    Gell, H.A.

    1980-09-30

    A metal hydride fuel system is described that incorporates a plurality of storage elements that may be individually replaced to provide a hydrogen fuel system for combustion engines having a capability of partial refueling is presented.

  17. Information retrieval system

    Science.gov (United States)

    Berg, R. F.; Holcomb, J. E.; Kelroy, E. A.; Levine, D. A.; Mee, C., III

    1970-01-01

    Generalized information storage and retrieval system capable of generating and maintaining a file, gathering statistics, sorting output, and generating final reports for output is reviewed. File generation and file maintenance programs written for the system are general purpose routines.

  18. Contingent Information Systems Development

    NARCIS (Netherlands)

    van Slooten, C.; Schoonhoven, Bram

    1996-01-01

    Situated approaches based on project contingencies are becoming more and more an important research topic for information systems development organizations. The Information Services Organization, which was investigated, has recognized that it should tune its systems development approaches to the

  19. Silver recovery system data

    Energy Technology Data Exchange (ETDEWEB)

    Boulineau, B.

    1991-08-26

    In August of 1990 the Savannah River Site Photography Group began testing on a different type of silver recovery system. This paper describes the baseline study and the different phases of installation and testing of the system.

  20. Drinking Water Distribution Systems

    Science.gov (United States)

    Learn about an overview of drinking water distribution systems, the factors that degrade water quality in the distribution system, assessments of risk, future research about these risks, and how to reduce cross-connection control risk.

  1. Renewable Energy Tracking Systems

    Science.gov (United States)

    Renewable energy generation ownership can be accounted through tracking systems. Tracking systems are highly automated, contain specific information about each MWh, and are accessible over the internet to market participants.

  2. Cross Disciplinary Biometric Systems

    CERN Document Server

    Liu, Chengjun

    2012-01-01

    Cross disciplinary biometric systems help boost the performance of the conventional systems. Not only is the recognition accuracy significantly improved, but also the robustness of the systems is greatly enhanced in the challenging environments, such as varying illumination conditions. By leveraging the cross disciplinary technologies, face recognition systems, fingerprint recognition systems, iris recognition systems, as well as image search systems all benefit in terms of recognition performance.  Take face recognition for an example, which is not only the most natural way human beings recognize the identity of each other, but also the least privacy-intrusive means because people show their face publicly every day. Face recognition systems display superb performance when they capitalize on the innovative ideas across color science, mathematics, and computer science (e.g., pattern recognition, machine learning, and image processing). The novel ideas lead to the development of new color models and effective ...

  3. Prosthetic Knee Systems

    Science.gov (United States)

    ... Facebook Google Bookmarks Technorati Yahoo MyWeb Prosthetic Knee Systems Translated into plain language by Helen Osborne of ... Consulting Original article by Bill Dupes Prosthetic knee systems are among the most complex of all components. ...

  4. BioSystems

    Data.gov (United States)

    U.S. Department of Health & Human Services — The NCBI BioSystems Database provides integrated access to biological systems and their component genes, proteins, and small molecules, as well as literature...

  5. Immune System and Disorders

    Science.gov (United States)

    Your immune system is a complex network of cells, tissues, and organs that work together to defend against germs. It ... t, to find and destroy them. If your immune system cannot do its job, the results can be ...

  6. Multiple System Atrophy (MSA)

    Science.gov (United States)

    Diseases and Conditions Multiple system atrophy (MSA) By Mayo Clinic Staff Multiple system atrophy (MSA) is a rare neurological disorder that impairs your body's involuntary (autonomic) functions, including blood ...

  7. Designing automatic resupply systems.

    Science.gov (United States)

    Harding, M L

    1999-02-01

    This article outlines the process for designing and implementing autoresupply systems. The planning process includes determination of goals and appropriate participation. Different types of autoresupply mechanisms include kanban, breadman, consignment, systems contracts, and direct shipping from an MRP schedule.

  8. Voluntary Service System (VSS)

    Data.gov (United States)

    Department of Veterans Affairs — Voluntary Service System (VSS) is a national-level application which replaced the site-based Voluntary Timekeeping System (VTK). VTK was used for many years at the...

  9. Audit Management System

    CERN Document Server

    Alconada, Federico

    2015-01-01

    In the need of renewing their system, the Internal Audit department has given a proposal for building a new one. Taking into consideration the problems of their system they elaborated a requirement's list with the functionalities and features they were expecting from the new management system. This new system would be primarily for the use of the Internal Audit staff but it would also support the follow-up of internal audit recommendations by potentially all CERN staff members.

  10. CCD digital radiography system

    Science.gov (United States)

    Wang, Yi; Kang, Xi; Li, Yuanjing; Cheng, Jianping; Hou, Yafei; Han, Haiwei

    2009-07-01

    Amorphous silicon flat-panel detector is the mainstream used in digital radiography (DR) system. In latest years, scintillation screen coupled with CCD DR is becoming more popular in hospital. Compared with traditional amorphous silicon DR, CCD-DR has better spatial resolution and has little radiation damage. It is inexpensive and can be operated easily. In this paper, A kind of CCD based DR system is developed. We describe the construction of the system, the system performances and experiment results.

  11. System programming languages

    OpenAIRE

    ŠMIT, MATEJ

    2016-01-01

    Most operating systems are written in the C programming language. Similar is with system software, for example, device drivers, compilers, debuggers, disk checkers, etc. Recently some new programming languages emerged, which are supposed to be suitable for system programming. In this thesis we present programming languages D, Go, Nim and Rust. We defined the criteria which are important for deciding whether programming language is suitable for system programming. We examine programming langua...

  12. Rainfed intensive crop systems

    DEFF Research Database (Denmark)

    Olesen, Jørgen E

    2014-01-01

    This chapter focuses on the importance of intensive cropping systems in contributing to the world supply of food and feed. The impact of climate change on intensive crop production systems is also discussed.......This chapter focuses on the importance of intensive cropping systems in contributing to the world supply of food and feed. The impact of climate change on intensive crop production systems is also discussed....

  13. Computational Systems Chemical Biology

    OpenAIRE

    Oprea, Tudor I.; Elebeoba E. May; Leitão, Andrei; Tropsha, Alexander

    2011-01-01

    There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically-based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology, SCB (Oprea et al., 2007).

  14. Linear system theory

    Science.gov (United States)

    Callier, Frank M.; Desoer, Charles A.

    1991-01-01

    The aim of this book is to provide a systematic and rigorous access to the main topics of linear state-space system theory in both the continuous-time case and the discrete-time case; and the I/O description of linear systems. The main thrusts of the work are the analysis of system descriptions and derivations of their properties, LQ-optimal control, state feedback and state estimation, and MIMO unity-feedback systems.

  15. Logistics Management Information System

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The logistics information is the logistics manageme nt 's inevitable request. The paper introduces several kinds of logistics informat ion system and their functions in the logistics management, such as the warehous e management system (WMS) in the delivery center, the control system for transpo rtation and delivery, the supply chain management (SCM), the optimization of th e logistics system, etc. In the author's opinion, the development of logistics could been divided into four phases. And the logistic...

  16. Space power systems technology

    Science.gov (United States)

    Coulman, George A.

    1994-01-01

    Reported here is a series of studies which examine several potential catalysts and electrodes for some fuel cell systems, some materials for space applications, and mathematical modeling and performance predictions for some solid oxide fuel cells and electrolyzers. The fuel cell systems have a potential for terrestrial applications in addition to solar energy conversion in space applications. Catalysts and electrodes for phosphoric acid fuel cell systems and for polymer electrolyte membrane (PEM) fuel cell and electrolyzer systems were examined.

  17. Computer system identification

    OpenAIRE

    Lesjak, Borut

    2008-01-01

    The concept of computer system identity in computer science bears just as much importance as does the identity of an individual in a human society. Nevertheless, the identity of a computer system is incomparably harder to determine, because there is no standard system of identification we could use and, moreover, a computer system during its life-time is quite indefinite, since all of its regular and necessary hardware and software upgrades soon make it almost unrecognizable: after a number o...

  18. Open quantum system identification

    CERN Document Server

    Schirmer, Sophie G; Zhou, Weiwei; Gong, Erling; Zhang, Ming

    2012-01-01

    Engineering quantum systems offers great opportunities both technologically and scientifically for communication, computation, and simulation. The construction and operation of large scale quantum information devices presents a grand challenge and a major issue is the effective control of coherent dynamics. This is often in the presence of decoherence which further complicates the task of determining the behaviour of the system. Here, we show how to determine open system Markovian dynamics of a quantum system with restricted initialisation and partial output state information.

  19. Quantum System Identification

    OpenAIRE

    Burgarth, Daniel; Yuasa, Kazuya

    2011-01-01

    The aim of quantum system identification is to estimate the ingredients inside a black box, in which some quantum-mechanical unitary process takes place, by just looking at its input-output behavior. Here we establish a basic and general framework for quantum system identification, that allows us to classify how much knowledge about the quantum system is attainable, in principle, from a given experimental setup. Prior knowledge on some elements of the black box helps the system identification...

  20. Content management systems (CMS)

    OpenAIRE

    Oriahi, Harrison

    2014-01-01

    This thesis describes the three most common and widely used content management systems (CMS) used to power several millions of business websites on the internet. Since there are many other content managements systems online, this report provides some helpful guides on each of the three most used systems and the web design projects that each of them maybe most suitable. There are plenty of options when it comes to selecting a content management system for a development project and this the...

  1. Human Resource Management System

    OpenAIRE

    Navaz, A. S. Syed; Fiaz, A. S. Syed; Prabhadevi, C.; V.Sangeetha; Gopalakrishnan,S.

    2013-01-01

    The paper titled HUMAN RESOURCE MANAGEMENT SYSTEM is basically concerned with managing the Administrator of HUMAN RESOURCE Department in a company. A Human Resource Management System, refers to the systems and processes at the intersection between human resource management and information technology. It merges HRM as a discipline and in particular its basic HR activities and processes with the information technology field, whereas the programming of data processing systems evolved into standa...

  2. Electric Vehicle Propulsion System

    OpenAIRE

    2014-01-01

    Electric vehicles are being considered as one of the pillar of eco-friendly solutions to overcome the problem of global pollution and radiations due to greenhouse gases. Present thesis work reports the improvement in overall performance of the propulsion system of an electric vehicle by improving autonomy and torque-speed characteristic. Electric vehicle propulsion system consists of supply and traction system, and are coordinated by the monitoring & control system. Case of light electric veh...

  3. The DISCUS Hardware System,

    Science.gov (United States)

    1982-07-01

    it physically impossible for one processor to access another’s local program or workspace. It should be noted that the system - generator should handle...this gateway would be complex and how it would be used and linked to the system generator would also be difficult. Because of this it worth asking...which is by no means trivial to write, identified several faults in the system generator and operating system that would have otherwise been

  4. Hybrid Action Systems

    DEFF Research Database (Denmark)

    Ronkko, Mauno; Ravn, Anders P.

    1997-01-01

    a differential action, which allows differential equations as primitive actions. The extension allows us to model hybrid systems with both continuous and discrete behaviour. The main result of this paper is an extension of such a hybrid action system with parallel composition. The extension does not change...... the original meaning of the parallel composition, and therefore also the ordinary action systems can be composed in parallel with the hybrid action systems....

  5. Wireless power transfer system

    OpenAIRE

    Arai, Hiroyuki

    2012-01-01

    This paper presents a survey of recent wireless power transfer systems. The issue of wireless power transfer is to achieve a highly efficient system with small positioning errors of the facilities setting. Several theories have been presented to obtain precise system design. This paper presents a summary of design theory for short range power transfer systems and detailed formulations based on a circuit model and an array of infinitesimal dipoles. In addition to these theories, this paper in...

  6. Spacecraft Energy Storage Systems

    OpenAIRE

    Robinson, Wilf; Hanks, James; Spina, Len; Havenhill, Doug; Gisler, Gary; Ginter, Steve; Brault, Sharon

    1997-01-01

    Flywheel Energy Storage Systems represent an exciting alternative to traditional battery storage systems used to power satellites during periods of eclipse. The increasing demand for reliable communication and data access is driving explosive growth in the number of satellite systems being developed as well as their performance requirements. Power on orbit is the key to this performance, and batteries are becoming increasingly unattractive as an energy storage media. Flywheel systems offer ve...

  7. Unix operating system

    CERN Document Server

    Liu, Yukun; Guo, Liwei

    2011-01-01

    ""UNIX Operating System: The Development Tutorial via UNIX Kernel Services"" introduces the hierarchical structure, principles, applications, kernel, shells, development, and management of the UNIX operation systems multi-dimensionally and systematically. It clarifies the natural bond between physical UNIX implementation and general operating system and software engineering theories, and presents self-explanatory illustrations for readers to visualize and understand the obscure relationships and intangible processes in UNIX operating system. This book is intended for engineers and researchers

  8. Radiant Floor Cooling Systems

    DEFF Research Database (Denmark)

    Olesen, Bjarne W.

    2008-01-01

    In many countries, hydronic radiant floor systems are widely used for heating all types of buildings such as residential, churches, gymnasiums, hospitals, hangars, storage buildings, industrial buildings, and smaller offices. However, few systems are used for cooling.This article describes a floor...... cooling system that includes such considerations as thermal comfort of the occupants, which design parameters will influence the cooling capacity and how the system should be controlled. Examples of applications are presented....

  9. Lithium battery management system

    Science.gov (United States)

    Dougherty, Thomas J [Waukesha, WI

    2012-05-08

    Provided is a system for managing a lithium battery system having a plurality of cells. The battery system comprises a variable-resistance element electrically connected to a cell and located proximate a portion of the cell; and a device for determining, utilizing the variable-resistance element, whether the temperature of the cell has exceeded a predetermined threshold. A method of managing the temperature of a lithium battery system is also included.

  10. Collaborative Micropayment Systems

    NARCIS (Netherlands)

    Parhonyi, R.; Pras, Aiko; Quartel, Dick; Yim, C.H.

    Around the world many different micropayment systems are in use. Because of this variety, content providers and customers may rely on different systems. As a result, customers may be unable to buy content from providers using a different system. This paper proposes a novel approach that allows

  11. Controllability of Quantum Systems

    CERN Document Server

    Schirmer, S G; Solomon, A I

    2003-01-01

    An overview and synthesis of results and criteria for open-loop controllability of Hamiltonian quantum systems obtained using Lie group and Lie algebra techniques is presented. Negative results for open-loop controllability of dissipative systems are discussed, and the superiority of closed-loop (feedback) control for quantum systems is established.

  12. LOFAR Information System

    NARCIS (Netherlands)

    Begeman, K.; Belikov, A. N.; Boxhoorn, D. R.; Dijkstra, F.; Holties, H.; Meyer-Zhao, Z.; Renting, G. A.; Valentijn, E. A.; Vriend, W. -J.

    2011-01-01

    In this paper, we present a newly designed and implemented scientific information system for the LOFAR Long Term Archive. It is a distributed multi-tier storage and data processing system that allows a number of users to process Petabytes of data. The LOFAR Information System is designed on the base

  13. The Quality System

    DEFF Research Database (Denmark)

    Brogaard Buus, Daniel; Eland, Morten Vestergaard; Lystlund, Rasmus

    2015-01-01

    In this article, we present our efforts to try to increase cohesiveness and connectivity between quests generated by a recreation of an existing procedural quest generation system, with an addition of a progressive tier system called Quality System. A study gave strong indications that the Quality...

  14. Endocrine System (For Parents)

    Science.gov (United States)

    ... of or replacing specific hormones can treat many endocrine disorders in children and adolescents, some of which include: ... System Your Child's Growth Female Reproductive System Activity: Endocrine System Word! Hormones Diabetes Center Thyroid Disorders Type 2 Diabetes: What Is It? Your Endocrine ...

  15. Flexible energy systems

    DEFF Research Database (Denmark)

    Lund, Henrik

    2003-01-01

    The paper discusses and analyses diffent national strategies and points out key changes in the energy system in order to achieve a system which can benefit from a high percentage of wind and CHP without having surplus production problems, introduced here as a flexible energy system....

  16. LED system reliability

    NARCIS (Netherlands)

    Driel, W.D. van; Yuan, C.A.; Koh, S.; Zhang, G.Q.

    2011-01-01

    This paper presents our effort to predict the system reliability of Solid State Lighting (SSL) applications. A SSL system is composed of a LED engine with micro-electronic driver(s) that supplies power to the optic design. Knowledge of system level reliability is not only a challenging scientific ex

  17. Imaging systems and applications.

    Science.gov (United States)

    Catrysse, Peter B; Imai, Francisco H; Linne von Berg, Dale C; Sheridan, John T

    2013-03-01

    Imaging systems have numerous applications in industrial, military, consumer, and medical settings. Assembling a complete imaging system requires the integration of optics, sensing, image processing, and display rendering. This issue features original research ranging from fundamental theories to novel imaging modalities and provides a systems perspective to imaging.

  18. Personal Food System Mapping

    Science.gov (United States)

    Wilsey, David; Dover, Sally

    2014-01-01

    Personal food system mapping is a practical means to engage community participants and educators in individualized and shared learning about food systems, decisions, and behaviors. Moreover, it is a useful approach for introducing the food system concept, which is somewhat abstract. We developed the approach to capture diversity of personal food…

  19. Control Oriented System Identification

    Science.gov (United States)

    1993-08-01

    The research goals for this grant were to obtain algorithms for control oriented system identification is to construct dynamical models of systems...and measured information. Algorithms for this type of nonlinear system identification have been given that produce models suitable for gain scheduled

  20. Compositional asynchronous membrane systems

    Institute of Scientific and Technical Information of China (English)

    Cosmin Bonchis; Cornel Izbasa; Gabriel Ciobanu

    2007-01-01

    This paper presents an algorithmic way of building complex membrane systems by coupling elementary membranes. Its application seems particularly valuable in the case of asynchronous membrane systems, since the resulting membrane system remains asynchronous. The composition method is based on a handshake mechanism implemented by using antiport rules and promoters.